scholarly journals Serotonin and Melatonin Biosynthesis in Plants: Genome-Wide Identification of the Genes and Their Expression Reveal a Conserved Role in Stress and Development

2021 ◽  
Vol 22 (20) ◽  
pp. 11034
Author(s):  
Bidisha Bhowal ◽  
Annapurna Bhattacharjee ◽  
Kavita Goswami ◽  
Neeti Sanan-Mishra ◽  
Sneh L. Singla-Pareek ◽  
...  
Keyword(s):  
Target Genes ◽  
Functional Characterization ◽  
Gene Families ◽  
Pcr Analysis ◽  
Tryptophan Decarboxylase ◽  
Cellular Processes ◽  
Genome Wide ◽  
A Genome ◽  
Suitable Target

Serotonin (Ser) and melatonin (Mel) serve as master regulators of plant growth and development by influencing diverse cellular processes. The enzymes namely, tryptophan decarboxylase (TDC) and tryptamine 5-hydroxylase (T5H) catalyse the formation of Ser from tryptophan. Subsequently, serotonin N-acetyl transferase (SNAT) and acetyl-serotonin methyltransferase (ASMT) form Mel from Ser. Plant genomes harbour multiple genes for each of these four enzymes, all of which have not been identified. Therefore, to delineate information regarding these four gene families, we carried out a genome-wide analysis of the genes involved in Ser and Mel biosynthesis in Arabidopsis, tomato, rice and sorghum. Phylogenetic analysis unravelled distinct evolutionary relationships among these genes from different plants. Interestingly, no gene family except ASMTs showed monocot- or dicot-specific clustering of respective proteins. Further, we observed tissue-specific, developmental and stress/hormone-mediated variations in the expression of the four gene families. The light/dark cycle also affected their expression in agreement with our quantitative reverse transcriptase-PCR (qRT-PCR) analysis. Importantly, we found that miRNAs (miR6249a and miR-1846e) regulated the expression of Ser and Mel biosynthesis under light and stress by influencing the expression of OsTDC5 and OsASMT18, respectively. Thus, this study may provide opportunities for functional characterization of suitable target genes of the Ser and Mel pathway to decipher their exact roles in plant physiology.

scholarly journals Genome-Wide Identification and Characterization of Hsf and Hsp Gene Families and Gene Expression Analysis under Heat Stress in Eggplant (Solanum melongema L.)

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 149
Author(s):  
Chao Gong ◽  
Qiangqiang Pang ◽  
Zhiliang Li ◽  
Zhenxing Li ◽  
Riyuan Chen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Gene Families ◽  
High Temperature Stress ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Genome Wide ◽  
Motif Composition ◽  
Hsp Genes ◽  
Identification And Characterization

Under high temperature stress, a large number of proteins in plant cells will be denatured and inactivated. Meanwhile Hsfs and Hsps will be quickly induced to remove denatured proteins, so as to avoid programmed cell death, thus enhancing the thermotolerance of plants. Here, a comprehensive identification and analysis of the Hsf and Hsp gene families in eggplant under heat stress was performed. A total of 24 Hsf-like genes and 117 Hsp-like genes were identified from the eggplant genome using the interolog from Arabidopsis. The gene structure and motif composition of Hsf and Hsp genes were relatively conserved in each subfamily in eggplant. RNA-seq data and qRT-PCR analysis showed that the expressions of most eggplant Hsf and Hsp genes were increased upon exposure to heat stress, especially in thermotolerant line. The comprehensive analysis indicated that different sets of SmHsps genes were involved downstream of particular SmHsfs genes. These results provided a basis for revealing the roles of SmHsps and SmHsp for thermotolerance in eggplant, which may potentially be useful for understanding the thermotolerance mechanism involving SmHsps and SmHsp in eggplant.

scholarly journals Chromatin architectural proteins regulate flowering time by precluding gene looping

2021 ◽  
Vol 7 (24) ◽  
pp. eabg3097
Author(s):  
Bo Zhao ◽  
Yanpeng Xi ◽  
Junghyun Kim ◽  
Sibum Sung
Keyword(s):  
Chromatin Structure ◽  
Cellular Processes ◽  
Genome Wide ◽  
A Genome ◽  
Evolutionarily Conserved ◽  
Architectural Proteins ◽  
Floral Repressor ◽  
Flanking Regions ◽  
Genome Wide Study

Chromatin structure is critical for gene expression and many other cellular processes. In Arabidopsis thaliana, the floral repressor FLC adopts a self-loop chromatin structure via bridging of its flanking regions. This local gene loop is necessary for active FLC expression. However, the molecular mechanism underlying the formation of this class of gene loops is unknown. Here, we report the characterization of a group of linker histone-like proteins, named the GH1-HMGA family in Arabidopsis, which act as chromatin architecture modulators. We demonstrate that these family members redundantly promote the floral transition through the repression of FLC. A genome-wide study revealed that this family preferentially binds to the 5′ and 3′ ends of gene bodies. The loss of this binding increases FLC expression by stabilizing the FLC 5′ to 3′ gene looping. Our study provides mechanistic insights into how a family of evolutionarily conserved proteins regulates the formation of local gene loops.

scholarly journals Genome-Wide Identification and Analysis of VQ Motif-containing Gene Family in Brassica napus and Functional Characterization of BnMKS1 in Response to Leptosphaeria maculans

2020 ◽  
Author(s):  
Zhongwei Zou ◽  
Fei Liu ◽  
Shuanglong Huang ◽  
DILANTHA GERARD FERNANDO
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Functional Characterization ◽  
Leptosphaeria Maculans ◽  
Defense Responses ◽  
Marker Genes ◽  
Blackleg Disease ◽  
Genome Wide ◽  
A Genome

Proteins containing Valine-glutamine (VQ) motifs play important roles in plant growth and development, as well as in defense responses to both abiotic and biotic stresses. Blackleg disease, which is caused by Leptosphaeria maculans, is the most important disease in canola (Brassica napus L.) worldwide. H; however, the identification of B. napus VQs and their functions in response to blackleg disease have not yet been reported. In this study, we conducted a genome genome-wide identification and characterization of the VQ gene family in B. napus, including chromosome location, phylogenetic relations, gene structure, motif domain, synteny analysis, and cis-elements categorization of their promoter regions. To understand B. napus VQ gene function in response to blackleg disease, we overexpressed BnVQ7 (BnaA01g36880D, also known as the mitogen-activated protein kinase4 substrate1 (MKS1) gene) in a blackleg-susceptible canola variety Westar. Overexpression The overexpression of BnMKS1 in canola did not improve its resistance to blackleg disease at the seedling stage. H; however, transgenic canola plants overexpressing BnMKS1 displayed an enhanced resistance to L. maculans infection at the adult plant stage. Expression levels of downstream and defense marker genes in cotyledons increased significantly at the necrotrophic stage of L. maculans infection in the overexpression line of BnMKS1, suggesting that the SA salicylic acid (SA)- and jasmonic acid (JA )-mediated signaling pathways were both involved in the defense responses. Together, these results suggest that BnMKS1 might play an important role in the defense against L. maculans.

scholarly journals Genome-Wide Identification, Expression Pattern Analysis and Evolution of the Ces/Csl Gene Superfamily in Pineapple (Ananas comosus)

Plants ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 275 ◽  
Author(s):  
Cao ◽  
Cheng ◽  
Zhang ◽  
Aslam ◽  
Yan ◽  
...  
Keyword(s):  
Plant Cell Wall ◽  
Developmental Stages ◽  
Functional Characterization ◽  
Gene Families ◽  
Cellulose Synthase ◽  
Ananas Comosus ◽  
Tropical Fruit ◽  
Genome Wide ◽  
Gene Structures

The cellulose synthase (Ces) and cellulose synthase-like (Csl) gene families belonging to the cellulose synthase gene superfamily, are responsible for the biosynthesis of cellulose and hemicellulose of the plant cell wall, and play critical roles in plant development, growth and evolution. However, the Ces/Csl gene family remains to be characterized in pineapple, a highly valued and delicious tropical fruit. Here, we carried out genome-wide study and identified a total of seven Ces genes and 25 Csl genes in pineapple. Genomic features and phylogeny analysis of Ces/Csl genes were carried out, including phylogenetic tree, chromosomal locations, gene structures, and conserved motifs identification. In addition, we identified 32 pineapple AcoCes/Csl genes with 31 Arabidopsis AtCes/Csl genes as orthologs by the syntenic and phylogenetic approaches. Furthermore, a RNA-seq investigation exhibited the expression profile of several AcoCes/Csl genes in various tissues and multiple developmental stages. Collectively, we provided comprehensive information of the evolution and function of pineapple Ces/Csl gene superfamily, which would be useful for screening out and characterization of the putative genes responsible for tissue development in pineapple. The present study laid the foundation for future functional characterization of Ces/Csl genes in pineapple.

scholarly journals Presence and Transmission of Mitochondrial Heteroplasmic Mutations in Human Populations of European and African Ancestry

2020 ◽  
Author(s):  
Chunyu Liu ◽  
Jessica L. Fetterman ◽  
Yong Qian ◽  
Xianbang Sun ◽  
Kaiyu Yan ◽  
...  
Keyword(s):  
Tyrosine Phosphatase ◽  
African Ancestry ◽  
Functional Characterization ◽  
Nuclear Genome ◽  
Human Populations ◽  
Sibling Pairs ◽  
Coding Regions ◽  
Genome Wide ◽  
A Genome

ABSTRACTWe investigated the concordance of mitochondrial DNA heteroplasmic mutations (heteroplasmies) in different types of maternal pairs (n=6,745 pairs) of European (EA, n=4,718 pairs) and African (AA, n=2,027 pairs) Americans with whole genome sequences (WGSs). The average concordance rate of heteroplasmies was highest between mother-offspring pairs, followed by sibling-sibling pairs and more distantly related maternal pairs in both EA and AA participants. The allele fractions of concordant heteroplasmies exhibited high correlation (R2=0.8) between paired individuals. Compared to concordant heteroplasmies, discordant ones were more likely to locate in coding regions, be nonsynonymous or nonsynonymous-deleterious (p<0.001). The average number of heteroplasmies per individual (i.e. heteroplasmic burden) was at a similar level until older age (70-80 years old) and increased significantly thereafter (p<0.01). The burden of deleterious heteroplasmies (combined annotation-dependent depletion score≥15), however, was significantly correlated with advancing age (20-44, 45-64, ≥65 years, p-trend=0.01). A genome-wide association analysis of the heteroplasmic burden identified many significant (P<5e-8) common variants (minor allele frequency>0.05) at 11p11.12. Many of the top SNPs act as strong long-range cis regulators of protein tyrosine phosphatase receptor type J. This study provides further evidence that mtDNA heteroplasmies may be inherited or somatic. Somatic heteroplasmic variants increase with advancing age and are more likely to have an adverse impact on mitochondrial function. Further studies are warranted for functional characterization of the deleterious heteroplasmies occurring with advancing age and the association of the 11p11.12 region of the nuclear genome with mtDNA heteroplasmy.

scholarly journals Genome-wide analysis and expression profiles of PdeMYB transcription factors in colored-leaf poplar (Populus deltoids)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Weibing Zhuang ◽  
Xiaochun Shu ◽  
Xinya Lu ◽  
Tao Wang ◽  
Fengjiao Zhang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Green Leaf ◽  
Myb Transcription Factor ◽  
Pcr Analysis ◽  
Genome Wide ◽  
Populus Deltoids

Abstract Background MYB transcription factors, comprising one of the largest transcription factor families in plants, play many roles in secondary metabolism, especially in anthocyanin biosynthesis. However, the functions of the PdeMYB transcription factor in colored-leaf poplar remain elusive. Results In the present study, genome-wide characterization of the PdeMYB genes in colored-leaf poplar (Populus deltoids) was conducted. A total of 302 PdeMYB transcription factors were identified, including 183 R2R3-MYB, five R1R2R3-MYB, one 4R-MYB, and 113 1R-MYB transcription factor genes. Genomic localization and paralogs of PdeMYB genes mapped 289 genes on 19 chromosomes, with collinearity relationships among genes. The conserved domain, gene structure, and evolutionary relationships of the PdeMYB genes were also established and analyzed. The expression levels of PdeMYB genes were obtained from previous data in green leaf poplar (L2025) and colored leaf poplar (QHP) as well as our own qRT-PCR analysis data in green leaf poplar (L2025) and colored leaf poplar (CHP), which provide valuable clues for further functional characterization of PdeMYB genes. Conclusions The above results provide not only comprehensive insights into the structure and functions of PdeMYB genes but also provide candidate genes for the future improvement of leaf colorization in Populus deltoids.

scholarly journals Identification of the WUSCHEL-Related Homeobox (WOX) Gene Family, and Interaction and Functional Analysis of TaWOX9 and TaWUS in Wheat

2020 ◽  
Vol 21 (5) ◽  
pp. 1581 ◽  
Author(s):  
Zheng Li ◽  
Dan Liu ◽  
Yu Xia ◽  
Ziliang Li ◽  
Doudou Jing ◽  
...  
Keyword(s):  
Gene Family ◽  
Oryza Sativa L ◽  
Dynamic Balance ◽  
Functional Characterization ◽  
Gene Families ◽  
Triticum Aestivum L ◽  
Genome Wide ◽  
A Genome ◽  
Paralogous Copy ◽  
Duplication Events

The WUSCHEL-related homeobox (WOX) is a family of plant-specific transcription factors, with important functions, such as regulating the dynamic balance of division and differentiation of plant stem cells and plant organ development. We identified 14 distinct TaWOX genes in the wheat (Triticum aestivum L.) genome, based on a genome-wide scan approach. All of the genes under evaluation had positional homoeologs on subgenomes A, B and D except TaWUS and TaWOX14. Both TaWOX14a and TaWOX14d had a paralogous copy on the same genome due to tandem duplication events. A phylogenetic analysis revealed that TaWOX genes could be divided into three groups. We performed functional characterization of TaWOX genes based on the evolutionary relationships among the WOX gene families of wheat, rice (Oryza sativa L.), and Arabidopsis. An overexpression analysis of TaWUS in Arabidopsis revealed that it affected the development of outer floral whorl organs. The overexpression analysis of TaWOX9 in Arabidopsis revealed that it promoted the root development. In addition, we identified some interaction between the TaWUS and TaWOX9 proteins by screening wheat cDNA expression libraries, which informed directions for further research to determine the functions of TaWUS and TaWOX9. This study represents the first comprehensive data on members of the WOX gene family in wheat.

scholarly journals Comprehensive Genome-Wide Identification and Transcript Profiling of GABA Pathway Gene Family in Apple (Malus domestica)

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1973
Author(s):  
Qingbo Zheng ◽  
Shenghui Su ◽  
Zhe Wang ◽  
Yongzhang Wang ◽  
Xiaozhao Xu
Keyword(s):  
Amino Acid ◽  
Gene Family ◽  
Alternative Pathway ◽  
Functional Characterization ◽  
Gaba Shunt ◽  
Gaba Transporters ◽  
Pathway Gene ◽  
Genome Wide ◽  
A Genome

γ-Aminobutyric Acid (GABA), a four-carbon non-protein amino acid, is a significant component of the free amino acid pool in most prokaryotic and eukaryotic organisms. GABA is involved in pH regulation, maintaining C/N balance, plant development and defence, as well as a compatible osmolyte and an alternative pathway for glutamate utilization via anion flux. Glutamate decarboxylase (GAD, EC 4.1.1.15) and GABA transaminase (GABA-T, EC 2.6.1.19) are two key enzymes involved in the synthesis and metabolism of GABA. Recently, GABA transporters (GATs), protein and aluminium-activated malate transporter (ALMT) proteins which function as GABA receptors, have been shown to be involved in GABA regulation. However, there is no report on the characterization of apple GABA pathway genes. In this study, we performed a genome-wide analysis and expression profiling of the GABA pathway gene family in the apple genome. A total of 24 genes were identified including five GAD genes (namely MdGAD 1–5), two GABA-T genes (namely MdGABA-T 1,2), 10 GAT genes (namely GAT 1–10) and seven ALMT genes (namely MdALMT1–7). These genes were randomly distributed on 12 chromosomes. Phylogenetic analyses grouped GABA shunt genes into three clusters—cluster I, cluster II, and cluster III—which had three, four, and five genes, respectively. The expression profile analysis revealed significant MdGAD4 expression levels in both fruit and flower organs, except pollen. However, there were no significant differences in the expression of other GABA shunt genes in different tissues. This work provides the first characterization of the GABA shunt gene family in apple and suggests their importance in apple response to abiotic stress. These results can serve as a guide for future studies on the understanding and functional characterization of these gene families.

scholarly journals Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks

2021 ◽  
Vol 11 ◽  
Author(s):  
Maud Fagny ◽  
Marieke Lydia Kuijjer ◽  
Maike Stam ◽  
Johann Joets ◽  
Olivier Turc ◽  
...  
Keyword(s):  
Regulatory Network ◽  
Regulatory Networks ◽  
Target Genes ◽  
Cell Wall Modification ◽  
Regulatory Modules ◽  
Genome Wide ◽  
A Genome ◽  
Spatio Temporal ◽  
Enhancer Sequences

Enhancers are key players in the spatio-temporal coordination of gene expression during numerous crucial processes, including tissue differentiation across development. Characterizing the transcription factors (TFs) and genes they connect, and the molecular functions underpinned is important to better characterize developmental processes. In plants, the recent molecular characterization of enhancers revealed their capacity to activate the expression of several target genes. Nevertheless, identifying these target genes at a genome-wide level is challenging, particularly for large-genome species, where enhancers and target genes can be hundreds of kilobases away. Therefore, the contribution of enhancers to plant regulatory networks remains poorly understood. Here, we investigate the enhancer-driven regulatory network of two maize tissues at different stages: leaves at seedling stage (V2-IST) and husks (bracts) at flowering. Using systems biology, we integrate genomic, epigenomic, and transcriptomic data to model the regulatory relationships between TFs and their potential target genes, and identify regulatory modules specific to husk and V2-IST. We show that leaves at the V2-IST stage are characterized by the response to hormones and macromolecules biogenesis and assembly, which are regulated by the BBR/BPC and AP2/ERF TF families, respectively. In contrast, husks are characterized by cell wall modification and response to abiotic stresses, which are, respectively, orchestrated by the C2C2/DOF and AP2/EREB families. Analysis of the corresponding enhancer sequences reveals that two different transposable element families (TIR transposon Mutator and MITE Pif/Harbinger) have shaped part of the regulatory network in each tissue, and that MITEs have provided potential new TF binding sites involved in husk tissue-specificity.

scholarly journals PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243791
Author(s):  
Caitlin Mills ◽  
Anushya Muruganujan ◽  
Dustin Ebert ◽  
Crystal N. Marconett ◽  
Juan Pablo Lewinger ◽  
...  
Keyword(s):  
Target Gene ◽  
Target Genes ◽  
Specific Gene ◽  
Web Interface ◽  
Protein Coding ◽  
Cellular Processes ◽  
Genome Wide ◽  
A Genome ◽  
Dna Elements ◽  
Cell Type Specific

Enhancers are powerful and versatile agents of cell-type specific gene regulation, which are thought to play key roles in human disease. Enhancers are short DNA elements that function primarily as clusters of transcription factor binding sites that are spatially coordinated to regulate expression of one or more specific target genes. These regulatory connections between enhancers and target genes can therefore be characterized as enhancer-gene links that can affect development, disease, and homeostatic cellular processes. Despite their implication in disease and the establishment of cell identity during development, most enhancer-gene links remain unknown. Here we introduce a new, publicly accessible database of predicted enhancer-gene links, PEREGRINE. The PEREGRINE human enhancer-gene links interactive web interface incorporates publicly available experimental data from ChIA-PET, eQTL, and Hi-C assays across 78 cell and tissue types to link 449,627 enhancers to 17,643 protein-coding genes. These enhancer-gene links are made available through the new Enhancer module of the PANTHER database and website where the user may easily access the evidence for each enhancer-gene link, as well as query by target gene and enhancer location.

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