Bioinformatic landscapes for plant transcription factor system research

MtTCP18 Regulates Plant Structure in Medicago truncatula

Plant structure has a large influence on crop yield formation, with branching and plant height being the important factors that make it up. We identified a gene, MtTCP18, encoding a TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factor highly conserved with Arabidopsis gene BRC1 (BRANCHED1) in Medicago truncatula. Sequence analysis revealed that MtTCP18 included a conserved basic helix-loop-helix (BHLH) motif and R domain. Expression analysis showed that MtTCP18 was expressed in all organs examined, with relatively higher expression in pods and axillary buds. Subcellular localization analysis showed that MtTCP18 was localized in the nucleus and exhibited transcriptional activation activity. These results supported its role as a transcription factor. Meanwhile, we identified a homozygous mutant line (NF14875) with a mutation caused by Tnt1 insertion into MtTCP18. Mutant analysis showed that the mutation of MtTCP18 altered plant structure, with increased plant height and branch number. Moreover, we found that the expression of auxin early response genes was modulated in the mutant. Therefore, MtTCP18 may be a promising candidate gene for breeders to optimize plant structure for crop improvement.

A matter of time: regulatory events behind the synchronization of C4 and crassulacean acid metabolism in Portulaca oleracea

Portulaca species can switch between C4 and crassulacean acid metabolism (CAM) depending on environmental conditions. However, the regulatory mechanisms behind this rare photosynthetic adaptation remain elusive. Using Portulaca oleracea as a model system, here we investigated the involvement of the circadian clock, plant hormones, and transcription factors in coordinating C4 and CAM gene expression. Free-running experiments in constant conditions suggested that C4 and CAM gene expression are intrinsically connected to the circadian clock. Detailed time-course, drought, and rewatering experiments revealed distinct time frames for CAM induction and reversion (days versus hours, respectively), which were accompanied by changes in abscisic acid (ABA) and cytokinin metabolism and signaling. Exogenous ABA and cytokinins were shown to promote and repress CAM expression in P. oleracea, respectively. Moreover, the drought-induced decline in C4 transcript levels was completely recovered upon cytokinin treatment. The ABA-regulated transcription factor genes HB7, NFYA7, NFYC9, TT8, and ARR12 were identified as likely candidate regulators of CAM induction following this approach, whereas NFYC4 and ARR9 were connected to C4 expression patterns. Therefore, we provide insights into the signaling events controlling C4-CAM transitions in response to water availability and over the day/night cycle, highlighting candidate genes for future functional studies in the context of facultative C4-CAM photosynthesis.

Transcriptome analyses reveal the expression profile of genes related to lignan biosynthesis in Anthriscus sylvestris L. Hoffm. Gen

Anthriscus sylvestris L. Hoffm. Gen (A. sylvestris) is a perennial herb widely used for antitussive and diuretic purposes in traditional Korean and Chinese medicine. Lignans are critical secondary metabolites with widely pharmacological activities in A. sylvestris. Using transcriptome data of A. sylvestris, we identified genes related to lignan biosynthesis. In all, 123,852 unigenes were obtained from the flowers, leaves, roots, and stems of A. sylvestris with the Illumina HiSeq 4000 platform. The average length of unigenes was 1,123 bp and 91,217 (73.65%) of them were annotated in public databases. Differentially expressed genes and root-specific genes were analyzed between roots and the other three tissue types by comparing gene expression profiles. Specifically, the key enzyme genes involved in lignan biosynthesis were identified and analyzed. The expression levels of some of these genes were highest in the roots, consistent with the accumulation of deoxypodophyllotoxin. These expression levels were experimentally verified via quantitative real-time polymerase chain reaction (qRT-PCR). This research provides valuable information on the transcriptome data of A. sylvestris and the identification of candidate genes associated with the biosynthesis of lignans, laying the foundation for further research on genomics in A. sylvestris and related species.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01156-w.

qTeller: a tool for comparative multi-genomic gene expression analysis

MOTIVATION

Over the last decade, RNA-Seq whole-genome sequencing has become a widely used method for measuring and understanding transcriptome-level changes in gene expression. Since RNA-Seq is relatively inexpensive, it can be used on multiple genomes to evaluate gene expression across many different conditions, tissues and cell types. Although many tools exist to map and compare RNA-Seq at the genomics level, few web-based tools are dedicated to making data generated for individual genomic analysis accessible and reusable at a gene-level scale for comparative analysis between genes, across different genomes and meta-analyses.

RESULTS

To address this challenge, we revamped the comparative gene expression tool qTeller to take advantage of the growing number of public RNA-Seq datasets. qTeller allows users to evaluate gene expression data in a defined genomic interval and also perform two-gene comparisons across multiple user-chosen tissues. Though previously unpublished, qTeller has been cited extensively in the scientific literature, demonstrating its importance to researchers. Our new version of qTeller now supports multiple genomes for intergenomic comparisons, and includes capabilities for both mRNA and protein abundance datasets. Other new features include support for additional data formats, modernized interface and back-end database and an optimized framework for adoption by other organisms' databases.

AVAILABILITY AND IMPLEMENTATION

The source code for qTeller is open-source and available through GitHub (https://github.com/Maize-Genetics-and-Genomics-Database/qTeller). A maize instance of qTeller is available at the Maize Genetics and Genomics database (MaizeGDB) (https://qteller.maizegdb.org/), where we have mapped over 200 unique datasets from GenBank across 27 maize genomes.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Genome-wide promoter analysis, homology modeling and protein interaction network of Dehydration Responsive Element Binding (DREB) gene family in Solanum tuberosum

Dehydration Responsive Element Binding (DREB) regulates the expression of numerous stress-responsive genes, and hence plays a pivotal role in abiotic stress responses and tolerance in plants. The study aimed to develop a complete overview of the cis-acting regulatory elements (CAREs) present in S. tuberosum DREB gene promoters. A total of one hundred and four (104) cis-regulatory elements (CREs) were identified from 2.5kbp upstream of the start codon (ATG). The in-silico promoter analysis revealed variable sets of cis-elements and functional diversity with the predominance of light-responsive (30%), development-related (20%), abiotic stress-responsive (14%), and hormone-responsive (12%) elements in StDREBs. Among them, two light-responsive elements (Box-4 and G-box) were predicted in 64 and 61 StDREB genes, respectively. Two development-related motifs (AAGAA-motif and as-1) were abundant in StDREB gene promoters. Most of the DREB genes contained one or more Myeloblastosis (MYB) and Myelocytometosis (MYC) elements associated with abiotic stress responses. Hormone-responsive element i.e. ABRE was found in 59 out of 66 StDREB genes, which implied their role in dehydration and salinity stress. Moreover, six proteins were chosen corresponding to A1-A6 StDREB subgroups for secondary structure analysis and three-dimensional protein modeling followed by model validation through PROCHECK server by Ramachandran Plot. The predicted models demonstrated >90% of the residues in the favorable region, which further ensured their reliability. The present study also anticipated pocket binding sites and disordered regions (DRs) to gain insights into the structural flexibility and functional annotation of StDREB proteins. The protein association network determined the interaction of six selected StDREB proteins with potato proteins encoded by other gene families such as MYB and NAC, suggesting their similar functional roles in biological and molecular pathways. Overall, our results provide fundamental information for future functional analysis to understand the precise molecular mechanisms of the DREB gene family in S. tuberosum.

Transcriptome profiling reveals key genes in regulation of the tepal trichome development in Lilium pumilum D.C

A number of potential genes and pathways involved in tepal trichome development were identified in a natural lily mutant by transcriptome analysis and were confirmed with trichome and trichomeless species. Trichome is a specialized structure found on the surface of the plant with an important function in survival against abiotic and biotic stress. It is also an important economic trait in crop breeding. Extensive research has investigated the foliar trichome in model plants (Arabidopsis and tomato). However, the developmental mechanism of tepal trichome remains elusive. Lilium pumilum is an edible ornamental bulb and a good breeding parent possessing cold and salt-alkali resistance. Here, we found a natural mutant of Lilium pumilum grown on a highland whose tepals are covered by trichomes. Our data indicate that trichomes of the mutant are multicellular and branchless. Notably, stomata are also developed on the tepal of the mutant as well, suggesting there may be a correlation between trichome and stomata regulation. Furthermore, we isolated 27 differentially expressed genes (DEGs) by comparing the transcriptome profiling between the natural mutant and the wild type. These 27 genes belong to 4 groups: epidermal cell cycle and division, trichome morphogenesis, stress response, and transcription factors. Quantitative real-time PCR in Lilium pumilum (natural mutant and the wild type) and other lily species (Lilium leichtlinii var. maximowiczii/trichome; Lilium davidii var. willmottiae/, trichomeless) confirmed the validation of RNA-seq data and identified several trichome-related genes.

Optimized combination methods for exploring and verifying disease-resistant transcription factors in melon

A large amount of omics data and number of bioinformatics tools has been produced. However, the methods for further exploring omics data are simple, in particular, to mine key regulatory genes, which are a priority concern in biological systems, and most of the specific functions are still unknown. First, raw data of two genotypes of melon (susceptible and resistant) were obtained by transcriptome analysis. Second, 391 transcription factors (TFs) were identified from the plant transcription factor database and cucurbit genomics database. Then, functional enrichment analysis indicated that these genes were mainly annotated in the process of transcription regulation. Third, 243 and 230 module-specific TFs were screened by weighted gene coexpression network analysis and short time series expression miner, respectively. Several TF genes, such as WRKYs and bHLHs, were regarded as key regulatory genes according to the values of significantly different modules. The coexpression network showed that these TF genes were significant correlated with resistance (R) genes, such as DRP2, RGA3, DRP1 and NB-ARC. Fourth, cis-acting element analysis illustrated that these R genes may bind to WRKY and bHLH. Finally, the expression of WRKY genes was verified by quantitative reverse transcription PCR (RT-qPCR). Phylogenetic analysis was carried out to further confirm that these TFs may play a critical role in Curcurbitaceae disease resistance. This study provides a new optimized combination strategy to explore the functions of TFs in a wide spectrum of biological processes. This strategy may also effectively predict potential relationships in the interactions of essential genes.

Transcriptome Analysis of the Cf-12-Mediated Resistance Response to Cladosporium fulvum in Tomato

Cf-12 is an effective gene for resisting tomato leaf mold disease caused by Cladosporium fulvum (C. fulvum). Unlike many other Cf genes such as Cf-2, Cf-4, Cf-5, and Cf-9, no physiological races of C. fulvum that are virulent to Cf-12 carrying plant lines have been identified. In order to better understand the molecular mechanism of Cf-12 gene resistance response, RNA-Seq was used to analyze the transcriptome changes at three different stages of C. fulvum infection (0, 4, and 8 days post infection [dpi]). A total of 9100 differentially expressed genes (DEGs) between 4 and 0 dpi, 8643 DEGs between 8 and 0 dpi and 2547 DEGs between 8 and 4 dpi were identified. In addition, we found that 736 DEGs shared among the above three groups, suggesting the presence of a common core of DEGs in response to C. fulvum infection. These DEGs were significantly enriched in defense-signaling pathways such as the calcium dependent protein kinases pathway and the jasmonic acid signaling pathway. Additionally, we found that many transcription factor genes were among the DEGs, indicating that transcription factors play an important role in C. fulvum defense response. Our study provides new insight on the molecular mechanism of Cf resistance to C. fulvum, especially the unique features of Cf-12 in responding to C. fulvum infection.

Membrane-bound NAC transcription factors in maize and their contribution to the oxidative stress response

NAC membrane-bound transcription factors (NTM1-like, NTL proteins) participate in the regulation of plant development and the abiotic stress response. While their function has been thoroughly explored in Arabidopsis thaliana, this is not the case in maize. Seven ZmNTL genes were identified by an in silico scan of relevant genome sequence. All seven included a NAC domain at their N terminus, and an α-helical membrane-bound structure domain in their C terminal region. Based on their gene structure and content of conserved motifs, the seven sequences were distributed into four clades. Six of the seven ZmNTLs were associated with the plasma membrane, and the remaining one with the endoplasmic reticulum. ZmNTL2-7 were more strongly transcribed in the stem than in either the leaf or root, while ZmNTL1 transcript abundance was highest in the leaf. When the plants were exposed to either abscisic acid or hydrogen peroxide treatment, all seven genes were up-regulated in the root and stem and down-regulated in the leaf. The heterologous expression of ZmNTL1-ΔTM, 2-ΔTM and 5-ΔTM in A. thaliana reduced the level of sensitivity of the plant to hydrogen peroxide.