Genome-Wide Analysis of Auxin Receptor Family Genes in Brassica juncea var. tumida

Comparative genomic profiling of transport inhibitor Response1/Auxin signaling F-box (TIR1/AFB) genes in eight Pyrus genomes revealed the intraspecies diversity and stress responsiveness patterns

In the genomics of plants and the phytoecosystem, Pyrus (pear) is among the most nutritious fruits and contains fiber that has great health benefits to humans. It is mostly cultivated in temperate regions and is one of the most cultivated pome fruits globally. Pears are highly subjected to biotic and abiotic stresses that affect their yield. TIR1/AFB proteins act as auxin co-receptors during the signaling of nuclear auxins and play a primary role in development-related regulatory processes and responses to biotic and abiotic stresses. However, this gene family and its members have not been explored in Pyrus genomes, and understanding these genes will help obtain useful insights into stress tolerance and ultimately help maintain a high yield of pears. This study reports a pangenome-wide investigation of TIR1/AFB genes from eight Pyrus genomes: Cuiguan (Pyrus pyrifolia), Shanxi Duli (P. betulifolia), Zhongai 1 [(P. ussuriensis × communis) × spp.], Nijisseiki (P. pyrifolia), Yunhong No.1 (P. pyrifolia), d'Anjou (P. communis), Bartlett v2.0 (P. communis), and Dangshansuli v.1.1 (P. bretschneideri). These genes were randomly distributed on 17 chromosomes in each genome. Based on phylogenetics, the identified TIR1/AFB genes were divided into six groups. Their gene structure and motif pattern showed the intraspecific structural conservation as well as evolutionary patterns of Pyrus TIR1/AFBs. The expansion of this gene family in Pyrus is mainly caused by segmental duplication; however, a few genes showed tandem duplication. Moreover, positive and negative selection pressure equally directed the gene's duplication process. The GO and PPI analysis showed that Pyrus TIR1/AFB genes are associated with abiotic stress- and development-related signaling pathways. The promoter regions of Pyrus TIR1/AFB genes were enriched in hormone-, light-, development-, and stress-related cis elements. Furthermore, publicly available RNA-seq data analysis showed that DaTIR1/AFBs have varied levels of expression in various tissues and developmental stages, fruit hardening disease conditions, and drought stress conditions. This indicated that DaTIR1/AFB genes might play critical roles in response to biotic and abiotic stresses. The DaTIR1/AFBs have similar protein structures, which show that they are involved in the same function. Hence, this study will broaden our knowledge of the TIR1/AFB gene family in Pyrus, elucidating their contribution to conferring resistance against various environmental stresses, and will also provide valuable insights for future researchers.

Genome-Wide Analysis Elucidates the Roles of GhTIR1/AFB Genes Reveals the Function of Gh_D08G0763 (GhTIR1) in Cold Stress in G. hirsutum

This study identified 13 GhTIR1/AFB members in G. hirsutum through bioinformatics methods and divided them into three subgroups by phylogenetic tree analysis. Motif and gene structure analysis showed that the genes in this family were highly conserved. Promoter cis-acting element analysis found that the promoters of GhTIR1/AFBs contained a large number of cis-acting elements in response to growth and development and abiotic stress. Further RT-qPCR results showed that GhTIR1/AFB genes responded to various abiotic stresses such as IAA, ABA, cold, and heat, and the expression levels of each gene changed obviously, especially Gh_D08G0763 (GhTIR1), which responded significantly to cold injury. Using VIGS (virus-induced gene silencing) technology to silence Gh_D08G0763 in the cold-tolerant cotton variety ZM36, it was found that the resistance of ZM36 to cold damage was significantly reduced. The physiological response mechanism of the Gh_D08G0763 in resisting cold damage was further analyzed through trypan blue staining of leaves and determination of enzyme activity levels. This study provided effective genetic resources for cotton cold-tolerance breeding.

Role of F-box E3-ubiquitin ligases in plant development and stress responses

KEY MESSAGE

F-box E3-ubiquitin ligases regulate critical biological processes in plant development and stress responses. Future research could elucidate why and how plants have acquired a large number of F-box genes. The ubiquitin-proteasome system (UPS) is a predominant regulatory mechanism employed by plants to maintain the protein turnover in the cells and involves the interplay of three classes of enzymes, E1 (ubiquitin-activating), E2 (ubiquitin-conjugating), and E3 ligases. The diverse and most prominent protein family among eukaryotes, F-box proteins, are a vital component of the multi-subunit SCF (Skp1-Cullin 1-F-box) complex among E3 ligases. Several F-box proteins with multifarious functions in different plant systems have evolved rapidly over time within closely related species, but only a small part has been characterized. We need to advance our understanding of substrate-recognition regulation and the involvement of F-box proteins in biological processes and environmental adaptation. This review presents a background of E3 ligases with particular emphasis on the F-box proteins, their structural assembly, and their mechanism of action during substrate recognition. We discuss how the F-box proteins regulate and participate in the signaling mechanisms of plant development and environmental responses. We highlight an urgent need for research on the molecular basis of the F-box E3-ubiquitin ligases in plant physiology, systems biology, and biotechnology. Further, the developments and outlooks of the potential technologies targeting the E3-ubiquitin ligases for developing crop improvement strategies have been discussed.

Insights of auxin signaling F-box genes in wheat (Triticum aestivum L.) and their dynamic expression during the leaf rust infection

The TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1/AFB) protein serves as auxin receptor and links with Aux/IAA repressor protein leading to its degradation via SKP-Cullin-F box (SCF^TIR1/AFB) complex in the auxin signaling pathway. Present study revealed 11 TIR1/AFB genes in wheat by genome-wide search using AFB HMM profile. Phylogenetic analysis clustered these genes in two classes. Several phytohormone, abiotic, and biotic stress responsive cis-elements were detected in promoter regions of TIR1/AFB genes. These genes were localized on homoeologous chromosome groups 2, 3, and 5 showing orthologous relation with other monocot plants. Most genes were interrupted by introns and the gene products were localized in cytoplasm, nucleus, and cell organelles. TaAFB3, TaAFB5, and TaAFB8 had nuclear localization signals. The evolutionary constraint suggested paralogous sister pairs and orthologous genes went through strong purifying selection process and are slowly evolving at protein level. Functional annotation revealed all TaAFB genes participated in auxin activated signaling pathway and SCF-mediated ubiquitination process. Furthermore, in silico expression study revealed their diverse expression profiles during various developmental stages in different tissues and organs as well as during biotic and abiotic stress. QRT-PCR based studies suggested distinct expression pattern of TIR1-1, TIR1-3, TaAFB1, TaAFB2, TaAFB3, TaAFB4, TaAFB5, TaAFB7, and TaAFB8 displaying maximum expression at 24 and 48 h post inoculation in both susceptible and resistant near isogenic wheat lines infected with leaf rust pathogen. Importantly, this also reflects coordinated responses in expression patterns of wheat TIR1/AFB genes during progression stages of leaf rust infection.

TIR1/AFB proteins: Active players in abiotic and biotic stress signaling

The TIR1/AFB family of proteins is a group of functionally diverse auxin receptors that are only found in plants. TIR1/AFB family members are characterized by a conserved N-terminal F-box domain followed by 18 leucine-rich repeats. In the past few decades, extensive research has been conducted on the role of these proteins in regulating plant development, metabolism, and responses to abiotic and biotic stress. In this review, we focus on TIR1/AFB proteins that play crucial roles in plant responses to diverse abiotic and biotic stress. We highlight studies that have shed light on the mechanisms by which TIR1/AFB proteins are regulated at the transcriptional and post-transcriptional as well as the downstream in abiotic or biotic stress pathways regulated by the TIR1/AFB family.

Molecular Aspects of MicroRNAs and Phytohormonal Signaling in Response to Drought Stress: A Review

Phytohormones play an essential role in plant growth and development in response to environmental stresses. However, plant hormones require a complex signaling network combined with other signaling pathways to perform their proper functions. Thus, multiple phytohormonal signaling pathways are a prerequisite for understanding plant defense mechanism against stressful conditions. MicroRNAs (miRNAs) are master regulators of eukaryotic gene expression and are also influenced by a wide range of plant development events by suppressing their target genes. In recent decades, the mechanisms of phytohormone biosynthesis, signaling, pathways of miRNA biosynthesis and regulation were profoundly characterized. Recent findings have shown that miRNAs and plant hormones are integrated with the regulation of environmental stress. miRNAs target several components of phytohormone pathways, and plant hormones also regulate the expression of miRNAs or their target genes inversely. In this article, recent developments related to molecular linkages between miRNAs and phytohormones were reviewed, focusing on drought stress.

Non-target-site resistance mechanism of barnyardgrass [Echinochloa crus-galli (L.) P. Beauv.] to florpyrauxifen-benzyl

BACKGROUND

Florpyrauxifen-benzyl (FPB) is an arylpicolinate herbicide (Group IV) for barnyardgrass control in rice. One susceptible (Sus) and three putative FPB-resistant (R1, R2, and R3) barnyardgrass biotypes were selected based on resistant/susceptible (R/S) ratios obtained from dose-response tests and used to investigate the potential resistance mechanisms.

RESULTS

Based on visual control results, the R/S ratios of barnyardgrass biotypes R1, R2, and R3 were 60-, 33-, and 16-fold greater than the Sus standard, respectively. Sequencing results of TIR1 and AFB genes in the tested barnyardgrass revealed no difference between Sus and R barnyardgrass biotypes. Absorption of [¹⁴ C]-FPB in Sus barnyardgrass increased over time and reached 90%, which was >10 percentage points greater than that in R biotypes. The [¹⁴ C]-FPB absorption in all R barnyardgrass equilibrated after 48 h. For both Sus and R barnyardgrass, most [¹⁴ C]-FPB absorbed was present in the treated leaf (79.8-88.8%), followed by untreated aboveground (9.5-18.6%) and belowground tissues (1.3-2.2%). No differences in translocation were observed. Differences between Sus and R barnyardgrass biotypes were found for FPB metabolism. Production of the active metabolite, florpyrauxifen-acid, was greater in Sus barnyardgrass (21.5-52.1%) than in R barnyardgrass (5.5-34.9%).

CONCLUSION

In conclusion, reductions in FPB absorption and florpyrauxifen-acid production may contribute to the inability to control barnyardgrass with FPB. © 2021 Society of Chemical Industry.

Auxin and its role in plant development: structure, signalling, regulation and response mechanisms

Auxins are plant hormones that play a central role in controlling plant growth and development across different environmental conditions. Even at low concentrations, auxins can regulate gene expression through specific transcription factors and proteins that are modulated to environmental responses in the signalling cascade. Auxins are synthesized in tissues with high cell division activity and distributed by specific transmembrane proteins that regulate efflux and influx. This review presents recent advances in understanding the biosynthetic pathways, both dependent and independent of tryptophan, highlighting the intermediate indole compounds (indole-3-acetamide, indole-3-acetaldoxime, indole-3-pyruvic acid and tryptamine) and the key enzymes for auxin biosynthesis, such as YUCs and TAAs. In relation to the signalling cascade, it has been shown that auxins influence gene expression regulation by the connection between synthesis and distribution. Moreover, the molecular action of the auxin response factors and auxin/indole-3-acetic acid transcription factors with the F-box TIR1/AFB auxin receptors regulates gene expression. In addition, the importance of microRNAs in the auxin signalling pathway and their influence on plant plasticity to environmental fluctuations is also demonstrated. Finally, this review describes the chemical and biological processes involving auxins in plants.

Genome-wide identification and characterization of NAC genes in Brassica juncea var. tumida

Background

NAC (NAM, ATAF1/2, and CUC2) transcription factors play an important role in plant growth and development. However, in tumorous stem mustard (Brassica juncea var. tumida), one of the economically important crops cultivated in southwest China and some southeast Asian countries, reports on the identification of NAC family genes are lacking. In this study, we conducted a genome-wide investigation of the NAC family genes in B. juncea var. tumida, based on its recently published genome sequence data.

Methods

The NAC genes were identified in B. juncea var. tumida using the bioinformatics approach on the whole genome level. Additionally, the expression of BjuNAC genes was analyzed under high- and low-temperature stresses by quantitative real-time PCR (qRT-PCR).

Results

A total of 300 BjuNAC genes were identified, of which 278 were mapped to specific chromosomes. Phylogenetic analysis of B. juncea var. tumida, Brassica rapa, Brassica nigra, rice and Arabidopsis thaliana NAC proteins revealed that all NAC genes were divided into 18 subgroups. Furthermore, gene structure analysis showed that most of the NAC genes contained two or three exons. Conserved motif analysis revealed that BjuNAC genes contain a conserved NAM domain. Additionally, qRT-PCR data indicated that thirteen BjuNAC genes with a varying degree of up-regulation during high-temperature stress. Conversely, four BjuNAC genes (BjuNAC006, BjuNAC083, BjuNAC170 and BjuNAC223) were up-regulated and two BjuNAC genes (BjuNAC074 and BjuNAC295) down-regulated under low temperature, respectively. Together, the results of this study provide a strong foundation for future investigation of the biological function of NAC genes in B. juncea var. tumida.

Expression and Role of Biosynthetic, Transporter, Receptor, and Responsive Genes for Auxin Signaling during Clubroot Disease Development

Auxins play a pivotal role in clubroot development caused by the obligate biotroph Plasmodiophora brassicae. In this study, we investigated the pattern of expression of 23 genes related to auxin biosynthesis, reception, and transport in Chinese cabbage (Brassica rapa) after inoculation with P. brassicae. The predicted proteins identified, based on the 23 selected auxin-related genes, were from protein kinase, receptor kinase, auxin responsive, auxin efflux carrier, transcriptional regulator, and the auxin-repressed protein family. These proteins differed in amino acids residue, molecular weights, isoelectric points, chromosomal location, and subcellular localization. Leaf and root tissues showed dynamic and organ-specific variation in expression of auxin-related genes. The BrGH3.3 gene, involved in auxin signaling, exhibited 84.4-fold increase in expression in root tissues compared to leaf tissues as an average of all samples. This gene accounted for 4.8-, 2.6-, and 5.1-fold higher expression at 3, 14, and 28 days post inoculation (dpi) in the inoculated root tissues compared to mock-treated roots. BrNIT1, an auxin signaling gene, and BrPIN1, an auxin transporter, were remarkably induced during both cortex infection at 14 dpi and gall formation at 28 dpi. BrDCK1, an auxin receptor, was upregulated during cortex infection at 14 dpi. The BrLAX1 gene, associated with root hair development, was induced at 1 dpi in infected roots, indicating its importance in primary infection. More interestingly, a significantly higher expression of BrARP1, an auxin-repressed gene, at both the primary and secondary phases of infection indicated a dynamic response of the host plant towards its resistance against P. brassicae. The results of this study improve our current understanding of the role of auxin-related genes in clubroot disease development.

Genome-wide identification and gene expression analysis of SOS family genes in tuber mustard (Brassica juncea var. tumida)

The Salt Overly Sensitive (SOS) pathway in Arabidopsis thaliana plays important roles in maintaining appropriate ion homeostasis in the cytoplasm and regulating plant tolerance to salinity. However, little is known about the details regarding SOS family genes in the tuber mustard crop (Brassica juncea var. tumida). Here, 12 BjSOS family genes were identified in the B. juncea var. tumida genome including two homologous genes of SOS1, one and three homologs of SOS2 and SOS3, two homologs of SOS4, two homologs of SOS5 and two homologs of SOS6, respectively. The results of conserved motif analysis showed that these SOS homologs contained similar protein structures. By analyzing the cis-elements in the promoters of those BjSOS genes, several hormone- and stress-related cis-elements were found. The results of gene expression analysis showed that the homologous genes were induced by abiotic stress and pathogen. These findings indicate that BjSOS genes play crucial roles in the plant response to biotic and abiotic stresses. This study provides valuable information for further investigations of BjSOS genes in tuber mustard.

Genome-Wide Identification and Characterization of the Vacuolar H+-ATPase Subunit H Gene Family in Crop Plants

The vacuolar H⁺-ATPase (V-ATPase) plays many important roles in cell growth and in response to stresses in plants. The V-ATPase subunit H (VHA-H) is required to form a stable and active V-ATPase. Genome-wide analyses of VHA-H genes in crops contribute significantly to a systematic understanding of their functions. A total of 22 VHA-H genes were identified from 11 plants representing major crops including cotton, rice, millet, sorghum, rapeseed, maize, wheat, soybean, barley, potato, and beet. All of these VHA-H genes shared exon-intron structures similar to those of Arabidopsis thaliana. The C-terminal domain of VHA-H was shorter and more conserved than the N-terminal domain. The VHA-H gene was effectively used as a genetic marker to infer the phylogenetic relationships among plants, which were congruent with currently accepted taxonomic groupings. The VHA-H genes from six species of crops (Gossypium raimondii, Brassica napus, Glycine max, Solanum tuberosum, Triticum aestivum, and Zea mays) showed high gene structural diversity. This resulted from the gains and losses of introns. Seven VHA-H genes in six species of crops (Gossypium raimondii, Hordeum vulgare, Solanum tuberosum, Setaria italica, Triticum aestivum, and Zea mays) contained multiple transcript isoforms arising from alternative splicing. The study of cis-acting elements of gene promoters and RNA-seq gene expression patterns confirms the role of VHA-H genes as eco-enzymes. The gene structural diversity and proteomic diversity of VHA-H genes in our crop sampling facilitate understanding of their functional diversity, including stress responses and traits important for crop improvement.