Genome-Wide Characterization, Evolution, and Expression Profiling of VQ Gene Family in Response to Phytohormone Treatments and Abiotic Stress in Eucalyptus grandis

The role and pathway of VQ family in plant growth, immunity, and stress response

MAIN CONCLUSION

This review provides a detailed description of the function and mechanism of VQ family gene, which is helpful for further research and application of VQ gene resources to improve crops. Valine-glutamine (VQ) motif-containing proteins are a large class of transcriptional regulatory cofactors. VQ proteins have their own unique molecular characteristics. Amino acids are highly conserved only in the VQ domain, while other positions vary greatly. Most VQ genes do not contain introns and the length of their proteins is less than 300 amino acids. A majority of VQ proteins are predicted to be localized in the nucleus. The promoter of many VQ genes contains stress or growth related elements. Segment duplication and tandem duplication are the main amplification mechanisms of the VQ gene family in angiosperms and gymnosperms, respectively. Purification selection plays a crucial role in the evolution of many VQ genes. By interacting with WRKY, MAPK, and other proteins, VQ proteins participate in the multiple signaling pathways to regulate plant growth and development, as well as defense responses to biotic and abiotic stresses. Although there have been some reports on the VQ gene family in plants, most of them only identify family members, with little functional verification, and there is also a lack of complete, detailed, and up-to-date review of research progress. Here, we comprehensively summarized the research progress of VQ genes that have been published so far, mainly including their molecular characteristics, biological functions, importance of VQ motif, and working mechanisms. Finally, the regulatory network and model of VQ genes were drawn, a precise molecular breeding strategy based on VQ genes was proposed, and the current problems and future prospects were pointed out, providing a powerful reference for further research and utilization of VQ genes in plant improvement.

Genomic Structure and Molecular Characterization of Toll-like Receptors in Black Scraper Thamnaconus Modestus and Their Expression Response to Two Types of Pathogens

The black scraper (Thamnaconus modestus) is an important commercial species in China. However, with the rapid expansion of aquaculture, the culture of this species faces substantial economic losses due to infectious diseases. Toll-like receptors (TLRs) recognize a wide range of pathogen-associated molecular patterns (PAMPs) and play a crucial role in disease resistance by initiating innate immune responses in the host. The genome of the black scraper comprises eight TLR members, which can be classified into five subfamilies based on evolutionary analysis. Moreover, the TmTLRs were identified on 6 out of the 20 chromosomes in the black scraper. The functional similarity within the same subfamilies is evident by conserved motifs and gene structures. The qRT-PCR experiments revealed diverse TmTLR expression patterns in the liver, intestine, spleen, head kidney, heart, and brain of black scrapers, with high expression levels observed in immune organs, suggesting that TmTLRs may participate in the regulation of immune mechanisms and other physiological functions in the black scraper. At least six TmTLRs showed significantly upregulated expression in response to poly (I: C) or lipopolysaccharide (LPS) stresses, thus indicating their potential roles in regulating abiotic stress responses. In conclusion, our findings not only provide a foundation for future research on the TLR gene family in the black scraper but also offer guidance for disease prevention and vaccine development.

Plant Genomics-Advancing Our Understanding of Plants

Plant genomics has made significant progress in recent years, enabling researchers to identify genes and genomic regions responsible for plant growth, development, and stress response [...].

Genome-wide characterization of the VQ genes in Triticeae and their functionalization driven by polyploidization and gene duplication events in wheat

Valine-glutamine motif-containing (VQ) proteins are transcriptional cofactors widely involved in plant growth, development, and response to various stresses. Although the VQ family has been genome-wide identified in some species, but the knowledge regarding duplication-driven functionalization of VQ genes among evolutionarily related species is still lacking. Here, 952 VQ genes have been identified from 16 species, emphasizing seven Triticeae species including the bread wheat. Comprehensive phylogenetic and syntenic analyses allow us to establish the orthologous relationship of VQ genes from rice (Oryza sativa) to bread wheat (Triticum aestivum). The evolutionary analysis revealed that whole-genome duplication (WGD) drives the expansion of OsVQs, while TaVQs expansion is associated with a recent burst of gene duplication (RBGD). We also analyzed the motif composition and molecular properties of TaVQ proteins, enriched biological functions, and expression patterns of TaVQs. We demonstrate that WGD-derived TaVQs have become divergent in both protein motif composition and expression pattern, while RBGD-derived TaVQs tend to adopt specific expression patterns, suggesting their functionalization in certain biological processes or in response to specific stresses. Furthermore, some RBGD-derived TaVQs are found to be associated with salt tolerance. Several of the identified salt-related TaVQ proteins were located in the cytoplasm and nucleus and their salt-responsive expression patterns were validated by qPCR analysis. Yeast-based functional experiments confirmed that TaVQ27 may be a new regulator to salt response and regulation. Overall, this study lays the foundation for further functional validation of VQ family members within the Triticeae species.

Genome-wide comparative analysis of the valine glutamine motif containing genes in four Ipomoea species

BACKGROUND

Genes with valine glutamine (VQ) motifs play an essential role in plant growth, development, and resistance to biotic and abiotic stresses. However, little information on the VQ genes in sweetpotato and other Ipomoea species is available.

RESULTS

This study identified 55, 58, 50 and 47 VQ genes from sweetpotato (I. batatas), I.triflida, I. triloba and I. nil, respectively. The phylogenetic analysis revealed that the VQ genes formed eight clades (I-VII), and the members in the same group exhibited similar exon-intron structure and conserved motifs distribution. The distribution of the VQ genes among the chromosomes of Ipomoea species was disproportional, with no VQ genes mapped on a few of each species' chromosomes. Duplication analysis suggested that segmental duplication significantly contributes to their expansion in sweetpotato, I.trifida, and I.triloba, while the segmental and tandem duplication contributions were comparable in I.nil. Cis-regulatory elements involved in stress responses, such as W-box, TGACG-motif, CGTCA-motif, ABRE, ARE, MBS, TCA-elements, LTR, and WUN-motif, were detected in the promoter regions of the VQ genes. A total of 30 orthologous groups were detected by syntenic analysis of the VQ genes. Based on the analysis of RNA-seq datasets, it was found that the VQ genes are expressed distinctly among different tissues and hormone or stress treatments. A total of 40 sweetpotato differentially expressed genes (DEGs) refer to biotic (sweetpotato stem nematodes and Ceratocystis fimbriata pathogen infection) or abiotic (cold, salt and drought) stress treatments were detected. Moreover, IbVQ8, IbVQ25 and IbVQ44 responded to the five stress treatments and were selected for quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis, and the results were consistent with the transcriptome analysis.

CONCLUSIONS

Our study may provide new insights into the evolution of VQ genes in the four Ipomoea genomes and contribute to the future molecular breeding of sweetpotatoes.

Comprehensive Identification and Expression Profiling of the VQ Motif-Containing Gene Family in Brassica juncea

Valine-glutamine (VQ) motif-containing proteins are a class of highly conserved transcriptional regulators in plants and play key roles in plant growth, development, and response to various stresses. However, the VQ family genes in mustard have not yet been comprehensively identified and analyzed. In this study, a total of 120 VQ family genes (BjuVQ1 to BjuVQ120), which were unevenly distributed on 18 chromosomes (AA_Chr01 to BB_Chr08), were characterized in mustard. A phylogenetic tree analysis revealed that the BjuVQ proteins were clustered into nine distinct groups (groups I to IX), and members in the same group shared a highly conserved motif composition. A gene structure analysis suggested that most BjuVQ genes were intronless. A gene duplication analysis revealed that 254 pairs of BjuVQ genes were segmentally duplicated and one pair was tandemly duplicated. Expression profiles obtained from RNA-seq data demonstrated that most BjuVQ genes have different gene expression profiles in different organs, including leaf, stem, root, flower bud, pod, and seed. In addition, over half of the BjuVQ genes were differentially expressed at some time points under low temperature treatment. The qRT-PCR data revealed that BjuVQ23, BjuVQ55, BjuVQ57, BjuVQ67, BjuVQ100, and BjuVQ117 were upregulated in response to cold stress. Taken together, our study provides new insights into the roles of different BjuVQ genes in mustard and their possible roles in growth and development, as well as in response to cold stress.

A Comprehensive Identification and Expression Analysis of VQ Motif-Containing Proteins in Sugarcane (Saccharum spontaneum L.) under Phytohormone Treatment and Cold Stress

The VQ motif-containing proteins play a vital role in various processes such as growth, resistance to biotic and abiotic stresses and development. However, there is currently no report on the VQ genes in sugarcane (Saccharum spp.). Herein, 78 VQ genes in Saccharum spontaneum were identified and classified into nine subgroups (I-IX) by comparative genomic analyses. Each subgroup had a similar structural and conservative motif. These VQ genes expanded mainly through whole-genome segmental duplication. The cis-regulatory elements (CREs) of the VQ genes were widely involved in stress responses, phytohormone responses and physiological regulation. The RNA-seq data showed that SsVQ gene expression patterns in 10 different samples, including different developmental stages, revealed distinct temporal and spatial patterns. A total of 23 SsVQ genes were expressed in all tissues, whereas 13 SsVQ genes were not expressed in any tissues. Sequence Read Archive (SRA) data showed that the majority of SsVQs responded to cold and drought stress. In addition, quantitative real-time PCR analysis showed that the SsVQs were variously expressed under salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA) and cold treatment. This study conducted a full-scale analysis of the VQ gene family in sugarcane, which could be beneficial for the functional characterization of sugarcane VQ genes and provide candidate genes for molecular resistance breeding in cultivated sugarcane in the future.

Genome-wide analysis of the VQ motif-containing gene family and expression profiles during phytohormones and abiotic stresses in wheat (Triticum aestivum L.)

BACKGROUND

VQ motif-containing (VQ) proteins are cofactors of transcriptional regulation that are widely involved in plant growth and development and respond to various stresses. The VQ gene family has been identified and characterized for many plants, but there is little research on VQ gene family proteins in wheat (Triticum aestivum L.).

RESULTS

In this study, 113 TaVQ genes (40 homoeologous groups) were identified in the wheat genome. TaVQ proteins all contain the conserved motif FxxhVQxhTG, and most of the TaVQ genes do not contain introns. Phylogenetic analysis demonstrated that TaVQ proteins can be divided into 8 subgroups (I-VIII). The chromosomal location mapping analysis indicated that TaVQ genes are disproportionally distributed on 21 wheat chromosomes. Gene duplication analysis revealed that segmental duplication significantly contributes to the expansion of the TaVQ gene family. Gene expression analysis demonstrated that the expression pattern of TaVQ genes varies in different tissues. The results of quantitative real-time PCR (qRT-PCR) found that TaVQ genes displayed different expression levels under different phytohormones and abiotic stresses. The cis-elements analysis of the promoter region demonstrated that stress responses, hormone responses, growth and development, and WRKY binding elements are all widely distributed. Additionally, a potential regulatory network between TaVQ proteins and WRKY transcription factors was visualized.

CONCLUSION

This study systematically analyzed the wheat TaVQ gene family, providing a reference for further functional characterization of TaVQ genes in wheat.

Activation of the VQ Motif-Containing Protein Gene VQ28 Compromised Nonhost Resistance of Arabidopsis thaliana to Phytophthora Pathogens

Nonhost resistance refers to resistance of a plant species to all genetic variants of a non-adapted pathogen. Such resistance has the potential to become broad-spectrum and durable crop disease resistance. We previously employed Arabidopsis thaliana and a forward genetics approach to identify plant mutants susceptible to the nonhost pathogen Phytophthora sojae, which resulted in identification of the T-DNA insertion mutant esp1 (enhanced susceptibility to Phytophthora). In this study, we report the identification of VQ motif-containing protein 28 (VQ28), whose expression was highly up-regulated in the mutant esp1. Stable transgenic A. thaliana plants constitutively overexpressing VQ28 compromised nonhost resistance (NHR) against P. sojae and P. infestans, and supported increased infection of P. parasitica. Transcriptomic analysis showed that overexpression of VQ28 resulted in six differentially expressed genes (DEGs) that are involved in the response to abscisic acid (ABA). High performance liquid chromatography-mass spectrometry (HPLC-MS) detection showed that the contents of endogenous ABA, salicylic acid (SA), and jasmonate (JA) were enriched in VQ28 overexpression lines. These findings suggest that overexpression of VQ28 may lead to an imbalance in plant hormone homeostasis. Furthermore, transient overexpression of VQ28 in Nicotiana benthamiana rendered plants more susceptible to Phytophthora pathogens. Deletion mutant analysis showed that the C-terminus and VQ-motif were essential for plant susceptibility. Taken together, our results suggest that VQ28 negatively regulates plant NHR to Phytophthora pathogens.

Genome-wide survey of the dehydrin genes in bread wheat (Triticum aestivum L.) and its relatives: identification, evolution and expression profiling under various abiotic stresses

BACKGROUND

Bread wheat (Triticum aestivum) is an important staple cereal grain worldwide. The ever-increasing environmental stress makes it very important to mine stress-resistant genes for wheat breeding programs. Therefore, dehydrin (DHN) genes can be considered primary candidates for such programs, since they respond to multiple stressors.

RESULTS

In this study, we performed a genome-wide analysis of the DHN gene family in the genomes of wheat and its three relatives. We found 55 DHN genes in T. aestivum, 31 in T. dicoccoides, 15 in T. urartu, and 16 in Aegilops tauschii. The phylogenetic, synteny, and sequence analyses showed we can divide the DHN genes into five groups. Genes in the same group shared similar conserved motifs and potential function. The tandem TaDHN genes responded strongly to drought, cold, and high salinity stresses, while the non-tandem genes respond poorly to all stress conditions. According to the interaction network analysis, the cooperation of multiple DHN proteins was vital for plants in combating abiotic stress.

CONCLUSIONS

Conserved, duplicated DHN genes may be important for wheat being adaptable to a different stress conditions, thus contributing to its worldwide distribution as a staple food. This study not only highlights the role of DHN genes help the Triticeae species against abiotic stresses, but also provides vital information for the future functional studies in these crops.

Valine-Glutamine Proteins in Plant Responses to Oxygen and Nitric Oxide

Multigene families coding for valine-glutamine (VQ) proteins have been identified in all kind of plants but chlorophytes. VQ proteins are transcriptional regulators, which often interact with WRKY transcription factors to regulate gene expression sometimes modulated by reversible phosphorylation. Different VQ-WRKY complexes regulate defense against varied pathogens as well as responses to osmotic stress and extreme temperatures. However, despite these well-known functions, new regulatory activities for VQ proteins are still to be explored. Searching public Arabidopsis thaliana transcriptome data for new potential targets of VQ-WRKY regulation allowed us identifying several VQ protein and WRKY factor encoding genes that were differentially expressed in oxygen-related processes such as responses to hypoxia or ozone-triggered oxidative stress. Moreover, some of those were also differentially regulated upon nitric oxide (NO) treatment. These subsets of VQ and WRKY proteins might combine into different VQ-WRKY complexes, thus representing a potential regulatory core of NO-modulated and O₂-modulated responses. Given the increasing relevance that gasotransmitters are gaining as plant physiology regulators, and particularly considering the key roles exerted by O₂ and NO in regulating the N-degron pathway-controlled stability of transcription factors, VQ and WRKY proteins could be instrumental in regulating manifold processes in plants.

Genome-wide identification, genomic organization and expression profiles of SlARR-B gene family in tomato

The type-B authentic response regulators (ARR-Bs) function as positive regulators of cytokinin signal transduction and play important roles in abiotic stress resistance and plant development. However, little of ARR-B family is known in tomato. In this study, we performed a comprehensive analysis of ARR-B family factors in tomato. In total, 12 genes encoding ARR-B transcription factors (named as SlARR-B1-SlARR-B12) were identified from tomato. We analyzed the structures, chromosome locations, phylogeny, protein motifs, and expression profiles of these SlARR-B genes. Gene structure analysis showed that 5-12 exons and 4-11 introns existed in the SlARR-B genes. These SlARR-B genes were asymmetrically distributed on eight chromosomes in tomato. Phylogenetic tree of SlARR-B genes from tomato and other plant species revealed that SlARR-B genes were classified into 6 subfamilies. SlARR-B proteins had typical conserved domains, including Motif 1 and Motif 2. The investigation of the expression profiles of SlARR-B genes in all the examined tissues demonstrated that these genes were differentially expressed, including roots, stems, leaves, flowers, and fruits at developmental stages. Notably, the expression of SlARR-B11 and SlARR-B12 exhibited high expression levels in flowers. Each gene was induced by at least one of different phytohormones (SA, IAA, ABA, IBA, 6-BA, JA, GA, and ETH) and four abiotic stress treatments (heat, drought, salt, and cold). This study sets a good foundation for further characterization of the SlARR-B transcription factors in plant development and abiotic stress responses of tomato.

Genome-Wide Identification of the VQ Protein Gene Family of Tobacco (Nicotiana tabacum L.) and Analysis of Its Expression in Response to Phytohormones and Abiotic and Biotic Stresses

VQ motif-containing proteins (VQ proteins) are transcriptional regulators that work independently or in combination with other transcription factors (TFs) to control plant growth and development and responses to biotic and abiotic stresses. VQ proteins contain a conserved FxxhVQxhTG amino acid motif that is the main element of its interaction with WRKY TFs. We identified 59 members of the tobacco (Nicotiana tabacum L.) NtVQ gene family by in silico analysis and examined their differential expression in response to phytohormonal treatments and following exposure to biotic and abiotic stressors. NtVQ proteins clustered into eight groups based upon their amino acid sequence and presence of various conserved domains. Groups II, IV, V, VI, and VIII contained the largest proportion of NtVQ gene family members differentially expressed in response to one or more phytohormone, and NtVQ proteins with similar domain structures had similar patterns of response to different phytohormones. NtVQ genes differentially expressed in response to temperature alterations and mechanical wounding were also identified. Over half of the NtVQ genes were significantly induced in response to Ralstonia solanacearum infection. This first comprehensive characterization of the NtVQ genes in tobacco lays the foundation for further studies of the NtVQ-mediated regulatory network in plant growth, developmental, and stress-related processes.