Autophagy is an evolutionarily conserved self-degradation process in eukaryotes. It not only plays a role in plant growth and development but also is involved in plant responses to biotic and abiotic stresses. Plants can initiate autophagy to degrade the surplus or damaged cytoplasmic materials and organelles, thus coping with abiotic and biotic stresses. The initiation of autophagy depends on autophagy-related genes (ATGs). The transcription factors can directly bind to the promoters of ATGs to activate autophagy and regulate their transcriptional levels and post-translational modifications. Furthermore, ATGs can directly or indirectly interact with plant hormones to regulate plant responses to stresses. When plants are exposed to salinity, drought, extreme temperatures, nutrient deficiencies, and pathogen stress, ATGs are significantly induced, which enhances the autophagy activity to facilitate the degradation of the denatured and misfolded proteins, thereby enhancing plant tolerance to adversity stresses. This article summarizes the discovery, structures, and classification of plant ATGs, reviews the research progress in the mechanisms of ATGs in plant responses to abiotic and biotic stresses, and prospects the future research directions. This review is expected to provide the genetic resources and a theoretical foundation for the genetic improvement of crops in responses to stress tolerance.
Autophagy/physiology* ; Stress, Physiological/genetics* ; Gene Expression Regulation, Plant ; Plants/metabolism* ; Transcription Factors/metabolism* ; Plant Proteins/genetics* ; Genes, Plant ; Plant Physiological Phenomena ; Droughts

Prunus mume is an ecologically and economically valuable plant with both medicinal and edible values. However, drought severely limits the promotion and cultivation of P. mume in the arid and semi-arid areas in northern China. In this study, we treated P. mume 'Meiren' with natural drought and then assessed photosynthetic and physiological indexes such as osmoregulatory substances, photosynthetic parameters, and antioxidant enzyme activities. Furthermore, we employed transcriptome sequencing to explore the internal regulatory mechanism of P. mume under drought stress. As the drought stress aggravated, the levels of chlorophyll a (Chla), chlorophyll b (Chlb), chlorophyll (a+b)[Chl(a+b)], and soluble protein (SP) in P. mume first elevated and then declined. The net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), maximum photochemical efficiency (Fv/Fm), effective photochemical quantum yield [Y(Ⅱ)], photochemical quenching (qP), and relative electron transport rate (ETR) all kept decreasing, while the levels of malondialdehyde, superoxide dismutase (SOD), peroxidase (POD), and osmoregulatory substances rose. Transcriptome sequencing revealed a total of 24 853 high-quality genes. Gene ontology (GO) enrichment showed that differentially expressed genes (DEGs) were the most under severe drought. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis showed that the DEGs during the four drought periods were mainly involved in the biosynthesis of secondary metabolites, plant-pathogen interaction, plant hormone signal transduction, starch and sucrose metabolism, and mitogen-activated protein kinase signaling pathways. Furthermore, we identified 16 key genes associated with the drought tolerance of P. mume 'Meiren'. This study discovered that P. mume might up-regulate or down-regulate the expression of drought tolerance-related genes such as SUS, P5CS, LEA, SOD, POD, SOD1, TPPD, and TPPA via transcription factors like MYB, ERF, bHLH, NAC, and WRKY to promote the accumulation of osmoregulatory substances like sucrose and enhance the activities of antioxidant enzymes such as SOD and POD, thus reducing the harm of reactive oxygen species and protecting the structure and function of the membrane system under drought stress. The findings provide theoretical references for further exploration of candidate genes of P. mume in response to drought stress and breeding of drought-tolerant varieties.
Droughts ; Photosynthesis/physiology* ; Gene Expression Regulation, Plant ; Stress, Physiological/genetics* ; Prunus/genetics* ; Chlorophyll/metabolism* ; Plant Proteins/genetics*

Beta-amylases (BAMs), key enzymes in starch hydrolysis, play an important role in plant growth, development, and resistance to abiotic stress. To mine the saline-alkali tolerance-related BAM genes in alfalfa (Medicago sativa L.), we identified MsBAM genes in the whole genome. The physicochemical properties, phylogeny, gene structures, conserved motifs, secondary structures, promoter cis-acting elements, chromosome localization, and gene replication relationships of BAM gene family members were analyzed. RNA-seq and quantitative real-time PCR (qRT-PCR) were employed to analyze the expression patterns of BAM family members under saline-alkali stress. The results showed that 54 BAM genes were identified in the genome, which were classified into 8 subgroups according to the phylogenetic tree. The members of the same subgroup had similar gene structures except that those of subgroups 1 and 7 had large differences. Conserved motif analysis showed that all MsBAM proteins had a typical glycohydrolysis domain. The chromosome localization analysis showed that MsBAM gene family members were unevenly distributed on 27 chromosomes. The duplication of gene segments led to the increase in BAM gene number in alfalfa. The promoters of BAM genes contained a large number of elements in response to plant hormones and stress. Transcriptome data and qRT-PCR results showed that the expression levels of most MsBAM genes were up-regulated in response to saline-alkali stress. Under the saline-alkali stress, the expression levels of 28 genes, including MsBAM6, were up-regulated on days 1 and 7, and those of 5 genes, including MsBAM9, were up-regulated by over 2 folds. In addition, under salt-alkali stress, BAM activity and soluble sugar content were significantly increased. These results indicate that BAM genes play a key role in alfalfa in response to saline-alkali stress, laying a foundation for further research in this field.
Medicago sativa/physiology* ; beta-Amylase/metabolism* ; Phylogeny ; Gene Expression Regulation, Plant ; Stress, Physiological/genetics* ; Multigene Family ; Alkalies ; Plant Proteins/genetics*

Picea mongolica, known for its remarkable tolerance to cold, drought, and salinity, is a key species for ecological restoration and urban greening in the "Three Norths" region of China. MYB transcription factors are involved in plant responses to abiotic stress and synthesis of secondary metabolites. However, studies are limited regarding the MYB transcription factors in P. mongolica and their roles in salt stress tolerance. In this study, 196 MYBs were identified based on the genome of Picea abies and the transcriptome of P. mongolica. Phylogenetic analysis classified the MYB transcription factors into seven subclasses. The R2R3-MYB subclass contained the maximum number of genes (84.77%), while the R-R and R1R2R3 subclasses each represented the smallest proportion, at about 0.51%. The MYB transcription factors within the same subclass were highly conserved, exhibiting similar motifs and gene structures. Experiments with varying salt stress gradients revealed that P. mongolica could tolerate the salt concentration up to 1 000 mmol/L. From the transcriptome data of P. mongolica exposed to salt stress (1 000 mmol/L) for 0, 3, 6, 12, and 24 h, a total of 34 differentially expressed MYBs were identified, which suggested that these MYBs played a key role in regulating the response to salt stress. The proteins encoded by these differentially expressed genes varied in length from 89 aa to 731 aa, with molecular weights ranging from 10.19 kDa to 79.73 kDa, isoelectric points between 4.80 and 9.91, and instability coefficients from 41.20 to 70.99. Subcellular localization analysis indicated that most proteins were localized in the nucleus, while three were found in the chloroplasts. Twelve MYBs were selected for quantitative real-time PCR (qRT-PCR), which showed that their expression patterns were consistent with the RNA-seq data. This study provides valuable data for further investigation into the functions and mechanisms of MYB family members in response to salt stress in P. mongolica.
Picea/physiology* ; Transcription Factors/classification* ; Salt Stress/genetics* ; Phylogeny ; Plant Proteins/genetics* ; Salt Tolerance/genetics* ; Gene Expression Regulation, Plant

Cucumber (Cucumis sativus L.) is one of the most widely cultivated vegetables in the world. High temperature and other stress conditions can affect the growth and development of this plant, even leading to the decreases in yield and quality. The mitogen-activated protein kinase (MAPK) family plays a crucial role in plant stress responses. However, the role of MPK4 in the stress response of cucumber remains to be reported. In this study, we cloned CsMPK4, which encoded 383 amino acid residues. The qRT-PCR results showed that the expression level of CsMPK4 was the highest in leaves and flowers, moderate in roots, and the lowest in stems and tendrils. CsMPK4 was located in the nucleus and cytoplasm, and it had a close relationship with CmMPK4 in muskmelon. The cucumber plants overexpressing CsMPK4 became stronger and shorter, with reduced length and quantity of tendrils. Moreover, the transgenic seedlings were more resistant to high temperatures, with decreased malondialdehyde (MDA) content and increased activities of peroxidase (POD) and superoxide dismutase (SOD) in young leaves. Furthermore, the protein-protein interaction between CsMPK4 and CsVQ10, a member of the valine-glutamine family, was confirmed by yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays. The results suggested that CsVQ10 cooperated with CsMPK4 in response to the high temperature stress in cucumber. This study laid a foundation for the further study on the stress response mechanism of CsMPK4 and the breeding of stress-resistant cucumber varieties.
Cucumis sativus/metabolism* ; Mitogen-Activated Protein Kinases/physiology* ; Plant Proteins/metabolism* ; Plants, Genetically Modified/metabolism* ; Gene Expression Regulation, Plant ; Stress, Physiological/genetics* ; Cloning, Molecular

Sucrose non-fermenting 1-related protein kinase 1 (SnRK1) is one of the highly conserved Ca²⁺ non-dependent serine/threonine protein kinases, playing a crucial role in regulating the stress responses, growth, and development of plants. SnRK1 is a three-subunit complex, and it is involved in responding to the signaling transduction induced by low-energy/low-sugar conditions. SnRK1 responds biotic and abiotic stress conditions (such as salt, drought, low/high temperatures, and diseases) through phosphorylation of key metabolic enzymes and regulatory proteins, regulation of transcription, and interactions with other proteins. Furthermore, SnRK1 is not only involved in hormone signaling pathways mediated by abscisic acid (ABA), jasmonic acid (JA) and salicylic acid (SA), but also regulates plant autophagy by inhibiting the activity of target of rapamycin (TOR). In this review, we summarized the current results of research on the discovery, structure, and classification of plant SnRK1 and its roles in the stress responses, growth, and development of plants. Furthermore, this article proposes the directions of future research. This review provides good genetic resources and a theoretical basis for the genetic improvement and biological breeding for enhancing the stress tolerance of crops.
Stress, Physiological/physiology* ; Protein Serine-Threonine Kinases/metabolism* ; Plant Development/genetics* ; Signal Transduction ; Gene Expression Regulation, Plant ; Plant Proteins/physiology* ; Plants/metabolism* ; Arabidopsis Proteins/physiology* ; Plant Growth Regulators/metabolism*

Small nuclear RNAs (snRNAs) refer to a class of highly abundant and functionally important non-coding small RNAs that are localized in the eukaryotic nucleus. These snRNAs are highly conserved in different eukaryotes during evolution and form complexes with specific chaperones to fulfill critical biological functions, including precursor messenger RNA (pre-mRNA) splicing and ribosomal RNA (rRNA) modification. Consequently, the regulation of snRNA gene expression is a crucial biological process for plants. In plants, the transcription and processing of snRNAs are regulated by RNA polymerase (Pol), snRNA-activating protein complex (SNAPc), defective in snRNA processing (DSP), and specific cis-elements in the snRNA promoter regions. Proper regulation of snRNA expression is essential for normal plant growth, development, and stress responses. This review summarizes the classification, structures, transcriptional regulation, and biological functions of plant snRNA genes, while outlining future research directions for snRNAs.
RNA, Small Nuclear/physiology* ; Gene Expression Regulation, Plant ; Transcription, Genetic ; Plants/metabolism* ; RNA, Plant/genetics*

Flowering and bolting are important agronomic traits in cruciferous crops such as Brassica juncea. Timely flowering can ensure the crop organ yield and quality, as well as seed propagation. The WRKY family plays an important role in regulating plant bolting and flowering, while the function and mechanism of WRKY12 in B. juncea remain unknown. To explore its function and mechanism in bolting and flowering of B. juncea, we cloned and characterized the BjuWRKY12 gene in B. juncea and found that its expression levels were significantly higher in flowers and inflorescences than in leaves. BjuWRKY12 belonged to the Ⅱc subfamily of the WRKY family, and subcellular localization indicated that the protein was located in the nucleus. Ectopic overexpression of BjuWRKY12 in transgenic lines promoted bolting and flowering, leading to significant increases in the expression levels of flowering integrators SOC1 and FUL. Furthermore, yeast one-hybrid and dual luciferase reporter system assays confirmed that BjuWRKY12 directly bound to the promoters of BjuSOC1 and BjuFUL, undergoing protein-DNA interactions. This discovery gives new insights into the regulation network and molecular mechanisms of BjuWRKY12, laying a theoretical foundation for the breeding of high-yield and high-quality varieties of B. juncea.
Mustard Plant/metabolism* ; Flowers/growth & development* ; Plant Proteins/physiology* ; Promoter Regions, Genetic/genetics* ; Gene Expression Regulation, Plant ; Plants, Genetically Modified/genetics* ; Transcription Factors/metabolism* ; MADS Domain Proteins/metabolism*

Stresses induced by the deficiency or excess of trace mineral elements, such as manganese (Mn), represent a common limiting factor for the production of crops like Brassica napus. To identify key genes involved in Mn allocation in B. napus and elucidate the underlying mechanisms, a member of the metal tolerance protein (MTP) family obtained in the previous screening of cDNA library of B. napus under Mn stress was selected as the research subject. Based on the sequence information and phylogenetic analysis, it was named as BnMTP10. It belongs to the Mn-cation diffusion facilitator (CDF) subfamily. Expression of BnMTP10 in yeast significantly improved the tolerance of transformants to excessive Mn and iron (Fe) and reduced the accumulation of Mn and Fe. However, the yeast transformants exhibited no significant changes in tolerance to excess cadmium, boron, aluminum, zinc, or copper. The qRT-PCR results demonstrated that the flowers of B. napus had the highest expression of BnMTP10, followed by roots and leaves. Subcellular localization studies revealed that BnMTP10 was localized in the endoplasmic reticulum (ER). Compared with wild-type plants, transgenic Arabidopsis overexpressing BnMTP10 exhibited enhanced tolerance to excessive Mn stress but showed no significant difference under Fe stress. Correspondingly, under excessive Mn stress, the Mn content in the roots of transgenic Arabidopsis increased significantly. However, under excessive Fe stress, the Fe content in transgenic Arabidopsis did not alter significantly. According to the results, we hypothesize that BnMTP10 may alleviate excessive Mn stress in plants by mediating Mn transport to the ER. This study facilitated our understanding of efficient mineral nutrients, and provided theoretical foundations and gene resources for breeding B. napus.
Brassica napus/genetics* ; Manganese/metabolism* ; Plants, Genetically Modified/genetics* ; Plant Proteins/physiology* ; Arabidopsis/metabolism* ; Gene Expression Regulation, Plant ; Phylogeny ; Cation Transport Proteins/metabolism* ; Stress, Physiological

The plant AT-rich sequence and zinc-binding protein (PLATZ) family is composed of plant-specific zinc finger-like transcription factors, which play important roles in plant growth, development, and stress tolerance. In this study, to gain a better understanding of the PLATZ gene in C. sinensis and elucidate its response under drought and high temperature conditions, the PLATZ gene family of the C. sinensis cultivar 'Tieguanyin' was systematically identified, and a total of 12 CsPLATZ family members were identified. Expasy online and other bioinformatics tools were used to analyze the members of the PLATZ gene family in terms of protein physicochemical properties, phylogenetic relationships, cis-acting elements, gene structures, and intra- and inter-species collinearity. The results of phylogenetic analysis classified the CsPLATZ family members into 2 subfamilies. The conserved domains and gene structures of PLATZ family members within the same subfamily had a high degree of consistency, whereas a certain degree of diversity was observed among the subfamilies. Twelve PLATZ genes were unevenly distributed across 7 chromosomes of C. sinensis and the promoter regions of these genes had multiple cis-acting elements related to hormone and stress responses. The collinearity analysis showed that there were 4 pairs of duplication events in the CsPLATZ gene family, all of which were segmental duplications. Based on this gene family, C. sinensis had a closer evolutionary relationship with A. thaliana than with O. sativa. The transcriptome analysis showed that the expression levels of CsPLATZ family members varied in different tissue samples of C. sinensis. 6 genes (CsPLATZ-1, CsPLATZ-2, CsPLATZ-3, CsPLATZ-4, CsPLATZ-6, and CsPLATZ-8) with high expression in shoots, young leaves, and roots were selected for high temperature and drought stress treatments, and their expression was quantified by qRT-PCR. The results indicated that the six genes might play important roles in the response to drought stress. In addition, CsPLATZ-2 and CsPLATZ-8 might have important functions in the response to high temperature stress. The results of this study will contribute to a better understanding of the biological functions of PLATZ genes and their possible roles in the growth, development, and stress responses of C. sinensis.
Droughts ; Camellia sinensis/physiology* ; Phylogeny ; Gene Expression Regulation, Plant ; Plant Proteins/genetics* ; Stress, Physiological/genetics* ; Multigene Family ; Transcription Factors/genetics* ; Hot Temperature ; Genes, Plant