INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
·
2022
·Vol. 23
·期 14
·7574
·
IF 6.208
Weizeng Lv,Xue He,Haojuan Guo,Haibin Lan,Yanqing Jiao,Le Li,Yanhao Lian,Zhiqiang Wang,Zeyu Xin,Yongzhe Ren,Tongbao Lin
Excessive input of nitrogen fertilizer not only causes a great waste of resources but brings about a series of ecological and environmental problems. AlthoughSmall Auxin Up-regulatedRNAs(SAURs) participate in diverse biological processes, the function ofSAURsin the nitrogen starvation response has not been well-studied. Here, we identified 308TaSAURs in wheat and divided them into 10 subfamilies. The promoter regions of mostTaSAURscontain hormone responsive elements, and their expression levels change under the treatment of different hormones, such as IAA, MeJA, and ABA. Interestingly, overexpression of one of theTaSAURfamily members, a nitrogen starvation responsive gene,TaSAUR66-5B, can promote the growth ofArabidopsisand wheat roots. In addition, overexpression ofTaSAUR66-5BinArabidopsisup-regulates the expression levels of auxin biosynthesis related genes, suggesting that overexpressionTaSAUR66-5Bmay promote root growth by increasing the biosynthesis of auxin. Furthermore, overexpression ofTaSAUR66-5Bin wheat can increase the biomass and grain yields of transgenic plants, as well as the nitrogen concentration and accumulation of both shoots and grains, especially under low nitrogen conditions. This study provides important genomic information of theTaSAURgene family and lays a foundation for elucidating the functions ofTaSAURsin improving nitrogen utilization efficiency in wheat.Keywords:TaSAURgene family;TaSAUR66-5B;root;nitrogen utilization efficiency
研究领域:
植物学
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遗传学
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分子生物学
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PubMed
高影响因子
JOURNAL OF PLANT BIOLOGY
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2024
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IF 2.2
Zhan Niheng,Zhao Ziyi,Ren Lingyan,Yang Fuxin,Zhang Chuhan,Qin Lijun,Gong Xian
NAC (NAM/ATAF1,2/CUC2) is one of the most important plant-specific transcription factors, playing a significant role in plant growth, morphogenesis, and stress resilience. In this investigation, 77 members of the NAC gene family were identified from the Eucommia ulmoides database, and these E. ulmoides NAC families were classified into 18 subfamilies based on their protein sequences. Currently, the architectural design, conserved domains, and cis -acting elements of EuNAC genes, as well as physicochemical properties of EuNAC proteins, have also been analyzed. In addition, the expression patterns of selected EuNAC genes under five heavy metal (Cu 2+ , Cd 2+ , Pb 2+ , Mn 2+ , and As 5+ ) imposed stresses were investigated. The results showed that the expression of EuNAC9 experienced a significant induction to upregulate under these five heavy metal stresses, suggesting that EuNAC9 may mediate the response to these five heavy metal stresses. In addition, the function of EuNAC9 was investigated in both transgenic yeasts and tobaccos. The transgenic yeasts exhibited enhanced resistance to Mn 2+ stress by increasing the expression of ScSMF1 and ScSOD2 , whereas the transgenic tobacco grew better under Mn 2+ stress and showed intense antioxidant enzyme activity to alleviate the accumulation of H 2 O 2 and O 2 − . Moreover, subcellular localization indicated EuNAC9 was a nuclear localization protein, and the transcriptional activity domain of EuNAC9 resided at the C-terminal. This study will provide a theoretical framework for analyzing the molecular regulatory mechanisms of plant responses to heavy metals mediated by EuNAC9 genes and elucidating the biological roles of E. ulmoides NACs in responding to heavy metal stress.
研究领域:
植物学
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遗传学
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分子生物学
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高影响因子
BMC GENOMICS
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2025
·Vol. 26
·期 1
·1-16
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IF 3.7
Liu Zhen,Ma Xiaoping,Zeng Xiangwen,Li Zhiguo,Liu Ruiguo,Luo Rongyan,Wang Weichen,Tahir Muhammad Salman,Wang Chengdong,Gu Yu
Alcohol dehydrogenase has been studied in regulation of fungal growth and development, stress response and pathogenesis, but its function in T. asahii remains unexplored. In this study, we analyzed the ADH gene family in T. asahii for the first time, identifying six ADH genes and containing conserved ADH_N and ADH_Zinc_N domains. We constructed an overexpression strain of the most significantly differentially expressed gene TaADH_like and compared its phenotypes with those of the wild-type strain, focusing on colony morphology, biofilm biomass, stress response, drug resistance, and pathogenicity. The results showed that TaADH_like overexpression reduced sensitivity to hypoxic conditions, altered the hyphae-to-yeast transition, and led to slower growth, decreased colonization ability, reduced tissue damage, and lower lethality. Increased osmotic stress sensitivity and the involvement of the HOG MAPK pathway in the hyphae-to-yeast conversion contributed to the reduced colonization capacity of T. asahii . Furthermore, the overexpression of TaADH_like promoted biofilm formation and led to a slight enhancement in fluconazole resistance in T. asahii . This study is the first to elucidate the function of the alcohol dehydrogenase gene in T. asahii , providing a foundation for future genetic research on this pathogen.
研究领域:
微生物学
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遗传学
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医学
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PubMed
高影响因子
Plants-Basel
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2025
·Vol. 14
·期 11
·1576
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IF 4.1
Zhangting Xu,Feixiong Zheng,Xiaoji Deng,Yiming Sun,Zhenming Yu,Xiaoxia Shen
Dendrobium officinale,which was rich in bioactive compounds such as polysaccharides, alkaloids, amino acids, and flavonoids, had significant medicinal value and ability to resist stresses. Studies had demonstrated thatGATAgenes were one of the crucial regulators in controlling plant development and growth and stress response. Genome-wide identification and characterization of the 18DoGATAgenes were displayed. According to phylogenetic relationships, theDoGATAfamily genes were divided into 4 groups and the conserved motifs ofDoGATA1–DoGATA18within the same group were similar. AllDoGATAgenes were localized in the nucleus and randomly mapped on 10 chromosomes. The GATA genes inD. officinaleexperienced one pair of tandem duplication and 4 pairs of segment duplications to expand the family genes. Additionally, we found that the 2000 bp upstream promoter region of theDoGATAgenes harbored 23 types ofcis-acting elements that were categorized into plant growth and development, phytohormone responsiveness, and stress responsiveness.DoGATA1–DoGATA18were diversely expressed across different tissues (root, leaf, stem, flower), exposed to salt stress, and following MeJA treatment. Co-expression analysis betweenDoGATAand enzyme-encoding genes involved in the biosynthesis of flavone showed thatDoCHI(LOC110104562) andDoGTMT(LOC110098370) may be potential downstream targets ofDoGATA16to regulate flavonoid biosynthesis to adapt to salt stress. Furthermore, we confirmed thatDoGATA16may act as a key member to resist stress. The collective findings of this study shed light on the function ofGATAgenes and molecular breeding ofD. officinale.
研究领域:
植物学
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分子生物学
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遗传学
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PubMed
高影响因子
Biology-Basel
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2025
·Vol. 14
·期 4
·411
·
IF 3.5
Qun Zhang,Xiuyue Xu,Ling Yang
Simple SummaryIn this study, theWOXgene family of Korean pine was analyzed, and 21 family members were identified using bioinformatics methods. The results showed that the total number of amino acids in all proteins is between 164 and 488 aa, with molecular weights between 18,456.30 and 53,893.18 Da and isoelectric point values between 5.56 and 9.80. According to the predicted results, the average hydrophilicity coefficient of thePkWOXproteins is between −0.993 and −0.565. The phylogenetic tree divides thePkWOXgenes into three sub-branches. A total of 21PkWOXgenes are unevenly distributed on 7 of 12 chromosomes. ThePkWOXpromoters contain cis-acting elements such as stress response, light response, hormone response, and meristem regulation. GO entry forPkWOXis a biological process and molecular function.PkWOX16was expressed in all tissues.PkWOX2,3had higher expression in the embryonic callus, non-embryonic callus, somatic embryo, and zygotic embryo.PkWOX2,3,and16were located in the nucleus and in the cell membrane. ThePkWOX2and3proteins exhibited transcriptional self-activation activity, whilePkWOX16did not. In this study, the members of the WOX transcription factor family were identified and systematically analyzed in Korean pine, laying a foundation for the research on their functions.(1) Background:WOX(WUSCHEL-related homologous box) is a plant-specific transcription factor involved in plant development and stress response. It has been reported to be involved in processes such as growth and development, stem cell division and differentiation, and organ development; (2) Methods: In this study, bioinformatics was used to identify and analyze theWOXgene family of Korean pine. The gene characteristics were identified and analyzed through yeast transcriptional activation assays as well as subcellular localization experiments; (3) Results: A total of 21 members of theWOXgene family of Korean pine were identified in this study. The phylogenetic tree divides thePkWOXgenes into three sub-branches. 21PkWOXgenes are unevenly distributed on 7 of the 12 chromosomes.PkWOX16was expressed in all tissues.PkWOX2,3had higher expression in the embryonic callus, non-embryonic callus, somatic embryo, and zygotic embryo.PkWOX2,3and16were located in the nucleus and in the cell membrane. ThePkWOX2and3proteins exhibited transcriptional self-activation activity, whilePkWOX16did not; (4) Conclusions: In this study, the members of the WOX transcription factor family in Korean pine were identified and systematically analyzed, laying a foundation for their subsequent functional research.
研究领域:
植物学
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遗传学
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分子生物学
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PubMed
高影响因子
BMC PLANT BIOLOGY
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2025
·Vol. 25
·期 1
·1-14
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IF 4.8
Chen Jing,Li Shoujie,Si Can,Liang Hanzhi,Duan Jun,He Chunmei
Background Abscisic acid (ABA) plays a crucial role in plant growth, development, and stress responses. The pyrabactin resistance-like (PYL) ABA receptor proteins, which are key components of ABA signal recognition and transmission. Dendrobium officinale is a precious traditional Chinese medicinal plant with known drought resistance. Nevertheless, the PYL genes of D. officinale, along with other orchid plants, remains unanalyzed.Results In this study, the PYL family was identified from D. officinale, consisting of 11 PYL proteins. A phylogenetic analysis showed that these DoPYL proteins were classified into three subfamilies. All the DoPYL proteins featured both Motif 1 and Motif 2. Notably, the members of subfamily I and III were intron-less, while those of subfamily II consistently displayed 2 introns. Analysis of expression patterns revealed that these DoPYL genes exhibit diverse spatiotemporal expression profiles in different organs. DoPYL1, DoPYL2, DoPYL4, DoPYL8 DoPYL9 and DoPYL10 followed a decreasing trend as protocorm-like bodies (PLBs) developed into plantlets. Under ABA and mannitol treatments, DoPYL1, DoPYL2, DoPYL4, DoPYL5, DoPYL6 and DoPYL10 exhibited significant down-regulation, while the expression of other genes remained unchanged. Following cold and salinity treatment, there was a notable up-regulation in the expression of the majority of DoPYL genes. PEG-simulated drought stress treatment led to the down-regulation of DoPYL genes. Furthermore, the DoPYL1 protein was localized in the cell membrane, cytoplasm and nucleus. During Yeast two-hybrid Library screening, we identified 40 potential interacting proteins of DoPYL1. Yeast two-hybrid verification confirmed that DoPYL1 interacted with DoRpb3, DoUbox, DoGrx, and DoATPsyn proteins.Conclusion Our results not only contribute to an understanding of the potential role of PYL proteins in growth, development and stress responses in Orchidaceae plants, but also provide additional theoretical guidance for breeding new varieties of D. officinale with resistance to abiotic stresses.
研究领域:
植物分子生物学
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药用植物学
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逆境生理学
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信号转导
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基因家族分析
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PubMed
高影响因子
Genes
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2025
·Vol. 16
·期 2
·184
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IF 2.8
Ruipeng Liu,Tingting Sun,Pengyu Du,Zengcai Liu,Yawei Li,Xinyu Tong,Li Zou
Background: Basic helix–loop–helix (bHLH) transcription factors (TFs) widely exist in eukaryotic organisms and play a key role in plant growth and development in response to environmental stresses.Sanghuangporus baumii, an important medicinal mushroom known for its anticancer properties, has limited research on the bHLH gene family. Methods: This research utilized the genomic data fromS. baumiito identify bHLH family members, and their gene structure, conserved motifs, and phylogenetic relationship were characterized. Additionally, we conducted an analysis of promoter cis-elements and predicted protein interaction networks. We also examined the expression profiles of bHLH genes during different developmental stages and in response to four abiotic stresses: heat, cold, oxidative stress, and heavy metal exposure. Finally, we overexpressed the candidate geneSbbHLH3in yeast to assess its tolerance to these different stress conditions. Results: A total of 12SbbHLHgenes were identified inS. baumii, and the members of the bHLH gene family displayed a variety of physicochemical characteristics, reflecting their diverse array of functions. Based on homology, the SbbHLH proteins are more closely related to those found inLentinula edodesandPleurotus ostreatus. The analysis of promoter cis-elements showed thatSbbHLHs contain several elements associated with abiotic stress response, and a network prediction identified 28 bHLH-interacting proteins. Expression pattern analysis revealed that mostSbbHLHgenes exhibited a positive response to different developmental stages and abiotic stresses. Notably, the overexpression ofSbbHLH3significantly enhanced stress tolerance in yeast. Conclusions: This study provides a comprehensive assessment of the bHLH family inS. baumii, delivering new genetic resources for breeding resistant varieties.
研究领域:
真菌学
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分子生物学
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遗传学
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PubMed
高影响因子
Horticulturae
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2024
·Vol. 10
·期 3
·252
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IF 3.1
Jinliao Chen,Fei Wang,Yangting Zhang,Ruiyue Zheng,Xiaopei Wu,Ye Ai,Sagheer Ahmad,Zhongjian Liu,Donghui Peng
ThePEBPgene family is involved in many biological processes in plants, including plant growth and development, flowering regulation, light response, and abiotic stress response. But there is little information about the role of thePEBPgene family inCymbidiumspecies. In this study, we identified 11, 9, and 7PEBPgenes inC. ensifolium,C. sinense, andC. goeringii, respectively, and mapped them to the chromosomes. We also studied the physicochemical characteristics of the proteins encoded by thesePEBPs and analyzed their intra-species collinearity, gene structure, conserved motifs, and cis-acting elements. Furthermore, a total of forty PEBP genes fromC. sinense,C. ensifolium,C. goeringii,Phalaenopsis, andArabidopsiswere divided into three clades based on the phylogenetic tree. The expression patterns of 11PEBPgenes in different tissues and organs ofC. ensifoliumwere analyzed based on transcriptome data, indicating that theCePEBPs might play an important role in the growth and development, especially in the flower bud organs (1–5 mm).CePEBP5plays an indispensable role in both the vegetative and reproductive growth cycles ofC. ensifolium.CePEBP1is essential for root development, whileCePEBP1,CePEBP3,CePEBP5, andCePEBP10regulate the growth and development of different floral organ tissues at various stages. The findings of this study can do a great deal to understand the roles of thePEBPgene family inCymbidium.
研究领域:
植物学
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分子生物学
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遗传学
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DOI
高影响因子
Aquaculture Reports
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2024
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IF 3.2
Yuru Zhang,Haiying Fan,Kedi Gao,Shibo Zhang,Ronghua Lu,Xianglin Cao,Xinxin Xu,Jiancheng Liu
The grass carp ( Ctenopharyngodon idella ) holds significant economic value worldwide. However, intensive farming practices often result in lipid metabolic disorder of fish. It is essential to explore the influence of pivotal genes in the process of fat accumulation, particularly from the perspective of fat transport. Fatty acid binding proteins (FABPs) are crucial for selectively binding and transporting free fatty acids (FAs) within cells. Nevertheless, the types of fabp genes in the grass carp genome and their responses to various FAs remain unclear. In the current study, exhaustive bioinformatic analysis identified nine fabp genes in the grass carp genome: fabp1a, fabp1b.1, fabp2, fabp3, fabp6, fabp7a, fabp10a, fabp11a, and fabp11b . Although these genes showed widespread expression across various tissues, each gene displayed distinct preferences for specific primary expression tissues. Notably, fabp1a exhibited prominent expression in muscle, fabp1b.1 in abdominal fat, fabp2 and fabp6 in the intestine, fabp7a in the brain, fabp10a in the hepatopancreas, and fabp11a showed maximal expression in the eye. Findings from primary grass carp hepatocytes revealed that the addition of palmitic acid (PA), high concentrations oleic acid (OA) and docosahexaenoic acid (DHA) (400 µM), significantly increased intracellular lipid accumulation. Intriguingly, the addition of PA resulted in increased expression of fabp2 and fabp11a , while DHA significantly enhanced the expression of fabp7a ( P < 0.01). Given that the accumulated FAs are primarily saturated fatty acids, these results suggest that regulating fabps , especially fabp2 and fabp11a, could be a strategy to control fat deposition in grass carp.
研究领域:
水产养殖学
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分子生物学
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DOI
高影响因子
PLANT PHYSIOLOGY AND BIOCHEMISTRY
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2021
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IF 4.27
Yu-Feng Xie,Rong-Xiang Zhang,Li-Jun Qin,La-la Song,De-Gang Zhao,Zhong-min Xia
MYB proteins play a crucial role in plant growth and development and stress responses. In this study, 160 members of the MYB gene family from the pepper genome database were used to analyze gene structures, chromosome localization, collinearity, genetic affinity and expression in response to heavy metals . The results identified R2R3-MYB members and further phylogenetically classified them into 35 subgroups based on highly conserved gene structures and motifs. Collinearity analysis showed that segmental duplication events played a crucial role in the functional expansion of the CaMYB gene family by intraspecific collinearity, and at least 12 pairs of CaMYB genes existed between species prior to the differentiation between monocots and dicots . Moreover, the upstream CaMYB genes were mainly localized to the phytohormone elements ABRE and transcription factor elements MYB and MYC. Further analysis revealed that MYB transcription factors were closely associated with a variety of abiotic stress-related proteins (e.g., MAC-complex and SKIP). Under the stress of five metal ions, Cd 2+ , Cu 2+ , Pb 2+ , Zn 2+ , and Fe 3+ , the expression levels of some CaMYB family genes were upregulated. Of these genes, pairing homologous 1 ( PH-1 ), PH-13 , and PH-15 in the roots of Capsicum annuum were upregulated to the greatest extent, indicating that these three MYB family members are particularly sensitive to these five metals. This study provides a theoretical reference for the analysis of the molecular regulatory mechanism of MYB family genes in mediating the response to heavy metals in plants. This study reveals the mode of interaction between MYB and a variety of abiotic stress proteins and clarifies the biological functions of CaMYB family members in the regulation of heavy metal stress.
研究领域:
植物学
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遗传学
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环境科学
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DOI
PubMed
高影响因子
MOLECULAR IMMUNOLOGY
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2024
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IF 3.2
Chaonan Zhu,Zhiquan Chen,Shuai Wang,Junmei Cao,Yuan Cheng,Maogen Zheng
Lung adenocarcinoma (LUAD) is a highly heterogeneous disease that threaten human life with serious incidence and high mortality. High heterogeneity of tumor microenvironment (TME) was reported in multiple studies. However, the factor of controlling the tumor migration progression between eary and late-stage LUAD is still not fully understood. In this study, we conducted a comprehensive analysis of single-cell RNA sequencing (scRNA-seq) data of LUAD obtained from the GEO database. The identification of cell clusters revealed significant expansion of epithelial cells in late-stage patients. Interpretation of the cell-cell communication results between early-stage and late-stage patient samples indicated that early tumor cells may interact with epithelial cells through the TGF-β pathway to promote tumor progression. The cell cycle analysis demonstrated a significant increase in the number of cells in the G2 and M phases in late-stage lung cancer. Further analysis using Non-negative Matrix Factorization (NMF) revealed early-stage cell-specific gene features involved in cell adhesion-related biological processes. Among these, the Tensin (TNS) gene family, particularly TNS1, showed high expression in epithelial cells and fibroblasts of early-stage samples, specifically associated with cell adhesion. Survival analysis using TCGA database for LUAD demonstrated that patients with high expression of TNS1 exhibited significantly higher overall survival rates compared to those with low expression. Immunofluorescence experiments have demonstrated co-expression of TNS1 with fibroblast and tumor cell markers (α-SMA and EPCAM). Immunohistochemistry experiments further validated the significantly higher expression levels of TNS1 in early-stage LUAD tissues compared to late-stage lung cancer tissues (P<0.05). Pathway experiments have shown that early-stage tumor patients with high expression of TNS1 exhibit stronger phosphorylation levels of Akt and mTOR, indicating a more potent activation of the Akt/mTOR signaling pathway. In conclusion, the results of this study demonstrate that TNS1 is an adhesive molecule in the immune microenvironment of early-stage tumor cells, and it may serve as a novel prognostic marker for lug cancer.
研究领域:
肿瘤学
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分子生物学
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基因组学
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细胞生物学
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癌症生物学
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DOI
PubMed
高影响因子
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
·
2024
·Vol. 25
·期 22
·11967
·
IF 4.9
Yuzhen Tian,Xizi Wang,Huoqing Huang,Xin Deng,Baihong Zhang,Yixuan Meng,Libo Wu,Hang Chen,Yun Zhong,Wenli Chen
Citrus Huanglongbing (HLB) is the most destructive citrus disease worldwide. The etiological agent responsible for this disease is “CandidatusLiberibacter asiaticus” (CLas), a phloem-restricted bacterium transmitted by psyllid vectors. To date, effective practical strategies for curing Citrus HLB remain elusive. Additionally, no susceptibility genes associated with HLB have been identified in Citrus species, thereby complicating the application of gene-editing techniques such as CRISPR-Cas9 to enhance resistance to HLB. The co-chaperoneDnaJplays a crucial role in protein folding and the regulation of various physiological activities, and it is also associated with multiple pathological processes.DnaJhas been extensively studied in many species, including Arabidopsis, rice, and wheat. However, there is limited information available regarding the DnaJ gene family in citrus. In this study, we conducted a comprehensive genome-wide analysis of the DnaJ family genes in various Citrus species. The Citrus genome was identified to contain 86DnaJgenes, which were unevenly distributed across nine chromosomes. Phylogenetic analysis indicated that these genes could be classified into six distinct groups. Furthermore, transcriptomic analysis revealed that nineDnaJgenes exhibited significantly higher induction in HLB-infected samples relative to non-HLB-infected Citrus.Cis-acting elements within the promoters ofDnaJgenes were also examined, revealing the presence of hormone and defense/stress responsiveness elements (TC-rich) distributed on theClDJC24gene. The results were validated using quantitative real-time PCR (qRT-PCR). Additionally, the silencing ofClDJC24suggested that this gene negatively regulates disease resistance in Citrus. Our study provided useful clues for further functional characterization and constructed a theoretical foundation for disease-resistant breeding in Citrus.
研究领域:
植物病理学
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分子生物学
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基因组学
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植物遗传学
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产品关联
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）