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学者姓名：马留银
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Abstract ：
Background Eucalyptus is one of the most important fast-growing tree species in the world, and its growth and development are significantly affected by nitrogen and phosphorus. The Amino acid/auxin permease (AAAP) gene family plays key roles in long-distance amino acid transport in plants, but their evolutionary diversity and gene expression analysis in Eucalyptus grandis under nutrient deficiency stress are largely unexplored. Results This study presents the first genome-wide identification and functional characterization of 78 AAAP family genes (EgAAAPs) in Eucalyptus grandis, classified into eight subfamilies. Phylogenetic analysis of 28 species across five evolutionary stages revealed the AAAP family's classification into three groups: Group III originating from green algae and Groups I-II from mosses. This study underscores lineage-specific expansions (e.g., Eucalyptus AAPs) and algal ancestors as pivotal drivers of functional diversification during early land plant adaptation. Structural analysis revealed subfamily-specific features, including conserved motifs, domain variations, and exon-intron heterogeneity, underpinning functional divergence. Tandem duplication dominated EgAAAP expansion, with syntenic conservation to Populus trichocarpa offering molecular insights into Myrtaceae-Salicaceae divergence. Transcriptional regulatory networks identified 166 transcription factors (MYBs, WRKYs, NACs), with subgroup-specific cis-element enrichment: WRKY binding in Group II and RGA-LIKE1 in Groups I/III, mechanistically linking phosphate/nitrogen signaling. Cross-species interaction hubs of key EgAAAPs (e.g., EgAAAP37, EgAAAP38, EgAAAP41, EgAAAP42, EgAAAP43 and EgAAAP78) with stress-responsive proteins (ABCG40, STP1), amino acid transporters (UMAMITs, CAT5/6), and metal carriers (YSLs) revealed woody plant-specific networks absent in Arabidopsis. Spatiotemporal expression profiling delineated six tissue-specific clusters and dynamic hormonal responses: SA/JA induced temporally distinct modules (early, sustained, delayed), while boron/nitrogen/phosphorus deficiency triggered subgroup- and tissue-dependent regulation. Conclusions Collectively, this study deciphers the evolutionary innovation, regulatory complexity, and functional specialization of AAAP transporters in Eucalyptus, providing a framework for understanding nutrient signaling and stress resilience in woody plants.
Keyword ：
Amino acid/Auxin permease Amino acid/Auxin permease Boron deficiency Boron deficiency Eucalyptus grandis Eucalyptus grandis Gene expression Gene expression Gene family evolution Gene family evolution Nitrogen deficiency Nitrogen deficiency Phosphate starvation Phosphate starvation
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| GB/T 7714 | Wei, Jiahui , Han, Yi , Xu, Huiming et al. AAAP gene family evolution and transcriptional regulation in Eucalyptus grandis under nitrogen, phosphate and boron deficiencies [J]. | BMC PLANT BIOLOGY , 2025 , 25 (1) . |
| MLA | Wei, Jiahui et al. "AAAP gene family evolution and transcriptional regulation in Eucalyptus grandis under nitrogen, phosphate and boron deficiencies" . | BMC PLANT BIOLOGY 25 . 1 (2025) . |
| APA | Wei, Jiahui , Han, Yi , Xu, Huiming , Deng, Lichuan , Li, Lu , Zhang, Shasha et al. AAAP gene family evolution and transcriptional regulation in Eucalyptus grandis under nitrogen, phosphate and boron deficiencies . | BMC PLANT BIOLOGY , 2025 , 25 (1) . |
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The phosphate starvation response (PHR) transcription factor family play central regulatory roles in nutrient signaling, but its relationship with other abiotic stress remains elusive. In the woody plant Eucalyptus grandis, we characterized 12 EgPHRs, which were phylogenetically divided into three groups, with group I exhibiting conserved structural features (e.g., unique motif composition and exon number). Notably, a protein-protein interaction network analysis revealed that EgPHR had a species-specific protein-protein interaction network: EgPHR6 interacted with SPX proteins of multiple species, while Eucalyptus and poplar PHR uniquely bound to TRARAC-kinesin ATPase, suggesting functional differences between woody and herbaceous plants. A promoter sequence analysis revealed a regulatory network of 59 transcription factors (TFs, e.g., BPC, MYBs, ERFs and WUS), mainly associated with tissue differentiation, abiotic stress, and hormonal responses that regulated EgPHRs' expression. Transcriptomics and RT-qPCR gene expression analyses showed that all EgPHRs dynamically responded to phosphate (Pi) starvation, with the expression of EgPHR2 and EgPHR6 exhibiting sustained induction, and were also regulated by salt, cold, jasmonic acid, and boron deficiency. Strikingly, nitrogen starvation suppressed most EgPHRs, highlighting crosstalk between nutrient signaling pathways. These findings revealed the multifaceted regulatory role of EgPHRs in adaptation to abiotic stresses and provided insights into their unique evolutionary and functional characteristics in woody plants.
Keyword ：
boron deficiency boron deficiency cold stress cold stress Eucalyptus grandis Eucalyptus grandis gene expression gene expression nitrogen starvation nitrogen starvation phosphate starvation phosphate starvation PHR PHR salt stress salt stress transcription factor transcription factor
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| GB/T 7714 | Xu, Huiming , Xing, Yifan , Li, Guangyou et al. Decoding PHR-Orchestrated Stress Adaptation: A Genome-Wide Integrative Analysis of Transcriptional Regulation Under Abiotic Stress in Eucalyptus grandis [J]. | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2025 , 26 (7) . |
| MLA | Xu, Huiming et al. "Decoding PHR-Orchestrated Stress Adaptation: A Genome-Wide Integrative Analysis of Transcriptional Regulation Under Abiotic Stress in Eucalyptus grandis" . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 26 . 7 (2025) . |
| APA | Xu, Huiming , Xing, Yifan , Li, Guangyou , Wang, Xin , Zhou, Xu , Lu, Zhaohua et al. Decoding PHR-Orchestrated Stress Adaptation: A Genome-Wide Integrative Analysis of Transcriptional Regulation Under Abiotic Stress in Eucalyptus grandis . | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES , 2025 , 26 (7) . |
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Malate dehydrogenases are pivotal in plant metabolism and stress responses, yet their evolutionary dynamics and functional diversification in woody angiosperms remain underexplored. This study comprehensively characterized the Eucalyptus grandis MDH (EgMDH) gene family to elucidate its roles in development and environmental adaptation. We identified 14 EgMDH genes and conducted phylogenetic, structural, and syntenic analyses to trace their evolutionary origins. Transcriptional networks were deciphered using cis-regulatory element analysis and protein interaction predictions. Spatiotemporal expression under hormone treatments (JA, SA), abiotic stresses (salt, cold), and nutrient deficiencies (phosphate, nitrogen, and boron) was profiled via transcriptome data or RT-qPCR experiments. Phylogenetics revealed three MDH clades: green algal-derived Groups I/II and red algal-derived Group III. Phylogenetics analysis with model plants revealed that Eucalyptus lacked Group III MDHs, while Poplar lacked Group II members, indicating lineage-specific gene loss in woody angiosperms. Four segmental duplicated paralog pairs (EgMDH1/3, 6/9, 10/11, 12/14) exhibited conserved motifs, exon distributions, and synteny with woody dicots, underscoring structural conservation across angiosperms. Sixty transcription factors (TFs) coordinated EgMDH expression, linking them to energy/stress adaptation and secondary metabolism. Subtype-specific regulators (e.g., GT-2, AIL6, NLP6) exclusively targeted Group II EgMDHs, indicating clade-divergent regulatory networks. EgMDHs showed tissue- and stage-dependent expression, particularly during late adventitious root development. EgMDH genes also exhibited temporally distinct expression patterns under JA treatment, SA treatment, salt stress and cold stress conditions. Notably, eleven EgMDH proteins interacted with PPC1/ASP3, coupling malate metabolism to nitrogen/phosphate homeostasis and C/N balance. Taken together, EgMDH genes displayed phased temporal and tissue-specific expression under Pi/N/B deficiencies. These results revealed that coordinated transcriptional reprogramming and protein interactions of EgMDHs were critical for nutrient stress adaptation. Overall, this study suggested that EgMDH genes underwent lineage-specific diversification and played important roles in development and stress resilience.
Keyword ：
boron deficiency boron deficiency cold stress cold stress Eucalyptus Grandis Eucalyptus Grandis gene expression regulation gene expression regulation MDH MDH nitrogen deficiency nitrogen deficiency phosphate starvation phosphate starvation salt stress salt stress
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| GB/T 7714 | Xing, Yifan , Xu, Huiming , Yang, Deming et al. Genome-wide identification and gene expression analysis of the malate dehydrogenase (MDH) gene family in Eucalyptus grandis [J]. | FRONTIERS IN PLANT SCIENCE , 2025 , 16 . |
| MLA | Xing, Yifan et al. "Genome-wide identification and gene expression analysis of the malate dehydrogenase (MDH) gene family in Eucalyptus grandis" . | FRONTIERS IN PLANT SCIENCE 16 (2025) . |
| APA | Xing, Yifan , Xu, Huiming , Yang, Deming , Deng, Lichuan , Li, Guolong , Zhao, Zhixin et al. Genome-wide identification and gene expression analysis of the malate dehydrogenase (MDH) gene family in Eucalyptus grandis . | FRONTIERS IN PLANT SCIENCE , 2025 , 16 . |
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Phosphorus (P), a critical macronutrient for plant growth and reproduction, is primarily acquired and translocated in the form of inorganic phosphate (Pi) by roots. Pi deficiency is widespread in many natural ecosystems, including forest plantations, due to its slow movement and easy fixation in soils. Plants have evolved complex and delicate regulation mechanisms on molecular and physiological levels to cope with Pi deficiency. Over the past two decades, extensive research has been performed to decipher the underlying molecular mechanisms that regulate the Pi starvation responses (PSR) in plants. This review highlights the prospects of Pi uptake, transport, and signaling in woody plants based on the backbone of model and crop plants. In addition, this review also highlights the interactions between phosphorus and other mineral nutrients such as Nitrogen (N) and Iron (Fe). Finally, this review discusses the challenges and potential future directions of Pi research in woody plants, including characterizing the woody-specific regulatory mechanisms of Pi signaling and evaluating the regulatory roles of Pi on woody-specific traits such as wood formation and ultimately generating high Phosphorus Use Efficiency (PUE) woody plants.
Keyword ：
Phosphorus Phosphorus Signaling Signaling Transport Transport Uptake Uptake Woody Plants Woody Plants
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| GB/T 7714 | Xingyan Fang , Deming Yang , Lichuan Deng et al. Phosphorus uptake, transport, and signaling in woody and model plants [J]. | Forestry Research , 2024 , 017 (4) : 0 . |
| MLA | Xingyan Fang et al. "Phosphorus uptake, transport, and signaling in woody and model plants" . | Forestry Research 017 . 4 (2024) : 0 . |
| APA | Xingyan Fang , Deming Yang , Lichuan Deng , Yaxin Zhang , Zhiyong Lin , Jingjing Zhou et al. Phosphorus uptake, transport, and signaling in woody and model plants . | Forestry Research , 2024 , 017 (4) , 0 . |
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Yaks are tough animals living in Tibet's hypoxic stress environment. However, the metabolite composition of yak milk and its role in hypoxic stress tolerance remains largely unexplored. The similarities and differences between yak and human milk in hypoxic stress tolerance are also unclear. This study explored yak colostrum (YC) and yak mature milk (YMM) using GC-MS, and 354 metabolites were identified in yak milk. A comparative metabolomic analysis of yak and human milk metabolites showed that over 70% of metabolites were species-specific. Yak milk relies mainly on essential amino acids- arginine and essential branched-chain amino acids (BCAAs): L-isoleucine, L-leucine, and L-valine tolerate hypoxic stress. To slow hypoxic stress, human breast milk relies primarily on the neuroprotective effects of non-essential amino acids or derivates, such as citrulline, sarcosine, and creatine. In addition, metabolites related to hypoxic stress were significantly enriched in YC than in YMM. These results reveal the unique metabolite composition of yak and human milk and provide practical information for applying yak and human milk to hypoxic stress tolerance.
Keyword ：
colostrum milk colostrum milk comparative metabolomics comparative metabolomics GC-MS GC-MS human breast human breast hypoxic stress tolerance hypoxic stress tolerance mature milk mature milk yak yak
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| GB/T 7714 | Li, Wenhao , Zeng, Weike , Zhang, Yanping et al. A comparative metabolomics analysis of domestic yak (Bos grunniens) milk with human breast milk [J]. | FRONTIERS IN VETERINARY SCIENCE , 2023 , 10 . |
| MLA | Li, Wenhao et al. "A comparative metabolomics analysis of domestic yak (Bos grunniens) milk with human breast milk" . | FRONTIERS IN VETERINARY SCIENCE 10 (2023) . |
| APA | Li, Wenhao , Zeng, Weike , Zhang, Yanping , Ma, Zhijie , Fang, Xingyan , Han, Yingcang et al. A comparative metabolomics analysis of domestic yak (Bos grunniens) milk with human breast milk . | FRONTIERS IN VETERINARY SCIENCE , 2023 , 10 . |
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| GB/T 7714 | Wang, Taotao , Ye, Wenbin , Zhang, Jiaxiang et al. Alternative 3′-untranslated regions regulate high-salt tolerance of Spartina alterniflora (vol 191, pg 2570, 2023) [J]. | PLANT PHYSIOLOGY , 2023 , 192 (3) : 2569-2569 . |
| MLA | Wang, Taotao et al. "Alternative 3′-untranslated regions regulate high-salt tolerance of Spartina alterniflora (vol 191, pg 2570, 2023)" . | PLANT PHYSIOLOGY 192 . 3 (2023) : 2569-2569 . |
| APA | Wang, Taotao , Ye, Wenbin , Zhang, Jiaxiang , Li, Han , Zeng, Weike , Zhu, Sheng et al. Alternative 3′-untranslated regions regulate high-salt tolerance of Spartina alterniflora (vol 191, pg 2570, 2023) . | PLANT PHYSIOLOGY , 2023 , 192 (3) , 2569-2569 . |
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Cryptochromes (CRYs) are vital regulators of blue light-dependent photoresponses, and multiple CRYs were characterized in basal eudicot-sacred lotus (Nelumbo nucifera). However, how blue light senses and regulates photomorphogenesis in sacred lotus remains unexplored. In this study, we found that sacred lotus Cryptochrome 1a (NnCRY1a) regulated photomorphogenesis in a blue light-dependent manner. Phylogenetic analysis revealed that NnCRY1a was closer to CRY1 from another basal eudicot. NnCRY1a showed a dynamic tissue expression pattern in the sacred lotus. NnCRY1a was sensitive to blue light but not in a dose-dependent manner. Over-expression of NnCRY1a in Arabidopsis led to a shorter hypocotyl length under blue light, and NnCRY1a partially rescued the long hypocotyl phenotype of the atcry1 mutant. NnCRY1a interacted with both AtCOP1 and NnCOP1 to deactivate the COP1/SPA complex, thus stimulating the accumulation of AtHY5 mRNAs under blue light. Overall, CRY1 has a conserved function in blue light-mediated hypocotyl elongation from core eudicot-Arabidopsis to the basal eudicot-sacred lotus.
Keyword ：
Blue light Blue light Hypocotyl elongation Hypocotyl elongation Nelumbo nucifera Nelumbo nucifera NnCRY1a NnCRY1a Regulates Regulates
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| GB/T 7714 | Yang, Yong , Guo, Yanan , Yin, Ziyuan et al. Cryptochrome 1 Ubiquitously Regulates Hypocotyl Elongation from Arabidopsis to Sacred Lotus (Nelumbo nucifera) [J]. | JOURNAL OF PLANT GROWTH REGULATION , 2023 , 42 (7) : 4570-4580 . |
| MLA | Yang, Yong et al. "Cryptochrome 1 Ubiquitously Regulates Hypocotyl Elongation from Arabidopsis to Sacred Lotus (Nelumbo nucifera)" . | JOURNAL OF PLANT GROWTH REGULATION 42 . 7 (2023) : 4570-4580 . |
| APA | Yang, Yong , Guo, Yanan , Yin, Ziyuan , Li, Han , Zeng, Weike , Zhang, Jiaxiang et al. Cryptochrome 1 Ubiquitously Regulates Hypocotyl Elongation from Arabidopsis to Sacred Lotus (Nelumbo nucifera) . | JOURNAL OF PLANT GROWTH REGULATION , 2023 , 42 (7) , 4570-4580 . |
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High-salt stress continues to challenge the growth and survival of many plants. Alternative polyadenylation (APA) produces mRNAs with different 3 '-untranslated regions (3 ' UTRs) to regulate gene expression at the post-transcriptional level. However, the roles of alternative 3 ' UTRs in response to salt stress remain elusive. Here, we report the function of alternative 3 ' UTRs in response to high-salt stress in S. alterniflora (Spartina alterniflora), a monocotyledonous halophyte tolerant of high-salt environments. We found that high-salt stress induced global APA dynamics, and similar to 42% of APA genes responded to salt stress. High-salt stress led to 3 ' UTR lengthening of 207 transcripts through increasing the usage of distal poly(A) sites. Transcripts with alternative 3 ' UTRs were mainly enriched in salt stress-related ion transporters. Alternative 3 ' UTRs of HIGH-AFFINITY K+ TRANSPORTER 1 (SaHKT1) increased RNA stability and protein synthesis in vivo. Regulatory AU-rich elements were identified in alternative 3 ' UTRs, boosting the protein level of SaHKT1. RNAi-knock-down experiments revealed that the biogenesis of 3 ' UTR lengthening in SaHKT1 was controlled by the poly(A) factor CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 30 (SaCPSF30). Over-expression of SaHKT1 with an alternative 3 ' UTR in rice (Oryza sativa) protoplasts increased mRNA accumulation of salt-tolerance genes in an AU-rich element-dependent manner. These results suggest that mRNA 3 ' UTR lengthening is a potential mechanism in response to high-salt stress. These results also reveal complex regulatory roles of alternative 3 ' UTRs coupling APA and regulatory elements at the post-transcriptional level in plants. Alternative 3 '-untranslated regions enable post-transcriptional gene expression regulation of high-salt-tolerant genes in Spartina alterniflora.
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| GB/T 7714 | Wang, Taotao , Ye, Wenbin , Zhang, Jiaxiang et al. Alternative 3′-untranslated regions regulate high-salt tolerance of Spartina alterniflora [J]. | PLANT PHYSIOLOGY , 2023 , 191 (4) : 2570-2587 . |
| MLA | Wang, Taotao et al. "Alternative 3′-untranslated regions regulate high-salt tolerance of Spartina alterniflora" . | PLANT PHYSIOLOGY 191 . 4 (2023) : 2570-2587 . |
| APA | Wang, Taotao , Ye, Wenbin , Zhang, Jiaxiang , Li, Han , Zeng, Weike , Zhu, Sheng et al. Alternative 3′-untranslated regions regulate high-salt tolerance of Spartina alterniflora . | PLANT PHYSIOLOGY , 2023 , 191 (4) , 2570-2587 . |
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NAC transcription factors play critical roles in regulating drought stress. However, the drought-responsive NAC transcription factors are largely unexplored in wheat. In this study, we isolated a NAC gene, TaNAC5D-2, and characterized the function of TaNAC5D-2 as a positive regulator of drought tolerance. The expression level of TaNAC5D-2 was induced under drought or abscisic acid treatment. Transient expression and transcriptional activity assays showed that TaNAC5D-2 is localized to the nucleus, and the C-terminal region exhibited transcriptional activity. Overexpression of TaNAC5D-2 in Arabidopsis thaliana led to greater drought tolerance, fresh weight and dry weight than wild-type plants, and the water loss was significant inhibited in the leaves of overexpression lines. Conversely, silencing of TaNAC5D-2 in wheat seedlings led to increased water loss and decreased growth compared to control and negative control plants under drought stress. RNA-Seq and RT-qPCR revealed that many Group A PP2C genes were upregulated in the TaNAC5D-2 silenced plants compared to negative control. And silencing TaNAC5D-2 negatively regulate ABA-induced stomatal closure that led to higher water loss. These data suggest that TaNAC5D-2 acts as a drought-responsive regulator, possibly by an abscisic acid-mediated stomatal closure to control water loss under drought condition.
Keyword ：
BSMV-VIGS BSMV-VIGS Drought stress Drought stress NAC transcription factor NAC transcription factor TaNAC5D-2 TaNAC5D-2
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| GB/T 7714 | Ma, Jianhui , Tang, Xiaoxiao , Sun, Bo et al. A NAC transcription factor, TaNAC5D-2, acts as a positive regulator of drought tolerance through regulating water loss in wheat (Triticum aestivum L.) [J]. | ENVIRONMENTAL AND EXPERIMENTAL BOTANY , 2022 , 196 . |
| MLA | Ma, Jianhui et al. "A NAC transcription factor, TaNAC5D-2, acts as a positive regulator of drought tolerance through regulating water loss in wheat (Triticum aestivum L.)" . | ENVIRONMENTAL AND EXPERIMENTAL BOTANY 196 (2022) . |
| APA | Ma, Jianhui , Tang, Xiaoxiao , Sun, Bo , Wei, Jituo , Ma, Liuyin , Yuan, Meng et al. A NAC transcription factor, TaNAC5D-2, acts as a positive regulator of drought tolerance through regulating water loss in wheat (Triticum aestivum L.) . | ENVIRONMENTAL AND EXPERIMENTAL BOTANY , 2022 , 196 . |
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Plants play a primary role for the global sulfur cycle in the earth ecosystems by reduction of inorganic sulfate from the soil to organic sulfur-containing compounds. How plants sense and transduce the sulfate availability to mediate their growth remains largely unclear. The target of rapamycin (TOR) kinase is an evolutionarily conserved master regulator of nutrient sensing and metabolic signaling to control cell proliferation and growth in all eukaryotes. By tissue-specific Western blotting and RNA-sequencing analysis, we investigated sulfate-TOR signal pathway in regulating shoot apex development. Here, we report that inorganic sulfate exhibits high potency activating TOR and cell proliferation to promote true leaf development in Arabidopsis in a glucose-energy parallel pathway. Genetic and metabolite analyses suggest that this sulfate activation of TOR is independent from the sulfate-assimilation process and glucose-energy signaling. Significantly, tissue specific transcriptome analyses uncover previously unknown sulfate-orchestrating genes involved in DNA replication, cell proliferation and various secondary metabolism pathways, which largely depends on TOR signaling. Systematic comparison between the sulfate- and glucose-TOR controlled transcriptome further reveals that TOR kinase, as the central growth integrator, responds to different nutrient signals to control both shared and unique transcriptome networks, therefore, precisely modulates plant proliferation, growth and stress responses.
Keyword ：
Arabidopsis Arabidopsis cell proliferation cell proliferation shoot apex activation shoot apex activation sulfate sulfate TOR TOR transcriptional reprogramming transcriptional reprogramming
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| GB/T 7714 | Yu, Yongdong , Zhong, Zhaochen , Ma, Liuyin et al. Sulfate-TOR signaling controls transcriptional reprogramming for shoot apex activation [J]. | NEW PHYTOLOGIST , 2022 , 236 (4) : 1326-1338 . |
| MLA | Yu, Yongdong et al. "Sulfate-TOR signaling controls transcriptional reprogramming for shoot apex activation" . | NEW PHYTOLOGIST 236 . 4 (2022) : 1326-1338 . |
| APA | Yu, Yongdong , Zhong, Zhaochen , Ma, Liuyin , Xiang, Chengbin , Chen, Jie , Huang, Xin-Yuan et al. Sulfate-TOR signaling controls transcriptional reprogramming for shoot apex activation . | NEW PHYTOLOGIST , 2022 , 236 (4) , 1326-1338 . |
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