International Journal of Molecular Sciences

Research

Jump to: Review

17 pages, 3581 KiB

Open AccessArticle

Role of GmFRI-1 in Regulating Soybean Nodule Formation Under Cold Stress

by Hongcai Zhang, Lin He, Huiyun Li, Nengfu Tao, Tianda Chang, Dongmei Wang, Yichu Lu, Zhenying Li, Chunhai Mai, Xiaorui Zhao, Bingjie Niu, Junkui Ma and Lixiang Wang

Int. J. Mol. Sci. 2025, 26(3), 879; https://doi.org/10.3390/ijms26030879 - 21 Jan 2025

Viewed by 855

Abstract

Symbiotic nitrogen fixation, recognized as the most efficient nitrogen assimilation system in ecosystems, is essential for soybean growth, as nodulation provides critical nitrogen to host cells. Soybeans thrive in warm and moist environments. However, they are highly susceptible to low temperatures, which impede [...] Read more.

Symbiotic nitrogen fixation, recognized as the most efficient nitrogen assimilation system in ecosystems, is essential for soybean growth, as nodulation provides critical nitrogen to host cells. Soybeans thrive in warm and moist environments. However, they are highly susceptible to low temperatures, which impede the formation and development of root nodules. The genetic basis and molecular mechanism underlying the inhibition of nodulation induced by low temperatures remain unclear. In this study, we conducted a comparative transcriptomic analysis of soybean roots inoculated with rhizobium at 1 DPI (Day Post Inoculation) under normal or cold treatments. We identified 39 up-regulated and 35 down-regulated genes associated with nodulation and nitrogen fixation. Notably, cold-responsive genes including three FRI (Frigida) family genes were identified among differentially expressed genes (DEGs). Further expression pattern analysis of GmFRI-1 demonstrated it being significantly responsive to rhizobium inoculation and its highest expression in nodules. Further investigation revealed that overexpression of GmFRI-1 led to an increase in the nodule number, while RNA interference (RNAi)-mediated gene editing of GmFRI-1 suppressed nodule formation. Additionally, GmFRI-1 overexpression may regulate soybean nodulation by modulating the expression of GmNIN (NODULE INCEPTION), GmNSP1 (nodulation signaling pathway 1), and GmHAP2-2 (histone- or haem-associated protein domain) in the nod factor signaling pathway. This study offers new insights into the genetic basis of nodulation regulation under cold stress in legumes and indicates that GmFRI-1 may serve as a key regulator of nodule formation under cold stress. Full article

(This article belongs to the Special Issue Plant–Microbe Interactions)

► Show Figures

Figure 1

16 pages, 2718 KiB

Open AccessArticle

Application of Synthetic Microbial Communities of Kalidium schrenkianum in Enhancing Wheat Salt Stress Tolerance

by Jing Zhu, Qiong Jia, Qi-Yong Tang, Ghenijan Osman, Mei-Ying Gu, Ning Wang and Zhi-Dong Zhang

Int. J. Mol. Sci. 2025, 26(2), 860; https://doi.org/10.3390/ijms26020860 - 20 Jan 2025

Viewed by 921

Abstract

Soil salinization poses a significant challenge to global agriculture, particularly in arid and semi-arid regions like Xinjiang. Kalidium schrenkianum, a halophytic plant adapted to saline-alkaline conditions, harbors endophytic microorganisms with potential plant growth-promoting properties. In this study, 177 endophytic bacterial strains were [...] Read more.

Soil salinization poses a significant challenge to global agriculture, particularly in arid and semi-arid regions like Xinjiang. Kalidium schrenkianum, a halophytic plant adapted to saline-alkaline conditions, harbors endophytic microorganisms with potential plant growth-promoting properties. In this study, 177 endophytic bacterial strains were isolated from K. schrenkianum, and 11 key strains were identified through functional screening based on salt tolerance, nutrient solubilization, and growth-promoting traits. Synthetic microbial communities (SMCs) were then constructed using these strains and optimized to enhance wheat growth under salt stress. The SMCs significantly improved seed germination, root length, and seedling vigor in both spring and winter wheat in hydroponic and pot experiments. Furthermore, the SMCs enhanced the activities of antioxidant enzymes, including superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and levels of malondialdehyde (MDA) and proline (PRO). They also reduced oxidative stress and improved chlorophyll content in wheat seedlings. These results demonstrate the potential of microbial consortia derived from extreme environments as eco-friendly biofertilizers for improving crop performance in saline soils, offering a sustainable alternative to chemical fertilizers and contributing to agricultural resilience and productivity. Full article

(This article belongs to the Special Issue Plant–Microbe Interactions)

► Show Figures

Figure 1

14 pages, 2069 KiB

Open AccessArticle

Transcriptomic Study of Nicotiana tabacum Treated with the Bacterial Protein CspD Reveals Some Specific Abiotic Stress Responses

by Denis Erokhin, Diana Baranova, Ksenia Sergeeva, Tatiana Pasechnik, Larisa Shcherbakova, Natalia Statsyuk and Vitaly Dzhavakhiya

Int. J. Mol. Sci. 2024, 25(23), 13015; https://doi.org/10.3390/ijms252313015 - 3 Dec 2024

Viewed by 885

Abstract

The ability of a cold-shock protein CspD from Bacillus thuringiensis to protect both dicots and monocots against various pathogens is well confirmed under both greenhouse and field conditions; however, the molecular basis of this phenomenon at the transcriptomic level still remains unexplored. Expression [...] Read more.

The ability of a cold-shock protein CspD from Bacillus thuringiensis to protect both dicots and monocots against various pathogens is well confirmed under both greenhouse and field conditions; however, the molecular basis of this phenomenon at the transcriptomic level still remains unexplored. Expression profiles of some marker genes associated with SAR/ISR nonspecific resistance pathways and ROS scavengers were examined in CspD-treated Nicotiana tabacum plants, and the RNA-seq analysis of CspD-treated plants was first carried out. The ISR markers PDF1.2 and PR4 were overexpressed locally in treated tobacco leaves with the maximum 2.4- and 5.7-fold change, respectively, reached 12 h after the leaf treatment with CspD; PDF1.2 was also up-regulated 4.8-fold four days after the inoculation of treated plants with TMV. The ROS scavenger analysis demonstrated overexpression of Cu-Zn superoxide dismutase in both treated (with the maximum 5.4-fold change observed 6 h after the treatment) leaves and leaves from the upper tier (“system” leaves, 6.5-fold change observed 4 days after the treatment). The ROS assay confirmed endogenous accumulation of superoxide in CspD-treated leaves 6 and 24 h after the treatment. An in silico comparative study of Arabidopsis orthologs of highly up-regulated tobacco genes induced by CspD with Arabidopsis genes activated by some other molecular patterns revealed the specific CspD-induced expression of Cu-Zn superoxide dismutase and some other genes associated with light and cold responses. This study may contribute to a better understanding of cross-talking between abiotic stress and nonspecific immunity in plants. Full article

(This article belongs to the Special Issue Plant–Microbe Interactions)

► Show Figures

Figure 1

15 pages, 3447 KiB

Open AccessArticle

Synthetic Microbial Community Isolated from Intercropping System Enhances P Uptake in Rice

by Huimin Ma, Hongcheng Zhang, Congcong Zheng, Zonghui Liu, Jing Wang, Ping Tian, Zhihai Wu and Hualiang Zhang

Int. J. Mol. Sci. 2024, 25(23), 12819; https://doi.org/10.3390/ijms252312819 - 28 Nov 2024

Cited by 1 | Viewed by 903

Abstract

Changes in root traits and rhizosphere microbiome are important ways to optimize plant phosphorus (P) efficiency and promote multifunctionality in intercropping. However, whether and how synthetic microbial communities isolated from polyculture systems can facilitate plant growth and P uptake are still largely unknown. [...] Read more.

Changes in root traits and rhizosphere microbiome are important ways to optimize plant phosphorus (P) efficiency and promote multifunctionality in intercropping. However, whether and how synthetic microbial communities isolated from polyculture systems can facilitate plant growth and P uptake are still largely unknown. A field experiment was first carried out to assess the rice yield and P uptake in the rice/soybean intercropping systems, and a synthetic microbial community (SynCom) isolated from intercropped rice was then constructed to elucidate the potential mechanisms of growth-promoting effects on rice growth and P uptake in a series of pot experiments. Our results showed that the yield and P uptake of intercropped rice were lower than those of rice grown in monoculture. However, bacterial networks in the rice rhizosphere were more stable in polyculture, exhibiting more hub nodes and greater modularity compared to the rice monoculture. A bacterial synthetic community (SynCom) composed of four bacterial strains (Variovorax paradoxus, Novosphingobium subterraneum, Hydrogenophaga pseudoflava, Acidovorax sp.) significantly enhanced the biomass and P uptake of potted rice plants. These growth-promoting effects are underpinned by multiple pathways, including the direct activation of soil available P, increased root surface area and root tip number, reduced root diameter, and promotion of root-to-shoot P translocation through up-regulation of Pi transporter genes (OsPht1;1, OsPht1;2, OsPht1;4, OsPht1;6). This study highlights the potential of harnessing synthetic microbial communities to enhance nutrient acquisition and improve crop production. Full article

(This article belongs to the Special Issue Plant–Microbe Interactions)

► Show Figures

Graphical abstract

16 pages, 6229 KiB

Open AccessArticle

Fusarium sacchari CFEM Proteins Suppress Host Immunity and Differentially Contribute to Virulence

by Tianshu Hong, Shichao Wang, Zhiyuan Luo, Qianqian Ren, Deng Wu, Lulu Wang, Yixue Bao, Wei Yao, Muqing Zhang and Qin Hu

Int. J. Mol. Sci. 2024, 25(23), 12805; https://doi.org/10.3390/ijms252312805 - 28 Nov 2024

Viewed by 799

Abstract

The pathogen Fusarium sacchari is responsible for the devastating pokkah boeng disease, which causes significant economic losses in sugarcane production. However, the mechanisms by which it affects plant immunity remain largely unknown. Common in Fungal Extracellular Membrane (CFEM) domain proteins have been implicated [...] Read more.

The pathogen Fusarium sacchari is responsible for the devastating pokkah boeng disease, which causes significant economic losses in sugarcane production. However, the mechanisms by which it affects plant immunity remain largely unknown. Common in Fungal Extracellular Membrane (CFEM) domain proteins have been implicated in fungal growth, infection processes, and pathogenicity. In this study, we identified three FsCFEM proteins (Fs08184, Fs10706, and Fs13617) that mediate the broad-spectrum suppression of the immune responses induced by typical effectors. A further analysis demonstrated that Fs08184, Fs10706, and Fs13617 suppressed host immunity through two potential iron-binding sites conserved in CFEM family members, characterized by Asp and Phe residues in Fs08184, Fs10706, and Fs13617. Additionally, the Asp and Phe residues within the iron-chelating site were necessary for the iron acquisition of F. sacchari and contributed to creating low-free-iron conditions at the interface of plant and pathogen interactions. It appeared that F. sacchari might employ Asp-Phe-type CFEM members to influence host iron homeostasis to suppress host immunity and to facilitate its successful colonization. Full article

(This article belongs to the Special Issue Plant–Microbe Interactions)

► Show Figures

Figure 1

18 pages, 8276 KiB

Open AccessArticle

Fusarium sacchari Effector FsMEP1 Contributes to Virulence by Disturbing Localization of Thiamine Thiazole Synthase ScTHI2 from Sugarcane

by Lulu Wang, Deng Wu, Tianshu Hong, Qianqian Ren, Shichao Wang, Yixue Bao, Wei Yao, Muqing Zhang and Qin Hu

Int. J. Mol. Sci. 2024, 25(22), 12075; https://doi.org/10.3390/ijms252212075 - 10 Nov 2024

Viewed by 1193

Abstract

Fusarium sacchari is a significant pathogenic fungus that causes sugarcane Pokkah Boeng. Proteins secreted by pathogenic fungi can be delivered into hosts to suppress plant immunity and establish infection. However, there is still much to be discovered regarding F. sacchari’s secreted effectors [...] Read more.

Fusarium sacchari is a significant pathogenic fungus that causes sugarcane Pokkah Boeng. Proteins secreted by pathogenic fungi can be delivered into hosts to suppress plant immunity and establish infection. However, there is still much to be discovered regarding F. sacchari’s secreted effectors in overcoming plant immunity. In this paper, we characterize a novel effector called FsMEP1, which is essential for the virulence of F. sacchari. FsMEP1 contains a conserved zinc-binding motif sequence, HEXXH, and is highly expressed during host infection. Using the Agrobacterium tumefaciens-mediated transient expression system, it was confirmed that FsMEP1 could suppress Bcl-2-associated X protein (BAX)-triggered cell death, callose deposition, and ROS explosion in Nicotiana benthamiana. Furthermore, the deletion of FsMEP1 demonstrated its requirement for contributing to the pathogenicity of F. sacchari in sugarcane. Further analysis revealed that FsMEP1 could interact with the sugarcane thiamine thiazole synthase ScTHI2 and disrupt its normal localization, thereby inhibiting the synthesis of thiamine and the defense responses mediated by ScTHI2. Based on these findings, we propose that ScTHI2 represents a potential molecular target for improving sugarcane resistance to Pokkah Boeng disease. Full article

(This article belongs to the Special Issue Plant–Microbe Interactions)

► Show Figures

Figure 1

13 pages, 3118 KiB

Open AccessArticle

Genome-Wide Identification and Analysis of Gene Family of Carbohydrate-Binding Modules in Ustilago crameri

by Dongyu Zhai, Deze Xu, Ting Xiang, Yu Zhang, Nianchen Wu, Fuqing Nie, Desuo Yin and Aijun Wang

Int. J. Mol. Sci. 2024, 25(21), 11790; https://doi.org/10.3390/ijms252111790 - 2 Nov 2024

Cited by 1 | Viewed by 999

Abstract

Ustilago crameri is a pathogenic basidiomycete fungus that causes foxtail millet kernel smut (FMKS), a devastating grain disease in most foxtail millet growing regions of the world. Carbohydrate-Binding Modules (CBMs) are one of the important families of carbohydrate-active enzymes (CAZymes) in fungi and [...] Read more.

Ustilago crameri is a pathogenic basidiomycete fungus that causes foxtail millet kernel smut (FMKS), a devastating grain disease in most foxtail millet growing regions of the world. Carbohydrate-Binding Modules (CBMs) are one of the important families of carbohydrate-active enzymes (CAZymes) in fungi and play a crucial role in fungal growth and development, as well as in pathogen infection. However, there is little information about the CBM family in U. crameri. Here, 11 CBM members were identified based on complete sequence analysis and functional annotation of the genome of U. crameri. According to phylogenetic analysis, they were divided into six groups. Gene structure and sequence composition analysis showed that these 11 UcCBM genes exhibit differences in gene structure and protein motifs. Furthermore, several cis-regulatory elements involved in plant hormones were detected in the promoter regions of these UcCBM genes. Gene ontology (GO) enrichment and protein–protein interaction (PPI) analysis showed that UcCBM proteins were involved in carbohydrate metabolism, and multiple partner protein interactions with UcCBM were also detected. The expression of UcCBM genes during U. crameri infection is further clarified, and the results indicate that several UcCBM genes were induced by U. crameri infection. These results provide valuable information for elucidating the features of U. crameri CBMs’ family proteins and lay a crucial foundation for further research into their roles in interactions between U. crameri and foxtail millet. Full article

(This article belongs to the Special Issue Plant–Microbe Interactions)

► Show Figures

Figure 1

18 pages, 4804 KiB

Open AccessArticle

Volatile Organic Compounds Produced by Co-Culture of Burkholderia vietnamiensis B418 with Trichoderma harzianum T11-W Exhibits Improved Antagonistic Activities against Fungal Phytopathogens

by Wenzhe Li, Xinyue Wang, Yanqing Jiang, Shuning Cui, Jindong Hu, Yanli Wei, Jishun Li and Yuanzheng Wu

Int. J. Mol. Sci. 2024, 25(20), 11097; https://doi.org/10.3390/ijms252011097 - 16 Oct 2024

Cited by 2 | Viewed by 1458

Abstract

Recently, there has been a growing interest in the biocontrol activity of volatile organic compounds (VOCs) produced by microorganisms. This study specifically focuses on the effects of VOCs produced by the co-culture of Burkholderia vietnamiensis B418 and Trichoderma harzianum T11-W for the control [...] Read more.

Recently, there has been a growing interest in the biocontrol activity of volatile organic compounds (VOCs) produced by microorganisms. This study specifically focuses on the effects of VOCs produced by the co-culture of Burkholderia vietnamiensis B418 and Trichoderma harzianum T11-W for the control of two phytopathogenic fungi, Botrytis cinerea and Fusarium oxysporum f. sp. cucumerium Owen. The antagonistic activity of VOCs released in mono- and co-culture modes was evaluated by inhibition assays on a Petri dish and in detached fruit experiments, with the co-culture demonstrating significantly higher inhibitory effects on the phytopathogens on both the plates and fruits compared with the mono-cultures. Metabolomic profiles of VOCs were conducted using the solid–liquid microextraction technique, revealing 341 compounds with significant changes in their production during the co-culture. Among these compounds, linalool, dimethyl trisulfide, dimethyl disulfide, geranylacetone, 2-phenylethanol, and acetophenone were identified as having strong antagonistic activity through a standard inhibition assay. These key compounds were found to be related to the improved inhibitory effect of the B418 and T11-W co-culture. Overall, the results suggest that VOCs produced by the co-culture of B. vietnamiensis B418 and T. harzianum T11-W possess great potential in biological control. Full article

(This article belongs to the Special Issue Plant–Microbe Interactions)

► Show Figures

Figure 1

Review

Jump to: Research

26 pages, 1308 KiB

Open AccessReview

The Role of Genetic Resistance in Rice Disease Management

by Andrews Danso Ofori, Tengda Zheng, John Kwame Titriku, Charlotte Appiah, Xing Xiang, Abdul Ghani Kandhro, Muhammad Irfan Ahmed and Aiping Zheng

Int. J. Mol. Sci. 2025, 26(3), 956; https://doi.org/10.3390/ijms26030956 - 23 Jan 2025

Cited by 1 | Viewed by 1097

Abstract

Rice (Oryza sativa) is a crucial staple crop for global food security, particularly in Asia. However, rice production faces significant challenges from various diseases that can cause substantial yield losses. This review explores the role of genetic resistance in rice disease [...] Read more.

Rice (Oryza sativa) is a crucial staple crop for global food security, particularly in Asia. However, rice production faces significant challenges from various diseases that can cause substantial yield losses. This review explores the role of genetic resistance in rice disease management, focusing on the molecular mechanisms underlying plant–pathogen interactions and strategies for developing resistant varieties. The paper discusses qualitative and quantitative resistance, emphasizing the importance of resistance (R) genes, defense-regulator genes, and quantitative trait loci (QTLs) in conferring broad-spectrum disease resistance. Gene-for-gene relationships in rice–pathogen interactions are examined, particularly for Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae. The review also covers recent advancements in breeding techniques, including marker-assisted selection, genetic engineering, and genome editing technologies like CRISPR-Cas. These approaches offer promising avenues for enhancing disease resistance in rice while maintaining yield potential. Understanding and exploiting genetic resistance mechanisms is crucial for developing durable and broad-spectrum disease-resistant rice varieties, essential for ensuring sustainable rice production and global food security in the face of evolving pathogen threats and changing environmental conditions. Full article

(This article belongs to the Special Issue Plant–Microbe Interactions)

► Show Figures

Figure 1

12 pages, 3128 KiB

Open AccessReview

The Multifaceted Ubiquitination of BIK1 During Plant Immunity in Arabidopsis thaliana

by Junhong Fu, Huihui Wang, Yuling Chen, Chunguang Zhang and Yanmin Zou

Int. J. Mol. Sci. 2024, 25(22), 12187; https://doi.org/10.3390/ijms252212187 - 13 Nov 2024

Viewed by 1275

Abstract

As sessile organisms, the plant immune system plays a vital role in protecting plants from the widespread pathogens in the environment. The Arabidopsis thaliana (Arabidopsis) receptor-like cytoplasmic kinase BOTRYTIS-INDUCED KINASE1 (BIK1) acts as a central regulator during plant immunity. As such, not only [...] Read more.

As sessile organisms, the plant immune system plays a vital role in protecting plants from the widespread pathogens in the environment. The Arabidopsis thaliana (Arabidopsis) receptor-like cytoplasmic kinase BOTRYTIS-INDUCED KINASE1 (BIK1) acts as a central regulator during plant immunity. As such, not only the BIK1 protein accumulation but also the attenuation is tightly regulated to ensure effective immune responses. Recent studies have highlighted the critical roles of ubiquitination in maintaining BIK1 homeostasis. Here, we review the latest advances in the ubiquitination of BIK1 in plant immunity, which is mediated by ubiquitin ligases PUB25/26, RHA3A/B, RGLG1/2, and PUB4. Additionally, we summarize and discuss the sites and types of BIK1 ubiquitination. Collectively, these analyses not only illustrate that the differential modifications on BIK1 by multiple ubiquitin ligases hold a crucial position in plant immunity but also provide a good example for future studies on ubiquitin-mediated modifications in plants. Full article

(This article belongs to the Special Issue Plant–Microbe Interactions)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Plant–Microbe Interactions

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (10 papers)

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI