Bacillus amyloliquefaciens LZ04 improves the resistance of Arabidopsis thaliana to high calcium stress and the potential role of lncRNA-miRNA-mRNA regulatory network in the resistance

Li, Fēi; Shi, Tianlong; He, Ao-Lei; Huang, Xiaolong; Gong, Jirui; Yi, Yin; Zhang, Jin‐Lin

doi:10.1016/j.plaphy.2020.03.022

Cited by 9 publications

(12 citation statements)

References 41 publications

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“…These observations signposted that LZ04 promoted the resistance and adaptation of A. thaliana to high calcium stress by regulating oxidative stress and lipid peroxidation in the high calcium-stressed plants. This study corroborated with our previous work ( Li et al, 2020a ) showing that the interaction between plants and microorganism is beneficial for plant to resist against numerous pathogens and biotic as well as abiotic stress conditions. Similarly to our findings, a large number of studies ( Qin et al, 2017 ; Wang et al, 2021 ) have shown that B. amyloliquefaciens strains are rhizosphere-promoting bacteria and that inoculation of these strains can promote plant growth, prevent soil-borne diseases and improve plant resistance to stress.…”

Section: Discussionsupporting

confidence: 92%

“…Previous studies have shown that the genes involved in calcium signaling play an important role in biotic and abiotic stresses. Up to date, only our previous study ( Li et al, 2020a ) gave an insight in the mechanism underlying the response of A. thaliana to calcium and the role of its interaction with B. amyloliquefaciens in the counteracting effect through lncRNA-miRNA-mRNA networks. Here, we focused on the expression of genes in calcium-related gene families in the roots of A. thaliana under high calcium stress and the effect of LZ04 on these genes were also explored.…”

Section: Discussionmentioning

confidence: 99%

“…Ascorbate peroxidase (APX) activity also followed a previously published protocol ( Dalton et al, 1987 ) whereas catalase (CAT) activity was evaluated by spectrophotical analysis of H 2 O 2 absorbance at 240 nm ( Zhang H. et al, 2005 ). The detailed information of high calcium stress and strain LZO4 treatment was as described in our previous work ( Li et al, 2020a ). We thank Professor Jinlin Zhang of Lanzhou University for providing the strain LZ04.…”

Section: Methodsmentioning

confidence: 99%

“…Illumina HiSeq 4,000 was used to perform strand-specific sequencing. The detailed information of the transcriptome analysis was as described in our previous work ( Li et al, 2020a ).…”

Section: Methodsmentioning

confidence: 99%

“…The transcriptome data was validated by RT-qPCR. Total RNA extraction and purification, reverse-transcription and amplification protocols and conditions conformed with those in our previous work ( Li et al, 2020a ). The forward and reverse sequences of primers used were as shown in Table 2 .…”

Section: Methodsmentioning

confidence: 99%

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Genome-Wide Identification and Characterization of Calcium Metabolism Related Gene Families in Arabidopsis thaliana and Their Regulation by Bacillus amyloliquefaciens Under High Calcium Stress

et al. 2021

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Several gene families involved in calcium signaling have been detected in plants, including calmodulin (CaM), calcium dependent protein kinases (CDPK), calcineurin B-like (CBL) and cyclic nucleotide-gated channels (CNGCs). In our previous study, we demonstrated that Bacillus amyloliquefaciens LZ04 (B. amyloliquefaciens LZ04) regulate genes involved in calcium stress in Arabidopsis thaliana (A. thaliana). Here, we aimed to explore the potential involvement of calcium-related gene families in the response of A. thaliana to calcium stress and the potential regulatory effects of B. amyloliquefaciens LZ04 on these genes. The structure, duplication, synteny, and expression profiles of 102 genes in calcium-related gene families in A. thaliana were investigated. Hidden Markov Models (HMMs) and BLASTP were used to predict candidate genes and conserved domains of the candidate genes were confirmed in SMART and NCBI CDD databases. Gene duplications and synteny were uncovered by BLASTP and phylogenetic analysis. The transcriptome expression profiles of candidate genes were investigated by strand-specific sequencing. Cluster analysis was used to find the expression profiles of calcium-related genes families under different treatment conditions. A total of 102 genes in calcium-related gene families were detected in A. thaliana genome, including 34 CDPK genes, 20 CNGC genes, 18 CIPK genes, 22 IQD genes, and 10 CBP genes. Additionally, of the 102 genes, 33 duplications (32.35%) and 26 gene pairs including 48 genes (47.06%) were detected. Treatment with B. amyloliquefaciens LZ04 enhanced the resistance of A. thaliana under high calcium stress by regulating some of the genes in the calcium-related gene families. Functional enrichment analysis revealed that the genes clustered in the 42nd expression profile which may be B. amyloliquefaciens-responsive genes under calcium stress were enriched in protein phosphorylation and protein modification process. Transcriptome data was validated by RT-PCR and the results generally corroborated the transcriptome sequencing results. These results may be useful for agricultural improvement in high calcium stress regions.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…Illumina HiSeq 4,000 was used to perform strand-specific sequencing. The detailed information of the transcriptome analysis was as described in our previous work ( Li et al, 2020a ).…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Genome-Wide Identification and Characterization of Calcium Metabolism Related Gene Families in Arabidopsis thaliana and Their Regulation by Bacillus amyloliquefaciens Under High Calcium Stress

et al. 2021

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Combined analysis of mRNA and miRNA reveals the banana potassium absorption regulatory network and validation of miRNA160a

et al. 2022

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Potassium (K) has an important effect on the growth and development of plants. Banana contains high K content than many other fruits, and its plant requires more K nutrient in soil. However, the soil in the banana-producing areas in China is generally de cient in K. Therefore, understanding the mechanism of banana K absorption may assis in providing effective strategy to solve this problem. This study used two banana varieties with contrasting K tolerance, 'Guijiao No. 1' (low-K tolerant), and 'Brazilian banana' (low-K sensitive)to investigate K absorption mechanisms in response to low K stress through miRNA and mRNA sequencing analysis. Under low K condition, 'Guijiao No.1' showed higher plant height, dry weight, tissue K content and ATPase activity. Transcription factor analysis results showed that it was mainly concentrated in MYB, AP2-EREBP, bHLH, etc. The sequencing results showed that 'Guijiao No. 1' had 776 differentially expressed genes (DEGs) and 27 differentially expressed miRNAs (DEMs), and 'Brazilian banana' had 71 DEGs and 14 DEMs. RT-qPCR results showed that all miRNAs and mRNAs showed similar expression patterns with RNA-Seq and transcriptome. miRNA regulatory network was constructed by integrated analysis of miRNA-mRNA data. miR160a was screened out as a key miRNA, and preliminary functional validation was performed. Arabidopsis overexpressed miRNA160a reduced tolerance to low K, and inhibited phenotypical traits such as root length, and reduced K accumulation. The overexpressed miR160a had a targeting relationship with ARF10 and ARF16 in Arabidopsis. These results indicate that miRNA160a may regulate K absorption in bananas through the auxin pathway. This study provides a theoretical basis for further research on the molecular mechanism underlying the response of banana plants to low-K stress and for molecular breeding.

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Biological function research of Fusarium oxysporum f. sp. cubense inducible banana long noncoding RNA Malnc2310 in Arabidopsis

Zhao

Sun

et al. 2023

Plant Mol Biol

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Bacillus amyloliquefaciens LZ04 improves the resistance of Arabidopsis thaliana to high calcium stress and the potential role of lncRNA-miRNA-mRNA regulatory network in the resistance

Cited by 9 publications

References 41 publications

Genome-Wide Identification and Characterization of Calcium Metabolism Related Gene Families in Arabidopsis thaliana and Their Regulation by Bacillus amyloliquefaciens Under High Calcium Stress

Genome-Wide Identification and Characterization of Calcium Metabolism Related Gene Families in Arabidopsis thaliana and Their Regulation by Bacillus amyloliquefaciens Under High Calcium Stress

Combined analysis of mRNA and miRNA reveals the banana potassium absorption regulatory network and validation of miRNA160a

Biological function research of Fusarium oxysporum f. sp. cubense inducible banana long noncoding RNA Malnc2310 in Arabidopsis

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