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Global transcriptome analysis of Mesorhizobium alhagi CCNWXJ12-2 under salt stress.

Liu X, Luo Y, Mohamed OA, Liu D, Wei G - BMC Microbiol. (2014)

Bottom Line: We have compared the transcriptome of M. alhagi growing in TY medium under high salt conditions (0.4 M NaCl) with salt free conditions as a control.Our results showed the complex mechanism of bacterial adaption to salt stress and it was a systematic work for bacteria to cope with the high salinity environmental problems.Therefore, these results could be helpful for further investigation of the bacterial salt resistance mechanism.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau,, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China. weigehong@nwsuaf.edu.cn.

ABSTRACT

Background: Mesorhizobium alhagi CCNWXJ12-2 is a α-proteobacterium which could be able to fix nitrogen in the nodules formed with Alhagi sparsifolia in northwest of China. Desiccation and high salinity are the two major environmental problems faced by M. alhagi CCNWXJ12-2. In order to identify genes involved in salt-stress adaption, a global transcriptional analysis of M. alhagi CCNWXJ12-2 growing under salt-free and high salt conditions was carried out. The next generation sequencing technology, RNA-Seq, was used to obtain the transcription profiles.

Results: We have compared the transcriptome of M. alhagi growing in TY medium under high salt conditions (0.4 M NaCl) with salt free conditions as a control. A total of 1,849 differentially expressed genes (fold change ≧ 2) were identified and 933 genes were downregulated while 916 genes were upregulated under high salt condition. Except for the upregulation of some genes proven to be involved in salt resistance, we found that the expression levels of protein secretion systems were changed under high salt condition and the expression levels of some heat shock proteins were reduced by salt stress. Notably, a gene encoding YadA domain-containing protein (yadA), a gene encoding trimethylamine methyltransferase (mttB) and a gene encoding formate--tetrahydrofolate ligase (fhs) were highly upregulated. Growth analysis of the three gene knockout mutants under salt stress demonstrated that yadA was involved in salt resistance while the other two were not.

Conclusions: To our knowledge, this is the first report about transcriptome analysis of a rhizobia using RNA-Seq to elucidate the salt resistance mechanism. Our results showed the complex mechanism of bacterial adaption to salt stress and it was a systematic work for bacteria to cope with the high salinity environmental problems. Therefore, these results could be helpful for further investigation of the bacterial salt resistance mechanism.

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Related in: MedlinePlus

The COG categories of all predicted genes and the DEGs. Summary of COG annotations for all the predicted genes and the number of differentially expressed genes in each COG category. The percentage of the the DEGs account for the predicted genes were shown up the bars.
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Fig2: The COG categories of all predicted genes and the DEGs. Summary of COG annotations for all the predicted genes and the number of differentially expressed genes in each COG category. The percentage of the the DEGs account for the predicted genes were shown up the bars.

Mentions: Cluster of orthologous groups (COG) is widely used to classify orthologous proteins [19]. Based on the conserved region, every protein is assumed to be evolved from an ancestor protein in COG database. Thus, this database is helpful to annotate the genes from poorly characterized genomes [20]. Aligned all of the predicted transcribed (RPKM > =20) genes against the COG database 4,022 genes obtained their COG codes. The Figure 2 presents the COG categories of all the proteins encoded by transcribed genes and the DEGs and the number of each category are shown in Additional file 2. The DEGs account for high ratios in most COG categories, which means the salt resistance mechanism in Mesorhizobium alhagi should be complex. Furthermore, among the total 1,849 differentially expressed genes (DEGs), 933 and 916 were significantly down-regulated and up-regulated response to salt stress, respectively. Consequently, this large number of DEGs suggested that not only the salt-specific stress responses but also the nonspecific responses were triggered. DEGs were then grouped by functional categories (Figure 3). Indeed, there are many genes involved in amino acid transport and metabolism, carbohydrate transport and metabolism, energy production and conversion and translation were induced by salt stress. The 184 genes of function unknown, 133 genes of general function predicted and 487 genes without COG codes indicated that Mesorhizobium alhagi XJ12-2 might have some unknown means to deal with the high salt condition.Figure 2


Global transcriptome analysis of Mesorhizobium alhagi CCNWXJ12-2 under salt stress.

Liu X, Luo Y, Mohamed OA, Liu D, Wei G - BMC Microbiol. (2014)

The COG categories of all predicted genes and the DEGs. Summary of COG annotations for all the predicted genes and the number of differentially expressed genes in each COG category. The percentage of the the DEGs account for the predicted genes were shown up the bars.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4302635&req=5

Fig2: The COG categories of all predicted genes and the DEGs. Summary of COG annotations for all the predicted genes and the number of differentially expressed genes in each COG category. The percentage of the the DEGs account for the predicted genes were shown up the bars.
Mentions: Cluster of orthologous groups (COG) is widely used to classify orthologous proteins [19]. Based on the conserved region, every protein is assumed to be evolved from an ancestor protein in COG database. Thus, this database is helpful to annotate the genes from poorly characterized genomes [20]. Aligned all of the predicted transcribed (RPKM > =20) genes against the COG database 4,022 genes obtained their COG codes. The Figure 2 presents the COG categories of all the proteins encoded by transcribed genes and the DEGs and the number of each category are shown in Additional file 2. The DEGs account for high ratios in most COG categories, which means the salt resistance mechanism in Mesorhizobium alhagi should be complex. Furthermore, among the total 1,849 differentially expressed genes (DEGs), 933 and 916 were significantly down-regulated and up-regulated response to salt stress, respectively. Consequently, this large number of DEGs suggested that not only the salt-specific stress responses but also the nonspecific responses were triggered. DEGs were then grouped by functional categories (Figure 3). Indeed, there are many genes involved in amino acid transport and metabolism, carbohydrate transport and metabolism, energy production and conversion and translation were induced by salt stress. The 184 genes of function unknown, 133 genes of general function predicted and 487 genes without COG codes indicated that Mesorhizobium alhagi XJ12-2 might have some unknown means to deal with the high salt condition.Figure 2

Bottom Line: We have compared the transcriptome of M. alhagi growing in TY medium under high salt conditions (0.4 M NaCl) with salt free conditions as a control.Our results showed the complex mechanism of bacterial adaption to salt stress and it was a systematic work for bacteria to cope with the high salinity environmental problems.Therefore, these results could be helpful for further investigation of the bacterial salt resistance mechanism.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau,, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China. weigehong@nwsuaf.edu.cn.

ABSTRACT

Background: Mesorhizobium alhagi CCNWXJ12-2 is a α-proteobacterium which could be able to fix nitrogen in the nodules formed with Alhagi sparsifolia in northwest of China. Desiccation and high salinity are the two major environmental problems faced by M. alhagi CCNWXJ12-2. In order to identify genes involved in salt-stress adaption, a global transcriptional analysis of M. alhagi CCNWXJ12-2 growing under salt-free and high salt conditions was carried out. The next generation sequencing technology, RNA-Seq, was used to obtain the transcription profiles.

Results: We have compared the transcriptome of M. alhagi growing in TY medium under high salt conditions (0.4 M NaCl) with salt free conditions as a control. A total of 1,849 differentially expressed genes (fold change ≧ 2) were identified and 933 genes were downregulated while 916 genes were upregulated under high salt condition. Except for the upregulation of some genes proven to be involved in salt resistance, we found that the expression levels of protein secretion systems were changed under high salt condition and the expression levels of some heat shock proteins were reduced by salt stress. Notably, a gene encoding YadA domain-containing protein (yadA), a gene encoding trimethylamine methyltransferase (mttB) and a gene encoding formate--tetrahydrofolate ligase (fhs) were highly upregulated. Growth analysis of the three gene knockout mutants under salt stress demonstrated that yadA was involved in salt resistance while the other two were not.

Conclusions: To our knowledge, this is the first report about transcriptome analysis of a rhizobia using RNA-Seq to elucidate the salt resistance mechanism. Our results showed the complex mechanism of bacterial adaption to salt stress and it was a systematic work for bacteria to cope with the high salinity environmental problems. Therefore, these results could be helpful for further investigation of the bacterial salt resistance mechanism.

Show MeSH
Related in: MedlinePlus