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Nitrogen starvation-induced transcriptome alterations and influence of transcription regulator mutants in Mycobacterium smegmatis.

Jeßberger N, Lu Y, Amon J, Titgemeyer F, Sonnewald S, Reid S, Burkovski A - BMC Res Notes (2013)

Bottom Line: This includes changes in the transcription of several hundred genes encoding e.g. transport proteins, proteins involved in nitrogen metabolism and regulation, energy generation and protein turnover.The specific nitrogen-related changes at the transcriptional level depend mainly on the presence of GlnR, while the AmtR protein controls only a small number of genes.M. smegmatis is able to metabolize a number of different nitrogen sources and nitrogen control in M. smegmatis is similar to control mechanisms characterized in streptomycetes, while the master regulator of nitrogen control in corynebacteria, AmtR, is plays a minor role in this regulatory network.

View Article: PubMed Central - HTML - PubMed

Affiliation: Lehrstuhl für Mikrobiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany. aburkov@biologie.uni-erlangen.de.

ABSTRACT

Background: As other bacteria, Mycobacterium smegmatis needs adaption mechanisms to cope with changing nitrogen sources and to survive situations of nitrogen starvation. In the study presented here, transcriptome analyses were used to characterize the response of the bacterium to nitrogen starvation and to elucidate the role of specific transcriptional regulators.

Results: In response to nitrogen deprivation, a general starvation response is induced in M. smegmatis. This includes changes in the transcription of several hundred genes encoding e.g. transport proteins, proteins involved in nitrogen metabolism and regulation, energy generation and protein turnover. The specific nitrogen-related changes at the transcriptional level depend mainly on the presence of GlnR, while the AmtR protein controls only a small number of genes.

Conclusions: M. smegmatis is able to metabolize a number of different nitrogen sources and nitrogen control in M. smegmatis is similar to control mechanisms characterized in streptomycetes, while the master regulator of nitrogen control in corynebacteria, AmtR, is plays a minor role in this regulatory network.

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The GlnR modulon of M. smegmatis. DNA microarray analyses were carried out with RNA isolated from nitrogen-starved wild-type SMR5 and glnR deletion strain MH1. Genes with decreased transcript levels in glnR deletion strain MH1 were classified according to functional categories [13].
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Figure 2: The GlnR modulon of M. smegmatis. DNA microarray analyses were carried out with RNA isolated from nitrogen-starved wild-type SMR5 and glnR deletion strain MH1. Genes with decreased transcript levels in glnR deletion strain MH1 were classified according to functional categories [13].

Mentions: In order to elucidate the specific nitrogen starvation response in more detail, the global transcription patterns of nitrogen-deprived wild-type and ΔglnR strain MH1 were compared. Transcripts of 125 genes were up-regulated and of six genes down-regulated by at least a factor of 3 in the wild-type in comparison to MH1, when the two strains were starved for nitrogen. The classification of these genes into COGs (Figure 2) gave a first hint that GlnR is not only involved in the regulation of ammonium assimilation, which was further supported by a detailed inspection of the DNA microarray results (Table 1). Putative GlnR regulated genes included the genes amtB (msmeg_2425, 56 x), glnK (msmeg_2426, 53 x), glnA (msmeg_4290, 34 x), glnD (msmeg_2427, 18 x) and amt1 (msmeg_6259, 12 x), which were described previously [11] besides others with obvious function in nitrogen metabolism. These include for example the nirBD gene cluster (msmeg_0427-0428) coding for nitrite reductase subunits, msmeg_0781, msmeg_1052, msmeg_2184 and msmeg_6735, encoding different putative permeases and transporter subunits involved in amino acid uptake, msmeg_1293, msmeg_2748, msmeg_4011, msmeg_5730 and msmeg_6660, encoding proteins putatively involved in purine and pyrimidine transport, as well as msmeg_2187, msmeg_2981 (urtB), msmeg_2982 (urtA) and msmeg_3626, encoding proteins for urea uptake and utilization. All in all, the results of transcriptome analyses of nitrogen-deprived wild-type and ΔglnR strain MH1 indicated a more global function of GlnR in the regulation of nitrogen metabolism. Similar results were obtained for S. coelicolor[3] and together indicate a more general role of GlnR in Actinobacteria.


Nitrogen starvation-induced transcriptome alterations and influence of transcription regulator mutants in Mycobacterium smegmatis.

Jeßberger N, Lu Y, Amon J, Titgemeyer F, Sonnewald S, Reid S, Burkovski A - BMC Res Notes (2013)

The GlnR modulon of M. smegmatis. DNA microarray analyses were carried out with RNA isolated from nitrogen-starved wild-type SMR5 and glnR deletion strain MH1. Genes with decreased transcript levels in glnR deletion strain MH1 were classified according to functional categories [13].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4222082&req=5

Figure 2: The GlnR modulon of M. smegmatis. DNA microarray analyses were carried out with RNA isolated from nitrogen-starved wild-type SMR5 and glnR deletion strain MH1. Genes with decreased transcript levels in glnR deletion strain MH1 were classified according to functional categories [13].
Mentions: In order to elucidate the specific nitrogen starvation response in more detail, the global transcription patterns of nitrogen-deprived wild-type and ΔglnR strain MH1 were compared. Transcripts of 125 genes were up-regulated and of six genes down-regulated by at least a factor of 3 in the wild-type in comparison to MH1, when the two strains were starved for nitrogen. The classification of these genes into COGs (Figure 2) gave a first hint that GlnR is not only involved in the regulation of ammonium assimilation, which was further supported by a detailed inspection of the DNA microarray results (Table 1). Putative GlnR regulated genes included the genes amtB (msmeg_2425, 56 x), glnK (msmeg_2426, 53 x), glnA (msmeg_4290, 34 x), glnD (msmeg_2427, 18 x) and amt1 (msmeg_6259, 12 x), which were described previously [11] besides others with obvious function in nitrogen metabolism. These include for example the nirBD gene cluster (msmeg_0427-0428) coding for nitrite reductase subunits, msmeg_0781, msmeg_1052, msmeg_2184 and msmeg_6735, encoding different putative permeases and transporter subunits involved in amino acid uptake, msmeg_1293, msmeg_2748, msmeg_4011, msmeg_5730 and msmeg_6660, encoding proteins putatively involved in purine and pyrimidine transport, as well as msmeg_2187, msmeg_2981 (urtB), msmeg_2982 (urtA) and msmeg_3626, encoding proteins for urea uptake and utilization. All in all, the results of transcriptome analyses of nitrogen-deprived wild-type and ΔglnR strain MH1 indicated a more global function of GlnR in the regulation of nitrogen metabolism. Similar results were obtained for S. coelicolor[3] and together indicate a more general role of GlnR in Actinobacteria.

Bottom Line: This includes changes in the transcription of several hundred genes encoding e.g. transport proteins, proteins involved in nitrogen metabolism and regulation, energy generation and protein turnover.The specific nitrogen-related changes at the transcriptional level depend mainly on the presence of GlnR, while the AmtR protein controls only a small number of genes.M. smegmatis is able to metabolize a number of different nitrogen sources and nitrogen control in M. smegmatis is similar to control mechanisms characterized in streptomycetes, while the master regulator of nitrogen control in corynebacteria, AmtR, is plays a minor role in this regulatory network.

View Article: PubMed Central - HTML - PubMed

Affiliation: Lehrstuhl für Mikrobiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany. aburkov@biologie.uni-erlangen.de.

ABSTRACT

Background: As other bacteria, Mycobacterium smegmatis needs adaption mechanisms to cope with changing nitrogen sources and to survive situations of nitrogen starvation. In the study presented here, transcriptome analyses were used to characterize the response of the bacterium to nitrogen starvation and to elucidate the role of specific transcriptional regulators.

Results: In response to nitrogen deprivation, a general starvation response is induced in M. smegmatis. This includes changes in the transcription of several hundred genes encoding e.g. transport proteins, proteins involved in nitrogen metabolism and regulation, energy generation and protein turnover. The specific nitrogen-related changes at the transcriptional level depend mainly on the presence of GlnR, while the AmtR protein controls only a small number of genes.

Conclusions: M. smegmatis is able to metabolize a number of different nitrogen sources and nitrogen control in M. smegmatis is similar to control mechanisms characterized in streptomycetes, while the master regulator of nitrogen control in corynebacteria, AmtR, is plays a minor role in this regulatory network.

Show MeSH
Related in: MedlinePlus