Limits...
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.

Show MeSH

Related in: MedlinePlus

Co-occurrence of amtR and AmtR-regulated genes in selected Actinobacteria. Genomic map of the highly conserved AmtR operon in K. radiotolerans(A), S. avermitilis(B) and M. smegmatis(C). The arrows indicate length and transcriptional orientation of annotated genes which are depicted by the respective orf number. Numbers in square brackets show the lengths of intergenic regions in bp. While the putative K. radiotolerans operon shows a subsequent series of genes with overlapping reading frames, the amtR gene is transcribed in opposite direction in S. avermitilis and the amino acid permease-encoding gene is located elsewhere, while in M. smegmatis, the amtR gene is not co-localized with the putatively AmtR-regulated genes (see Table 3 for details).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4222082&req=5

Figure 7: Co-occurrence of amtR and AmtR-regulated genes in selected Actinobacteria. Genomic map of the highly conserved AmtR operon in K. radiotolerans(A), S. avermitilis(B) and M. smegmatis(C). The arrows indicate length and transcriptional orientation of annotated genes which are depicted by the respective orf number. Numbers in square brackets show the lengths of intergenic regions in bp. While the putative K. radiotolerans operon shows a subsequent series of genes with overlapping reading frames, the amtR gene is transcribed in opposite direction in S. avermitilis and the amino acid permease-encoding gene is located elsewhere, while in M. smegmatis, the amtR gene is not co-localized with the putatively AmtR-regulated genes (see Table 3 for details).

Mentions: The experiments described above supported the idea that GlnR is a major nitrogen regulator in M. smegmatis, which consequently leads to the question of AmtR function in this organism. In a first approach to characterize the AmtR regulon, a bioinformatic analysis was carried out to identify AmtR-controlled genes in M. smegmatis. For this purpose, a co-occurrence analysis was carried out using the genome information of ten actinobacterial genomes, i.e. Arthrobacter aurescens, C. michiganensis, C. efficiens, Gordonia bronchialis, K. radiotolerans, M. smegmatis, Nocardia farcinica, Rhodococcus jostii, Streptomyces avermitilis and Tsukumurella paurometabola. From these genomes, one conserved operon was extracted, which (i) shows a high degree of co-occurrence with the amtR gene, (ii) shows co-localization with amtR in A. aurescens, Rhodococcus sp. RHA1 and S. avermitilis and (iii) seems to be involved in nitrogen metabolism based on their annotation (Table 3). K. radiotolerans features the most condensed AmtR gene cluster (Figure 7); all open reading frames of this putative operon feature overlapping start and stop codons (GTGA or ATGA). While AmtR and the amino acid permease are highly conserved and well consistently annotated in the different genomes, the exact functions of unknown reading frames urf1 and urf2, the urea carboxylase and the amidase are highly speculative and deduced from annotations (automatic and manual), domain analyses and PFAM searches. The location of these unknown reading frames in direct genomic neighborhood to the putative urea carboxylase-encoding gene is highly conserved in all investigated genomes, while the locations of the genes coding for amino acid permease and the amidase are more variable. Particularly the amtR gene can be found in close vicinity as well as completely elsewhere in the respective genome sequences (Table 3, Figure 7).


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)

Co-occurrence of amtR and AmtR-regulated genes in selected Actinobacteria. Genomic map of the highly conserved AmtR operon in K. radiotolerans(A), S. avermitilis(B) and M. smegmatis(C). The arrows indicate length and transcriptional orientation of annotated genes which are depicted by the respective orf number. Numbers in square brackets show the lengths of intergenic regions in bp. While the putative K. radiotolerans operon shows a subsequent series of genes with overlapping reading frames, the amtR gene is transcribed in opposite direction in S. avermitilis and the amino acid permease-encoding gene is located elsewhere, while in M. smegmatis, the amtR gene is not co-localized with the putatively AmtR-regulated genes (see Table 3 for details).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: Co-occurrence of amtR and AmtR-regulated genes in selected Actinobacteria. Genomic map of the highly conserved AmtR operon in K. radiotolerans(A), S. avermitilis(B) and M. smegmatis(C). The arrows indicate length and transcriptional orientation of annotated genes which are depicted by the respective orf number. Numbers in square brackets show the lengths of intergenic regions in bp. While the putative K. radiotolerans operon shows a subsequent series of genes with overlapping reading frames, the amtR gene is transcribed in opposite direction in S. avermitilis and the amino acid permease-encoding gene is located elsewhere, while in M. smegmatis, the amtR gene is not co-localized with the putatively AmtR-regulated genes (see Table 3 for details).
Mentions: The experiments described above supported the idea that GlnR is a major nitrogen regulator in M. smegmatis, which consequently leads to the question of AmtR function in this organism. In a first approach to characterize the AmtR regulon, a bioinformatic analysis was carried out to identify AmtR-controlled genes in M. smegmatis. For this purpose, a co-occurrence analysis was carried out using the genome information of ten actinobacterial genomes, i.e. Arthrobacter aurescens, C. michiganensis, C. efficiens, Gordonia bronchialis, K. radiotolerans, M. smegmatis, Nocardia farcinica, Rhodococcus jostii, Streptomyces avermitilis and Tsukumurella paurometabola. From these genomes, one conserved operon was extracted, which (i) shows a high degree of co-occurrence with the amtR gene, (ii) shows co-localization with amtR in A. aurescens, Rhodococcus sp. RHA1 and S. avermitilis and (iii) seems to be involved in nitrogen metabolism based on their annotation (Table 3). K. radiotolerans features the most condensed AmtR gene cluster (Figure 7); all open reading frames of this putative operon feature overlapping start and stop codons (GTGA or ATGA). While AmtR and the amino acid permease are highly conserved and well consistently annotated in the different genomes, the exact functions of unknown reading frames urf1 and urf2, the urea carboxylase and the amidase are highly speculative and deduced from annotations (automatic and manual), domain analyses and PFAM searches. The location of these unknown reading frames in direct genomic neighborhood to the putative urea carboxylase-encoding gene is highly conserved in all investigated genomes, while the locations of the genes coding for amino acid permease and the amidase are more variable. Particularly the amtR gene can be found in close vicinity as well as completely elsewhere in the respective genome sequences (Table 3, Figure 7).

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