Regulation of <scp>V</scp>‐nitrogenase genes in <i><scp>A</scp>nabaena variabilis</i> by <scp>RNA</scp> processing and by dual repressors

Pratte, Brenda S.; Sheridan, Ryan M.; James, Jessie A.; Thiel, Teresa

doi:10.1111/mmi.12197

Cited by 19 publications

(36 citation statements)

References 48 publications

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“…In contrast, we were able to verify primary transcription start sites upstream of nifB1 and hesA1 that matched the published sequence (7,39,46). Further, we demonstrated that the 5= ends of nifH1 and fdxH1 in the nif1 cluster, as well as the V-nitrogenase genes, vnfH and vnfDG, have processed RNA ends, not primary transcript ends (39,46,47). In a mutant strain that lacks xisA, the gene that makes the excisase that removes the 11-kb element from nifD1, the nifB1 promoter can no longer drive expression of the genes downstream from the excision element, resulting in little or no expression of those genes (46).…”

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confidence: 58%

Role of RNA Secondary Structure and Processing in Stability of the nifH1 Transcript in the Cyanobacterium Anabaena variabilis

2015

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In the cyanobacterium Anabaena variabilis ATCC 29413, aerobic nitrogen fixation occurs in micro-oxic cells called heterocysts. Synthesis of nitrogenase in heterocysts requires expression of the large nif1 gene cluster, which is primarily under the control of the promoter for the first gene, nifB1. Strong expression of nifH1 requires the nifB1 promoter but is also controlled by RNA processing, which leads to increased nifH1 transcript stability. The processing of the primary nifH1 transcript occurs at the base of a predicted stem-loop structure that is conserved in many heterocystous cyanobacteria. Mutations that changed the predicted secondary structure or changed the sequence of the stem-loop had detrimental effects on the amount of nifH1 transcript, with mutations that altered or destabilized the structure having the strongest effect. Just upstream from the transcriptional processing site for nifH1 was the promoter for a small antisense RNA, sava4870.1. This RNA was more strongly expressed in cells grown in the presence of fixed nitrogen and was downregulated in cells 24 h after nitrogen step down. A mutant strain lacking the promoter for sava4870.1 showed delayed nitrogen fixation; however, that phenotype might have resulted from an effect of the mutation on the processing of the nifH1 transcript. The nifH1 transcript was the most abundant and most stable nif1 transcript, while nifD1 and nifK1, just downstream of nifH1, were present in much smaller amounts and were less stable. The nifD1 and nifK1 transcripts were also processed at sites just upstream of nifD1 and nifK1. IMPORTANCEIn the filamentous cyanobacterium Anabaena variabilis, the nif1 cluster, encoding the primary Mo nitrogenase, functions under aerobic growth conditions in specialized cells called heterocysts that develop in response to starvation for fixed nitrogen. The large cluster comprising more than a dozen nif1 genes is transcribed primarily from the promoter for the first gene, nifB1; however, this does not explain the large amount of transcript for the structural genes nifH1, nifD1, and nifK1, which are also under the control of the distant nifB1 promoter. Here, we demonstrate the importance of a predicted stem-loop structure upstream of nifH1 that controls the abundance of nifH1 transcript through transcript processing and stabilization and show that nifD1 and nifK1 transcripts are also controlled by transcript processing.A nabaena variabilis is a filamentous cyanobacterium that fixes nitrogen under oxic growth conditions in cells called heterocysts. Heterocysts, which are specialized micro-oxic cells that develop in a semiregular pattern in the filament in response to nitrogen stress, fix atmospheric dinitrogen to ammonium using the enzyme nitrogenase (1-3). The micro-oxic conditions of the heterocyst result from the glycolipid layer that may restrict oxygen diffusion into the cell, the absence of oxygen-evolving photosystem II, and increased respiration, all of which serve to protect nitrogenase from oxygen (4-6). While all heter...

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confidence: 58%

Role of RNA Secondary Structure and Processing in Stability of the nifH1 Transcript in the Cyanobacterium Anabaena variabilis

2015

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“…The xisA deletion strain, BP669, was created by introducing the mobilizable plasmid pBP669 into strain FD by conjugation. Single recombinants were selected by erythromycin resistance (Em r ), followed by isolation of double-recombinant mutants with the deleted copy of xisA, using sacB with sucrose selection (38) as described previously (39).…”

Section: Methodsmentioning

confidence: 99%

Regulation of Nitrogenase Gene Expression by Transcript Stability in the Cyanobacterium Anabaena variabilis

Pratte

Thiel

2014

Journal of Bacteriology

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The nitrogenase gene cluster in cyanobacteria has been thought to comprise multiple operons; however, in Anabaena variabilis, the promoter for the first gene in the cluster, nifB1, appeared to be the primary promoter for the entire nif cluster. The structural genes nifHDK1 were the most abundant transcripts; however, their abundance was not controlled by an independent nifH1 promoter, but rather, by RNA processing, which produced a very stable nifH1 transcript and a moderately stable nifD1 transcript. There was also no separate promoter for nifEN1. In addition to the nifB1 promoter, there were weak promoters inside the nifU1 gene and inside the nifE1 gene, and both promoters were heterocyst specific. In an xisA mutant, which effectively separated promoters upstream of an 11-kb excision element in nifD1 from the downstream genes, the internal nifE1 promoter was functional. Transcription of the nif1 genes downstream of the 11-kb element, including the most distant genes, hesAB1 and fdxH1, was reduced in the xisA mutant, indicating that the nifB1 promoter contributed to their expression. However, with the exception of nifK1 and nifE1, which had no expression, the downstream genes showed low to moderate levels of transcription in the xisA mutant. The hesA1 gene also had a promoter, but the fdxH gene had a processing site just upstream of the gene. The processing of transcripts at sites upstream of nifH1 and fdxH1 correlated with increased stability of these transcripts, resulting in greater amounts than transcripts that were not close to processing sites.

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“…5). The assumption that V is acquired and the V-Nase genes are activated only when Mo becomes limiting for diazotrophic growth might be due to the oversimplified conditions used in laboratory experiments to study metal acquisition and homeostasis in A. vinelandii and other dinitrogen fixers (Bellenger et al, 2011;Pratte et al, 2013).…”

Section: Resultsmentioning

confidence: 99%

Effect of organic matter on nitrogenase metal cofactors homeostasis in Azotobacter vinelandii under diazotrophic conditions

Noumsi

Pourhassan

Darnajoux

et al. 2016

Environ Microbiol Rep

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Biological nitrogen fixation can be catalysed by three isozymes of nitrogenase: molybdenum (Mo)-nitrogenase, vanadium (V)-nitrogenase and iron-only (Fe)-nitrogenase. The activity of these isozymes strongly depends on their metal cofactors, molybdenum, vanadium and iron, and their bioavailability in ecosystems. Here, we show how metal bioavailability can be affected by the presence of tannic acid (organic matter), and the subsequent consequences on diazotrophic growth of the soil bacterium Azotobacter vinelandii. In the presence of tannic acids, A. vinelandii produces a higher amount of metallophores, which coincides with an active, regulated and concomitant acquisition of molybdenum and vanadium under cellular conditions that are usually considered not molybdenum limiting. The associated nitrogenase genes exhibit decreased nifD expression and increased vnfD expression. Thus, in limiting bioavailable metal conditions, A. vinelandii takes advantage of its nitrogenase diversity to ensure optimal diazotrophic growth.

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Regulation of V‐nitrogenase genes in Anabaena variabilis by RNA processing and by dual repressors

Cited by 19 publications

References 48 publications

Role of RNA Secondary Structure and Processing in Stability of the nifH1 Transcript in the Cyanobacterium Anabaena variabilis

Role of RNA Secondary Structure and Processing in Stability of the nifH1 Transcript in the Cyanobacterium Anabaena variabilis

Regulation of Nitrogenase Gene Expression by Transcript Stability in the Cyanobacterium Anabaena variabilis

Effect of organic matter on nitrogenase metal cofactors homeostasis in Azotobacter vinelandii under diazotrophic conditions

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