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

Pratte, Brenda S.; Thiel, Teresa

doi:10.1128/jb.02045-14

Cited by 14 publications

(47 citation statements)

References 55 publications

(85 reference statements)

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“…The apparent transcription start sites for nifB1 and nifH1 in A. variabilis are identical to those mapped in Anabaena sp. PCC 7120, and there are weak, heterocyst-specific promoters within the coding regions of nifU1 and nifE1 (7,39,46). However, we found no evidence for a promoter in the 300-bp nifU1-nifH1 intergenic region driving expression of nifH1 (39).…”

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confidence: 69%

“…However, we found no evidence for a promoter in the 300-bp nifU1-nifH1 intergenic region driving expression of nifH1 (39). 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).…”

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confidence: 60%

“…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). Even hesA1, which has its own promoter, is not expressed as well in the xisA mutant as in the wild-type (WT) strain, which suggests that the nifB1 promoter controls the expression of a gene that is 14 kb away.…”

mentioning

confidence: 89%

“…In A. variabilis, the nifH1 transcript is much more abundant than the other nif1 transcripts, even though nifH1 lacks its own promoter, because the transcript is very stable (39,46). The 5= end of the processed transcript is at the base of a predicted stem-loop structure that may be responsible for the stability of the transcript (39,46).…”

mentioning

confidence: 99%

“…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).…”

mentioning

confidence: 99%

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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: 69%