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Series GSE234075 Query DataSets for GSE234075
Status Public on Jun 07, 2023
Title A hybrid nitrogenase with regulatory elasticity in Azotobacter vinelandii
Organism Azotobacter vinelandii DJ
Experiment type Expression profiling by high throughput sequencing
Summary Biological nitrogen fixation, the microbial reduction of atmospheric nitrogen to bioavailable ammonia, represents both a major limitation on biological productivity and a highly desirable engineering target for synthetic biology. However, the engineering of nitrogen fixation requires an integrated understanding of how the gene regulatory dynamics of host diazotrophs respond across sequence-function space of its central catalytic metalloenzyme, nitrogenase. Here, we interrogate this relationship by analyzing the transcriptome of Azotobacter vinelandii engineered with a phylogenetically inferred ancestral nitrogenase protein variant. The engineered strain exhibits reduced cellular nitrogenase activity but recovers wild-type growth rates following an extended lag period. We find that expression of genes within the immediate nitrogen fixation network is resilient to the introduced nitrogenase sequence-level perturbations. Rather the sustained physiological compatibility with the ancestral nitrogenase variant is accompanied by reduced expression of genes that support trace metal and electron resource allocation to nitrogenase. Our results spotlight gene expression changes in cellular processes adjacent to nitrogen fixation as productive engineering considerations to improve compatibility between remodeled nitrogenase proteins and engineered host diazotrophs.

Azotobacter vinelandii is a key model bacterium for the study of biological nitrogen fixation, an important metabolic process catalyzed by nitrogenase enzymes. Here, we demonstrate that compatibilities between engineered A. vinelandii strains and nitrogenase variants can be modulated at the regulatory level. The engineered strain studied here responds by adjusting the expression of proteins involved in cellular processes adjacent to nitrogen fixation, rather than that of nitrogenase proteins themselves. These insights can inform future strategies to transfer nitrogenase variants to non-native hosts.
Overall design Comparative RNA-seq gene expression analysis for Azotobacter vinelandii WT and strain ancNif (ΔnifD) grown diaztrophically. Three biological replicates were sequenced and analyzed for each strain.
Web link
Contributor(s) Rivier AJ, Myers KS, Garcia AK, Sobol MS, Kacar B
Citation(s) 37702481
Submission date Jun 05, 2023
Last update date Sep 15, 2023
Contact name Betül Kaçar
Organization name University of Wisconsin-Madison
Department Department of Bacteriology
Lab Kaçar Lab
Street address 1550 Linden Dr.
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
Platforms (1)
GPL33461 Illumina NovaSeq 6000 (Azotobacter vinelandii DJ)
Samples (6)
GSM7445239 WT Rep 1
GSM7445240 WT Rep 2
GSM7445241 WT Rep 3
BioProject PRJNA980078

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Supplementary file Size Download File type/resource
GSE234075_FPKM-data.txt.gz 235.6 Kb (ftp)(http) TXT
GSE234075_HTSeq-counts.txt.gz 67.0 Kb (ftp)(http) TXT
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