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1. Regulatory response to a hybrid ancestral nitrogenase in Azotobacter vinelandii

   https://doi.org/10.1128/spectrum.02815-23  

   Rivier, Alex J.; Myers, Kevin S.; Garcia, Amanda K.; Sobol, Morgan S.; Kaçar, Betül (October 2023, Microbiology Spectrum)

   Youssef, Noha H. (Ed.)

   ABSTRACT 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 ofAzotobacter vinelandiiengineered 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. IMPORTANCEAzotobacter vinelandiiis 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 engineeredA. vinelandiistrains 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. 

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2. Reconstructing the evolutionary history of nitrogenases: Evidence for ancestral molybdenum‐cofactor utilization

   https://doi.org/10.1111/gbi.12381  

   Garcia, Amanda K.; McShea, Hanon; Kolaczkowski, Bryan; Kaçar, Betül (February 2020, Geobiology)

   Abstract The nitrogenase metalloenzyme family, essential for supplying fixed nitrogen to the biosphere, is one of life's key biogeochemical innovations. The three forms of nitrogenase differ in their metal dependence, each binding either a FeMo‐, FeV‐, or FeFe‐cofactor where the reduction of dinitrogen takes place. The history of nitrogenase metal dependence has been of particular interest due to the possible implication that ancient marine metal availabilities have significantly constrained nitrogenase evolution over geologic time. Here, we reconstructed the evolutionary history of nitrogenases, and combined phylogenetic reconstruction, ancestral sequence inference, and structural homology modeling to evaluate the potential metal dependence of ancient nitrogenases. We find that active‐site sequence features can reliably distinguish extant Mo‐nitrogenases from V‐ and Fe‐nitrogenases and that inferred ancestral sequences at the deepest nodes of the phylogeny suggest these ancient proteins most resemble modern Mo‐nitrogenases. Taxa representing early‐branching nitrogenase lineages lack one or more biosyntheticnifEandnifNgenes that both contribute to the assembly of the FeMo‐cofactor in studied organisms, suggesting that early Mo‐nitrogenases may have utilized an alternate and/or simplified pathway for cofactor biosynthesis. Our results underscore the profound impacts that protein‐level innovations likely had on shaping global biogeochemical cycles throughout the Precambrian, in contrast to organism‐level innovations that characterize the Phanerozoic Eon. 

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3. Reconstruction of Nitrogenase Predecessors Suggests Origin from Maturase-Like Proteins

   https://doi.org/10.1093/gbe/evac031  

   Garcia, Amanda K; Kolaczkowski, Bryan; Kaçar, Betül (March 2022, Genome Biology and Evolution)

   Archibald, John (Ed.)

   Abstract The evolution of biological nitrogen fixation, uniquely catalyzed by nitrogenase enzymes, has been one of the most consequential biogeochemical innovations over life’s history. Though understanding the early evolution of nitrogen fixation has been a longstanding goal from molecular, biogeochemical, and planetary perspectives, its origins remain enigmatic. In this study, we reconstructed the evolutionary histories of nitrogenases, as well as homologous maturase proteins that participate in the assembly of the nitrogenase active-site cofactor but are not able to fix nitrogen. We combined phylogenetic and ancestral sequence inference with an analysis of predicted functionally divergent sites between nitrogenases and maturases to infer the nitrogen-fixing capabilities of their shared ancestors. Our results provide phylogenetic constraints to the emergence of nitrogen fixation and are consistent with a model wherein nitrogenases emerged from maturase-like predecessors. Though the precise functional role of such a predecessor protein remains speculative, our results highlight evolutionary contingency as a significant factor shaping the evolution of a biogeochemically essential enzyme. 

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4. Characterization of a Nitrogenase Iron Protein Substituted with a Synthetic [Fe ₄ Se ₄ ] Cluster

   https://doi.org/10.1002/anie.202202271  

   Solomon, Joseph B.; Tanifuji, Kazuki; Lee, Chi Chung; Jasniewski, Andrew J.; Hedman, Britt; Hodgson, Keith O.; Hu, Yilin; Ribbe, Markus W. (March 2022, Angewandte Chemie International Edition)

   Abstract The Fe protein of nitrogenase plays multiple roles in substrate reduction and cluster maturation via its redox‐active [Fe₄S₄] cluster. Here we report the synthesis and characterization of a water‐soluble [Fe₄Se₄] cluster that is used to substitute the [Fe₄S₄] cluster of theAzotobacter vinelandiiFe protein (AvNifH). Biochemical, EPR and XAS/EXAFS analyses demonstrate the ability of the [Fe₄Se₄] cluster to adopt the super‐reduced, all‐ferrous state upon its incorporation intoAvNifH. Moreover, these studies reveal that the [Fe₄Se₄] cluster inAvNifH already assumes a partial all‐ferrous state ([Fe₄Se₄]⁰) in the presence of dithionite, where its [Fe₄S₄] counterpart inAvNifH exists solely in the reduced state ([Fe₄S₄]¹⁺). Such a discrepancy in the redox properties of theAvNifH‐associated [Fe₄Se₄] and [Fe₄S₄] clusters can be used to distinguish the differential redox requirements for the substrate reduction and cluster maturation of nitrogenase, pointing to the utility of chalcogen‐substituted FeS clusters in future mechanistic studies of nitrogenase catalysis and assembly. 

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5. Evolution recovers the fitness of Acinetobacter baylyi strains with large deletions through mutations in deletion-specific targets and global post-transcriptional regulators

   https://doi.org/10.1371/journal.pgen.1011306  

   Gifford, Isaac; Suárez, Gabriel A; Barrick, Jeffrey E (September 2024, PLOS Genetics)

   Didelot, Xavier (Ed.)

   Organelles and endosymbionts have naturally evolved dramatically reduced genome sizes compared to their free-living ancestors. Synthetic biologists have purposefully engineered streamlined microbial genomes to create more efficient cellular chassis and define the minimal components of cellular life. During natural or engineered genome streamlining, deletion of many non-essential genes in combination often reduces bacterial fitness for idiosyncratic or unknown reasons. We investigated how and to what extent laboratory evolution could overcome these defects in six variants of the transposon-freeAcinetobacter baylyistrain ADP1-ISx that each had a deletion of a different 22- to 42-kilobase region and two strains with larger deletions of 70 and 293 kilobases. We evolved replicate populations of ADP1-ISx and each deletion strain for ~300 generations in a chemically defined minimal medium or a complex medium and sequenced the genomes of endpoint clonal isolates. Fitness increased in all cases that were examined except for two ancestors that each failed to improve in one of the two environments. Mutations affecting nine protein-coding genes and two small RNAs were significantly associated with one of the two environments or with certain deletion ancestors. The global post-transcriptional regulatorsrnd(ribonuclease D),csrA(RNA-binding carbon storage regulator), andhfq(RNA-binding protein and chaperone) were frequently mutated across all strains, though the incidence and effects of these mutations on gene function and bacterial fitness varied with the ancestral deletion and evolution environment. Mutations in this regulatory network likely compensate for how an earlier deletion of a transposon in the ADP1-ISx ancestor of all the deletion strains restoredcsrAfunction. More generally, our results demonstrate that fitness lost during genome streamlining can usually be regained rapidly through laboratory evolution and that recovery tends to occur through a combination of deletion-specific compensation and global regulatory adjustments. 

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