scholarly journals Suppression ofhesAmutation on nitrogenase activity inPaenibacillus polymyxaWLY78 with the addition of high levels of molybdate or cystine

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6294 ◽  
Author(s):  
Xiaomeng Liu ◽  
Xiyun Zhao ◽  
Xiaohan Li ◽  
Sanfeng Chen
Keyword(s):  
Nitrogen Fixation ◽  
Gene Cluster ◽  
Nitrogenase Activity ◽  
Reductase Activity ◽  
Klebsiella Oxytoca ◽  
Paenibacillus Polymyxa ◽  
Gene Clusters ◽  
Nucleotide Binding Domain ◽  
Diazotrophic Cyanobacteria ◽  
Nitrogen Fixation Gene

The diazotrophicPaenibacillus polymyxaWLY78 possesses a minimal nitrogen fixation gene cluster consisting of nine genes (nifB nifH nifD nifK nifE nifN nifX hesAandnifV). Notably, thehesAgene contained within thenifgene cluster is also found withinnifgene clusters among diazotrophic cyanobacteria andFrankia. The predicted product HesA is a member of the ThiF-MoeB-HesA family containing an N-terminal nucleotide binding domain and a C-terminal MoeZ/MoeB-like domain. However, the function ofhesAgene in nitrogen fixation is unknown. In this study, we demonstrate that thehesAmutation ofP. polymyxaWLY78 leads to nearly complete loss of nitrogenase activity. The effect of the mutation can be partially suppressed by the addition of high levels of molybdate or cystine. However, the nitrogenase activity of thehesAmutant could not be restored byKlebsiella oxytoca nifQorEscherichia coli moeBcompletely. In addition, thehesAmutation does not affect nitrate reductase activity ofP. polymyxaWLY78. Our results demonstratehesAis a novel gene specially required for nitrogen fixation and its role is related to introduction of S and Mo into the FeMo-co of nitrogenase.

scholarly journals Molecular Components of Nitrogen Fixation Gene Cluster and Associated Enzymatic Activities of Non-Heterocystous Thermophilic Cyanobacterium Thermoleptolyngbya sp.

Life ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 640
Author(s):  
Meijin Li ◽  
Lei Cheng ◽  
Jie Tang ◽  
Maurycy Daroch
Keyword(s):  
Nitrogen Fixation ◽  
Gene Cluster ◽  
Microbial Mats ◽  
Hot Spring ◽  
Nitrogenase Activity ◽  
Second Phase ◽  
Two Phase ◽  
Fixation Capacity ◽  
Molecular Components ◽  
Nitrogen Fixation Gene

Thermoleptolyngbya is a genus of non-heterocystous cyanobacteria that are typical inhabitants of hot spring microbial mats. These filamentous cyanobacteria are capable of nitrogen fixation. In this study, we examined the genome sequences of five publicly available Thermoleptolyngbya strains to explore their nitrogen fixation gene cluster. Analysis of the nitrogen-fixation clusters in these extremophilic strains revealed that the cluster is located in a single locus in Thermoleptolyngbyace. The average nucleotide and amino acid identities of the nitrogen-fixation cluster combined with phylogenetic reconstructions support that nitrogen fixation genes in Thermoleptolyngbyaceae are closely related to one another but also heterogeneous within the genus. The strains from Asia, and China more specifically, generate a separate clade within the genus. Among these strains Thermoleptolyngbya sp. PKUAC-SCTB121 has been selected for experimental validation of clade’s nitrogen fixation capacity. The acetylene reduction experiments of that strain shown that the strain can reduce acetylene to ethylene, indicating a fully functional nitrogenase. The activity of nitrogenase has been tested using different gas compositions across 72 h and exhibited a two-phase trend, high nitrogenase activity at the beginning of the assay that slowed down in the second phase of the analysis.

Phenotypic reversion of nitrogenase in pleiotropic mutants of Rhizobium meliloti

1979 ◽  
Vol 25 (3) ◽  
pp. 298-301 ◽  
Author(s):  
Ilona Barabás ◽  
Tibor Sik
Keyword(s):  
Amino Acids ◽  
Nitrogen Fixation ◽  
Nitrate Reductase ◽  
Nitrate Reductase Activity ◽  
Symbiotic Nitrogen Fixation ◽  
Rhizobium Meliloti ◽  
Nitrogenase Activity ◽  
Reductase Activity ◽  
Amino Acid Utilization ◽  
Phenotypic Reversion

In two out of three pleiotropic mutants of Rhizobium meliloti, defective in nitrate reductase induced by amino acid utilization in vegetative bacteria and in symbiotic nitrogen fixation, nitrogenase activity could be restored completely by purines and partially by the amino acids L-glutamate, L-aspartate, L-glutamine, and L-asparagine. The compounds restoring effectiveness in nitrogen fixation did not restore nitrate reductase activity in vegetative bacteria. The restoration of effectiveness supports our earlier conclusion that the mutation is not in the structural gene for a suggested common subunit of nitrogenase and nitrate reductase.

Sequences of nifX, nifW, nifZ, nifB and two ORF in the frankia nitrogen fixation gene cluster

Gene ◽  
1995 ◽  
Vol 161 (1) ◽  
pp. 63-67 ◽  
Author(s):  
Olivia T. Harriott ◽  
Thomas J. Hosted ◽  
David R. Benson
Keyword(s):  
Nitrogen Fixation ◽  
Gene Cluster ◽  
Nitrogen Fixation Gene

scholarly journals The nif Gene Operon of the Methanogenic Archaeon Methanococcus maripaludis

1998 ◽  
Vol 180 (6) ◽  
pp. 1504-1511 ◽  
Author(s):  
Peter S. Kessler ◽  
Carrine Blank ◽  
John A. Leigh
Keyword(s):  
Nitrogen Fixation ◽  
Gene Cluster ◽  
Sequence Similarity ◽  
Methanogenic Archaea ◽  
Gene Clusters ◽  
Northern Analysis ◽  
Insertion Mutagenesis ◽  
Fragmentation Pattern ◽  
Methanococcus Maripaludis ◽  
Regulation Of Expression

ABSTRACT Nitrogen fixation occurs in two domains, Archaea andBacteria. We have characterized a nif(nitrogen fixation) gene cluster in the methanogenic archaeonMethanococcus maripaludis. Sequence analysis revealed eight genes, six with sequence similarity to known nif genes and two with sequence similarity to glnB. The gene order,nifH, ORF105 (similar to glnB),ORF121 (similar to glnB), nifD,nifK, nifE, nifN, andnifX, was the same as that found in part in other diazotrophic methanogens and except for the presence of theglnB-like genes, also resembled the order found in many members of the Bacteria. Using transposon insertion mutagenesis, we determined that an 8-kb region required for nitrogen fixation corresponded to the nif gene cluster. Northern analysis revealed the presence of either a single 7.6-kbnif mRNA transcript or 10 smaller mRNA species containing portions of the large transcript. Polar effects of transposon insertions demonstrated that all of these mRNAs arose from a single promoter region, where transcription initiated 80 bp 5′ tonifH. Distinctive features of the nif gene cluster include the presence of the six primary nif genes in a single operon, the placement of the two glnB-like genes within the cluster, the apparent physical separation of the cluster from any other nif genes that might be in the genome, the fragmentation pattern of the mRNA, and the regulation of expression by a repression mechanism described previously. Our study and others with methanogenic archaea reporting multiple mRNAs arising from gene clusters with only a single putative promoter sequence suggest that mRNA processing following transcription may be a common occurrence in methanogens.

scholarly journals The role of Fnr paralogs for controlling anaerobic metabolism in diazotroph Paenibacillus polymyxa WLY78

2020 ◽  
Author(s):  
Haowen Shi ◽  
Yongbin Li ◽  
Tianyi Hao ◽  
Xiaomeng Liu ◽  
Xiyun Zhao ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Nitrogen Fixation ◽  
Bacillus Cereus ◽  
Anaerobic Condition ◽  
Anaerobic Metabolism ◽  
Nitrogenase Activity ◽  
Paenibacillus Polymyxa ◽  
Transcription Analysis ◽  
Double Deletion ◽  
Expression Of Genes

ABSTRACTFnr is a transcriptional regulator that controls the expression of a variety of genes in response to oxygen limitation in bacteria. Genome sequencing revealed four genes (fnr1, fnr3, fnr5 and fnr7) coding for Fnr proteins in Paenibacillus polymyxa WLY78. Fnr1 and Fnr3 showed more similarity to each other than to Fnr5 and Fnr7. Also, Fnr1 and Fnr3 exhibited high similarity with Bacillus cereus Fnr and Bacillus subtilis Fnr in sequence and structures. Deletion analysis showed that the four fnr genes, especially fnr1 and fnr3, have significant impacts on the growth and nitrogenase activity. Single deletion of fnr1 or fnr3 led to 50% reduction in nitrogenase activity and double deletion of fnr1 and fnr3 resulted to 90% reduction in activity. Both of the aerobically purified His-tagged Fnr1 and His-tagged Fnr3 in Escherichia coli could bind to the specific DNA promoter. Genome-wide transcription analysis showed that Fnr1 and Fnr3 indirectly activated expression of nif (nitrogen fixation) genes and Fe transport genes under anaerobic condition. Fnr1 and Fnr3 inhibited expression of the genes involved in aerobic respiratory chain and activated expression of genes responsible for anaerobic electron acceptor genes.IMPORTANCEPaenibacillus is a genus of Gram-positive, facultative anaerobic and endospore-forming bacteria. The members of nitrogen-fixing Paenibacillus have great potential use as a bacterial fertilizer in agriculture. However, the functions of fnr gene(s) in nitrogen fixation and other metabolisms in Paenibacillus spp. are not known. Here, we revealed that copy numbers vary largely among different Paenibacillus species and strains. Deletion and complementation analysis demonstrated that fnr1 and fnr3 have significant impacts on the growth and nitrogenase activity. Both of the aerobically purified His-tagged Fnr1 and His-tagged Fnr3 purified in Escherichia coli could bind to the specific DNA promoter as Bacillus cereus Fnr did. Fnr1 and Fnr3 indirectly activated nif expression under anaerobic condition. Fnr1 and Fnr3 directly or indirectly activated or inhibited expression of many important genes involved in respiration, energy metabolism, Fe uptake and potentially specific electron transport for nitrogenase under anaerobic condition. This study not only reveals the roles of fnr genes in nitrogen fixation and anaerobic metabolism, but also provides insight into the evolution and regulatory mechanisms of fnr in Paenibacillus.

scholarly journals Evolution and Functional Analysis of orf1 Within nif Gene Cluster from Paenibacillus graminis RSA19

2019 ◽  
Vol 20 (5) ◽  
pp. 1145 ◽  
Author(s):  
Qin Li ◽  
Xiaomeng Liu ◽  
Haowei Zhang ◽  
Sanfeng Chen
Keyword(s):  
Nitrogen Fixation ◽  
Gene Cluster ◽  
Gene Clusters ◽  
Amino Acid Sequences ◽  
Transcriptional Analysis ◽  
Facultative Anaerobic ◽  
Orf1 Gene ◽  
Nif Gene ◽  
Nif Gene Cluster ◽  
Paenibacillus Species

Paenibacillus is a genus of Gram-positive, facultative anaerobic and endospore-forming bacteria. Genomic sequence analysis has revealed that a compact nif (nitrogen fixation) gene cluster comprising 9–10 genes nifBHDKENX(orf1)hesAnifV is conserved in diazotrophic Paenibacillus species. The evolution and function of the orf1 gene within the nif gene cluster of Paenibacillus species is unknown. In this study, a careful comparison analysis of the compositions of the nif gene clusters from various diazotrophs revealed that orf1 located downstream of nifENX was identified in anaerobic Clostridium ultunense, the facultative anaerobic Paenibacillus species and aerobic diazotrophs (e.g., Azotobacter vinelandii and Azospirillum brasilense). The predicted amino acid sequences encoded by the orf1 gene, part of the nif gene cluster nifBHDKENXorf1hesAnifV in Paenibacillus graminis RSA19, showed 60–90% identity with those of the orf1 genes located downstream of nifENX from different diazotrophic Paenibacillus species, but shared no significant identity with those of the orf1 genes from different taxa of diazotrophic organisms. Transcriptional analysis showed that the orf1 gene was expressed under nitrogen fixation conditions from the promoter located upstream from nifB. Mutational analysis suggested that the orf1 gene functions in nitrogen fixation in the presence of a high concentration of O2.

scholarly journals Horizontal transfer of the nitrogen fixation gene cluster in the cyanobacterium Microcoleus chthonoplastes

2009 ◽  
Vol 4 (1) ◽  
pp. 121-130 ◽  
Author(s):  
Henk Bolhuis ◽  
Ina Severin ◽  
Veronique Confurius-Guns ◽  
Ute I A Wollenzien ◽  
Lucas J Stal
Keyword(s):  
Nitrogen Fixation ◽  
Gene Cluster ◽  
Horizontal Transfer ◽  
Microcoleus Chthonoplastes ◽  
Nitrogen Fixation Gene

scholarly journals Nitrogen Fixation by Paenibacillus Polymyxa WLY78 is Responsible for Cucumber Growth Promotion

2021 ◽  
Author(s):  
Shuang Liu ◽  
Qin Li ◽  
Yongbin Li ◽  
Tianyi Hao ◽  
Sanfeng Chen
Keyword(s):  
Nitrogen Fixation ◽  
Plant Growth ◽  
Gene Cluster ◽  
Isotope Dilution ◽  
Laser Scanning ◽  
Growth Promotion ◽  
Nitrogenase Activity ◽  
Confocal Laser ◽  
Greenhouse Experiments ◽  
Dilution Experiments

Abstract Aims To study nitrogen contribution to cucumber derived from nitrogen fixation of Paenibacillus polymyxa WLY78.Methods The nif gene cluster deletion mutant (ΔnifB-V) of P. polymyxa WLY78 is constructed by a homologous recombination method. The GFP-labeled ΔnifB-V mutant was used to inoculate cucumber and to study colonization by confocal laser scanning microscope. The effects of plant-growth promotion were investigated by greenhouse experiments. The nitrogen fixation contribution was estimated by 15N isotope dilution experiments. Results Deletion of nif gene cluster of P. polymyxa WLY78 resulted in complete loss of nitrogenase activity. Observation by laser confocal microscopy revealed ΔnifB-V mutant can effectively colonize cucumber root, stem and leaf tissues, like wild-type P. polymyxa WLY78. Greenhouse experiments showed that inoculation with P. polymyxa WLY78 can significantly enhance the lengths and dry weights of cucumber roots and shoots, but inoculation with ΔnifB-V mutant can not. 15N isotope dilution experiments showed that cucumber plants derive 25.93% nitrogen from nitrogen fixation performed by P. polymyxa WLY78, but the ΔnifB-V mutant nearly can not provide nitrogen for plant growth. Conclusions This present study demonstrates that nitrogen fixation performed by P. polymyxa WLY78 is responsible for cucumber growth promotion.

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