- Open Access
Unraveling the molecular mechanisms of nitrogenase conformational protection against oxygen in diazotrophic bacteria
- Letícia MS Lery†1Email author,
- Mainá Bitar†1,
- Mauricio GS Costa†1,
- Shaila CS Rössle2 and
- Paulo M Bisch1
© Lery et al; licensee BioMed Central Ltd. 2010
- Published: 22 December 2010
G. diazotrophicus and A. vinelandii are aerobic nitrogen-fixing bacteria. Although oxygen is essential for the survival of these organisms, it irreversibly inhibits nitrogenase, the complex responsible for nitrogen fixation. Both microorganisms deal with this paradox through compensatory mechanisms. In A. vinelandii a conformational protection mechanism occurs through the interaction between the nitrogenase complex and the FeSII protein. Previous studies suggested the existence of a similar system in G. diazotrophicus, but the putative protein involved was not yet described. This study intends to identify the protein coding gene in the recently sequenced genome of G. diazotrophicus and also provide detailed structural information of nitrogenase conformational protection in both organisms.
Genomic analysis of G. diazotrophicus sequences revealed a protein coding ORF (Gdia0615) enclosing a conserved “fer2” domain, typical of the ferredoxin family and found in A. vinelandii FeSII. Comparative models of both FeSII and Gdia0615 disclosed a conserved beta-grasp fold. Cysteine residues that coordinate the 2[Fe-S] cluster are in conserved positions towards the metallocluster. Analysis of solvent accessible residues and electrostatic surfaces unveiled an hydrophobic dimerization interface. Dimers assembled by molecular docking presented a stable behaviour and a proper accommodation of regions possibly involved in binding of FeSII to nitrogenase throughout molecular dynamics simulations in aqueous solution. Molecular modeling of the nitrogenase complex of G. diazotrophicus was performed and models were compared to the crystal structure of A. vinelandii nitrogenase. Docking experiments of FeSII and Gdia0615 with its corresponding nitrogenase complex pointed out in both systems a putative binding site presenting shape and charge complementarities at the Fe-protein/MoFe-protein complex interface.
The identification of the putative FeSII coding gene in G. diazotrophicus genome represents a large step towards the understanding of the conformational protection mechanism of nitrogenase against oxygen. In addition, this is the first study regarding the structural complementarities of FeSII-nitrogenase interactions in diazotrophic bacteria. The combination of bioinformatic tools for genome analysis, comparative protein modeling, docking calculations and molecular dynamics provided a powerful strategy for the elucidation of molecular mechanisms and structural features of FeSII-nitrogenase interaction.
- Biological Nitrogen Fixation
- Ramachandran Plot
- Docking Calculation
- Diazotrophic Bacterium
- Rhodobacter Capsulatus
Nitrogen is a component of nucleic acids, proteins and many other biological molecules thus, it is an essential element for all living organisms. Although the N2 gas is abundant in the atmosphere, it can not be readily used by most organisms. Nitrogen fixation is a key process in which molecular nitrogen is reduced to form ammonia, which is the form used by living systems for the synthesis of many organic compounds . Biological nitrogen fixation is catalyzed by the oxygen-sensitive enzyme nitrogenase present in some microorganisms known as diazotrophs, mainly bacteria [2–4].
The most abundant and extensively studied nitrogenase is the molybdenum (Mo)-dependent enzyme . It is composed of two metalloproteins: the MoFe-protein (also called dinitrogenase or component I) and the Fe-protein (also called dinitrogenase reductase or component II) . Both the MoFe and Fe-protein are irreversibly damaged by oxygen . O2 exposure leads to inappropriate oxidation of the metalloclusters, decrease of protein secondary structure and further degradation .
Yet, several nitrogen-fixing bacteria are aerobic and demand high O2 flux for proper cellular metabolism. Therefore these bacteria present mechanisms to solve this apparent paradox. Under high O2 concentration, they increase metabolism and consume more carbon source than needed to satisfy its energy requirement for growth in order to decrease O2 pressure [7, 8]. Subtle adjustments in the composition and functioning of the respiratory chain, mainly differential expression of cytochromes, were described [9–11]. Additionally, diazotrophs grown in air secrete abundant extracellular polysaccharides and live inside colonies that help to produce a local microaerobic environment [12, 13].
Besides the respiratory protection mechanism, it was shown that a few nitrogen-fixing bacteria present a conformational protection mechanism of nitrogenase against O2[14–17]. Such system involves the interaction of a ferredoxin protein (FeSII or Shethna protein) with the nitrogenase complex that results in stabilization of a reversibly inactive complex. The ferredoxin protein is found as an homodimer that contains a 2[Fe-S] cluster and interacts specifically and reversibly with the nitrogenase complex .
Similar mechanisms were described in Azotobacter chroococcum, Azotobacter vinelandii, Clostridium pasteurianum[19, 20] and Klebsiella pneumoniae. The FeSII protein was mainly studied in A. vinelandii[18, 21, 22]. Site-directed mutagenesis and crosslinking experiments revealed two residues possibly with fundamental roles on the interaction of FeSII with nitrogenase [20, 23].
Previous studies have shown evidences of a similar mechanism of conformational protection in Gluconacetobacter diazotrophicus, however the putative FeSII protein was not yet identified .
Due to the great importance of biological nitrogen fixation for sustainable crop production, advances have been achieved in genetics and biochemistry, culminating in the determination of the crystallographic structures of both nitrogenase components [24–26]. However, studies on protein regulation and dynamics need to be carried out to a complete understanding of the molecular nature of the process.
In order to gain knowledge on structure and function of the proteins involved in the conformational protection of nitrogenase, we performed bioinformatic analysis on the whole genome sequence of G. diazotrophicus and identified a putative FeSII protein. In addition, molecular modeling, dynamics and docking studies on both A. vinelandii and G. diazotrophicus FeSII proteins and nitrogenases were carried out, elucidating molecular aspects of protein-protein interaction.
Gdia0615 codes for a putative FeSII protein of G. diazotrophicus
C. pasteurianum and A. vinelandii FeSII proteins were target of several theoretical and experimental studies [15, 19–23, 25]. Thus, its primary sequences were used to search for an homologue in G. diazotrophicus. Searches were performed on both versions of G. diazotrophicus complete genome sequence available, containing 3852 (Riogene; ) and 3501 (DOE) predicted protein coding genes. However, similarity searches on predicted protein sequences or raw genomic sequence did not return any hit with high sequence similarity (>30% identity) and coverage (>70%).
In order to follow up the search for a putative FeSII in G. diazotrophicus the functional properties of FeSII proteins were analyzed. For instance, A. vinelandii FeSII protein presents 13 kDa and a fer2 domain , found in ferredoxins that are electron carrier proteins with a 2Fe-2S cofactor acting in a wide variety of metabolic reactions. The members of this family are proteins of approximately one hundred aminoacids with four conserved cysteine residues that coordinate the 2[Fe-S] cluster and have a general core structure consisting of beta(2)-alpha-beta(2) .
Accordingly, Ureta et al, 2002  have shown the co-precipitation of a 14 kDa protein with nitrogenase of G. diazotrophicus cells grown diazotrophically under high oxygen concentration. This result suggested a conformational protection mechanism of nitrogenase in G. diazotrophicus, involving a 14 kDa protein.
In a second attempt to identify the G. diazotrophicus FeSII protein, we have analyzed the whole genome sequences for ferredoxin proteins. From the 7353 ORFs analyzed, a search for textual annotation with the “ferredoxin” or “2Fe-2S” syntax revealed 16 putative ferredoxins. From these, only 8 present predicted molecular weight between 9 and 20 kDa, around the expected size for a putative 2[Fe-S] Shethna protein. Analysis of these 8 ferredoxins for the presence of functional domains disclosed two ORFs in G. diazotrophicus genome with high score for the fer2 domain (Protein Family PF00111; Gdi2370 and Gdia0615 both presented an e-value of 7.2e-17). However, they correspond to the same protein, as they come from one of each complete genome sequence available. They are 99% identical and the only difference is that Gdia0615 is 3 aminoacids longer (initial MPH sequence) than Gdi2370. Thus, Gdia0615 was chosen for further analysis.
Following this analysis, the functional conserved residues from A. vinelandii FeSII were investigated for corresponding residues on the putative G. diazotrophicus sequence. Lou et al 1999  described the importance of two lysine residues (K14 and K15) crucial for FeSII interaction with nitrogenase. Interestingly, Gdia0615 presents two arginine residues (R13 and R14) in a conserved position (Fig. 1). K and R are both basic residues and might encompass same function in the protein context. Besides, A. vinelandii FeSII presents 4 cysteine residues at positions 42, 47, 50 and 102, that coordinate the metal cluster, essential for plenty function of FeSII . Gdia0615 also presents this 4 cysteine residues well conserved in structure (C39, C45, C48 and C85; Fig. 1). Altogether, these results strongly suggest that Gdia0615 is the gene that codes for the putative FeSII in G. diazotrophicus.
FeSII molecular models revealed a conserved β-grasp core structure
The results discussed above strongly suggest that Gdia0615 is the putative FeSII protein of G. diazotrophicus. However, there are no structural information available for both A. vinelandii FeSII and Gdia0615. It is far known that protein structure is a determinant of protein function and three-dimensional structure is more conserved than protein sequence. Thus, as a support to the above predictions, 3D comparative models for Gdia0615, as well as for A. vinelandii FeSII, were constructed.
The first step in comparative modeling is the definition of a template sequence. The template sequence must have its 3D structure experimentally determined with high accuracy and present sequence similarity with the target. The quality of 3D structure (resolution of the template structure) and the alignment between template and target sequences are crucial for the model quality. Therefore, several alignments were generated for the FeSII sequences, using information from sequence database searches, secondary structure prediction and available homologues with resolved 3D structures. Alignments were then manually optimized in order to minimize gaps and assert that the conserved domain residues are aligned. Although Gdia0615 and A. vinelendii FeSII might both perform the conformational protection of nitrogenase, they share low sequence similarity (18% identity and 42% similarity). Therefore, template structures chosen for comparative modeling of each of them were different. Gdia0615 chosen template is FdvI protein (48% identity and 67% similarity), a 2[Fe-S] ferredoxin essential for growth of Rhodobacter capsulatus, also a diazotrophic bacterium. A. vinelandii FeSII chosen template is E. coli Fdx (20% identity and 36% similarity), an adrenodoxin-type 2[Fe-S] ferredoxin with an essential role in the maturation of various iron-sulfur (Fe-S) proteins . This two template proteins share some structural similarity and both coordinate a 2[Fe-S] cluster.
The A. vinelandii FeSII model (deposited at Protein Model DataBase at identification number PM0075978) exhibited high stereochemical quality (97% of residues in the allowed regions of Ramachandran plot) and a high probability to represent a native-like conformation (Dope-score -3.7493 and ProSa Z-score -5.06). The average distance deviation between backbone equivalent atoms (RMSD - Root Mean Square Deviation) measures the similarity between 3D structures after optimal superposition; the RMSD score for FeSII proposed model vs. the crystal structure of Fdx was 0.53 Å, a further indication of the high quality of the model . A remarkable feature of this model is a large loop region, comprising aminoacids 77-90, as expected from the observed gap in sequence alignment. In overall, this represents a structure of high quality.
The Gdia0615 model (deposited at PMDB at identification number PM0075980) also presented high stereochemical quality (100% of residues in the allowed regions of Ramachandran plot) and is a highly probable native-like structure (Dope-score -4.0447 and ProSa Z-score -6.57). The RMSD between Gdia0615 model and FdvI crystal structure is 0.46 Å, representing the overall quality of the model.
Additionally, the 4 cysteine residues are positioned towards the 2[Fe-S] cluster, as was expected, in both models (Fig. 2). The 2 lysine (K14 and K15) residues of A. vinelandii FeSII and the corresponding 2 arginine (R13 and R14) of G. diazotrophicus are positioned at exposed surface and might be involved in nitrogenase interaction, as suggested before.
Altogether these results provide evidence that FeSII and Gdia0615 could perform same molecular function.
FeSII dimer is the stable functional unit
G. diazotrophicus nitrogenase complex structure is close related to A. vinelandii nitrogenase
In order to better understand the conformational protection mechanism of nitrogenase from oxygen damage, analysis of FeSII-nitrogenase interaction is required. The protection is due to the formation of an oxygen-tolerant three-component nitrogenase complex (Fe-protein + MoFe-protein + FeSII protein) [16, 32]. Crystal structures of A. vinelandii nitrogenase complex were already determined and presented insights on multiple docking sites of nucleotides [33, 34]. Mutant forms of nitrogenase proteins were also studied and revealed key residues for nucleotide-protein interaction . In contrast, FeSII interaction with nitrogenase complex was not yet studied in respect to structural aspects. In addition, it lacks information on 3D structure of G. diazotrophicus nitrogenase complex.
As a strategy to fulfill this gap, a molecular model of G. diazotrophicus nitrogenase complex was built through comparative modeling. The Fe-protein presents 70% identity and 85% positivity with the A. vinelandii homologue. The MoFe-protein α-subunit shows 71% identity and 81% similarity with the A. vinelandii counterpart. The β-subunit of MoFe-protein is 52% identical and 70% similar to the A. vinelandii protein. In summary, all components of nitrogenase complex from G. diazotrophicus and A. vinelandii share high sequence similarity. Therefore, the template structures for both components of nitrogenase complex were the A. vinelandii subunits.
In consequence of this high degree of similarity between target and template sequences, the molecular model of G. diazotrophicus nitrogenase complex presented high stereochemical quality. Molecular models of Fe-protein (deposited at PMDB at identification number PM0075981), MoFe-protein α and β-subunits (deposited at PMDB at identification numbers PM0075982 and PM0075983, respectively) presented 99%, 98% and 99% of residues in allowed regions of Ramachandran plot. The overall RMSD between each crystal structure and the proposed model is 0.41, 0.31 and 0.54 Å, respectively. Such a high quality model is suitable for protein-protein interaction analysis.
A negative pocket anchors the FeSII positive region near the Fe-protein/MoFe-protein interface in the nitrogenase complex
As mentioned before, a few studies reported the interaction of FeSII with nitrogenase. Nitrogenase protein is found as an oligomer (two Fe-protein homodimers + one heterotetramer of MoFe-protein). The binding site of FeSII in nitrogenase is not clearly described. It was shown that a 2[Fe-S] ferredoxin of C. pasteurianum binds the MoFe-protein at a site involving both subunits of the MoFe-protein . However, in A. vinelandii and A. chroococcum it was demonstrated that FeSII binds to the nitrogenase complex, but not to each individual subunit [23, 32, 36]. Apparently, the formation of a three-component nitrogenase complex (Fe-protein + MoFe-protein + FeSII) is essential for nitrogenase oxygen tolerance and suggests that FeSII interacts near the subunits interface of nitrogenase complex [32, 36]. Furthermore, in A. vinelandii, several site-directed mutants were constructed and tested for its FeSII capability of interaction with nitrogenase . Two of those (K14 and K15) lost ability of interaction. This experiment showed the importance of these two K residues for interaction. However, it was not shown if is due to direct contact or allosteric effect.
G. diazotrophicus Gdia0615-nitrogenase interaction was also analyzed. The surface electrostatic potential and structural shape of both were manually inspected. As observed in A. vinelandii proteins, there is a small negative pocket on the interface of Fe-protein and MoFe-protein. This region is completely complementary in shape and charge to the unique positive region of Gdia0615, corresponding to R13 and R14 neighborhood. Such suspicious analysis suggests these arginine residues are directly involved in the nitrogenase oxygen-stable three-component complex formation in G. diazotrophicus (Fig. 4).
FeSII and nitrogenase interacting residues
H-bond (side chain-side chain)
H-bond (side chain-backbone)
H-bond (backbone-side chain)
H-bond (side chain-side chain)
H-bond (side chain-backbone)
H-bond (side chain-side chain)
From the 1000 complexes generated, 49 are clustered in the same docking site and show a very similar conformational structure. They also represent the lowest energy complexes obtained and the best one is shown on figure 4 (Haddock score = -59.8 with standard deviation of 2.6). The complex structure presented energy values of: -763.5 +/- 41.8 (electrostatic contribution), -26.8 +/- 6.3 (van de Waals), 102.8 +/- 12.4 (desolvation energy) and 169.4 +/- 47.81 (restraints penalty energy). Analysis of these energetic components of FeSII-nitrogenase complex confirmed that interaction is mainly due to electrostatic potential. This result explains previous experimental data which shows that an increase in ionic strength disrupts the FeSII-nitrogenase complex [32, 36].
The nitrogenase conformational protection mechanism against oxygen is a bacterial strategy to avoid the enzyme degradation during a sudden increase in oxygen concentration. FeSII protein (Shethna protein) interacts with nitrogenase complex [19, 21]. The three-component complex keeps nitrogenase inactive but transiently protected from damage by oxygen . This oxygen-stable nitrogenase complex is formed only under conditions of low ionic strength in the presence of MgCl2, and requires all three components to be present in an oxidized state [32, 36].
A. vinelandii FeSII was target of a few studies regarding its function and regulation. This study contributed for the understanding of this mechanism with structural aspects. In contrast, G. diazotrophicus protein involved in nitrogenase conformational protection was not yet known. The results described herein present for the first time a putative FeSII protein for G. diazotrophicus. A detailed analysis of all predicted ORFs of complete genomic sequence revealed only one possible protein coding gene (Gdia0615) for the putative FeSII. Although Gdia0615 present low sequence similarity with A. vinelandii FeSII, all functional residues are well conserved. A comparative analysis of the 3D molecular models of Gdia0615 and FeSII support the hypothesis of Gdia0615 protective function. Both form a beta-grasp folding and present similar electrostatic properties. In addition, they are functional as symmetric homodimers that interact through a hydrophobic interface.
A. vinelandii FeSII docking with nitrogenase complex revealed a putative binding site near the Fe-protein/MoFe-protein interface, corroborating previous data on the three-component complex. This interaction is dependent of shape and charge complementarities. Two FeSII lysine residues (K14 and K15), as well as an histidine H55 participate actively on interaction. On the other hand, 3 glutamic acid residues of Fe-protein enclose a negative cavity for FeSII binding. In G. diazotrophicus we suggest that arginine residues R13 and R14, histidine H56 and adjacent regions compose the main region for Gdia0615 interaction with nitrogenase complex. In overall, this study provided the first molecular insights on structural properties of the conformational protection mechanism of nitrogenase against oxygen. Such study will certainly contribute to a better understanding of the biological nitrogen fixation process.
A. vinelandii FeSII (gi: 451865) and C. pasteurianum FeSII (gi: 119942) sequences are available. These sequences were used to scan the two public available complete genome sequences of G. diazotrophicus (gi: 162145846 and 209542188) for a putative FeSII protein. Both genome sequences present essentially the same genes. Therefore, most of the genes in one version have a matching in the other. Sequence similarity searches were performed using BLAST algorithms , for both aminoacids and nucleotides. Analysis of functional domains was performed in NCBI Conserved Domains (version 2.17; 31608 PSSMs; ) and Pfam databases (version 23.0; 10340 families; ). Protein secondary structure prediction based on position-specific scoring matrices was performed on PSI-PRED server .
The 3D molecular models of the FeSII (A. vinelandii), the putative FeSII, Fe-protein and MoFe-protein (G. diazotrophicus) were built by comparative modeling. The search for candidate template sequences was performed at the PDB database . Templates used for modeling were the Escherichia coli Fdx, (1I7H), the Rhodobacter capsulatus FdvI (1E9M) and A. vinelandii nitrogenase complex (1G20), respectively. Templates and target sequences were aligned using Promals3D  and manually optimized with the support of the DNATagger  by monitoring the alignment of cysteine residues and conservation of physicochemical properties of aligned residues. Molecular models were generated using the program Modeller (version 9.7; ), considering the presence of heteroatoms (2 [Fe-S] cluster) if suitable. Additionally, loop refinement of A. vinelandii FeSII loop region, comprising the residues 77 to 90 was performed. 100 candidate models were generated for each protein system and all of them were evaluated using stereochemical quality Ramachandran plots generated by Procheck (version 3.5.4; ) and energy values according to Modeller Dope-score  and Prosa (ProSa 2003; ). RMSD calculations, visualization and manipulation of molecular images were performed with Pymol (version 1.2; ).
Prediction of solvent accessible surface area (Naccess version 2.1.1; ) and evaluation of the electrostatic potential on the protein surface (APBS software package; ) were accounted to determine potential protein-protein binding sites. These results, together with literature information, were introduced as restraints to drive docking calculations with Haddock . The Haddock advanced guru interface was used in order to support the setting of active and passive residues. A list comprising the residues predicted by Naccess as directly involved in the interaction (active residues) and the surrounding residues within a radius of 6.5 angstrons around the active residues was defined. All additional parameters were used as default values. A set of probable complexes were generated and the results were analyzed through stereochemical, cluster-sizes and energy evaluations. A thousand structures were used for rigid body docking and 5 minimisation trials. Water was used as the solvent for the last iteration and 200 structures were selected for explicit solvent refinement. A 7.5 angstrons RMSD cutoff was set for clustering of at least 4 structures. A total of 200 structures were analyzed as final results from Haddock.
Molecular dynamics (MD) simulations, energy minimization and trajectory analyses were carried out with GROMACS 4.05 package , using GROMOS96 (G53a6) force field . Explicit SPC water molecules  were used in all simulations, in which a 14 Å layer of water molecules were added around the solute molecules, within a cubic water box, using periodic boundary conditions. Counter ions were inserted for system neutralization. LINCS  and SETTLE  were applied to constraint solute and solvent bond, respectively. Temperature was kept at 298 K by rescaling velocities with a stochastic term  and pressure at 1 atm using the Berendsen approach . Electrostatic interactions were corrected with PME method , using non-bonded cutoffs of 1.0 nm for Coulomb and 1.2 nm for van der Waals. MD integration time was 2 fs.
A 3-steps energy minimization protocol was used to avoid artifacts in atomic trajectories due to conversion of potential into kinetic energies: firstly, applying the steepest-descent algorithm: i. 5000 steps with solute heavy atom positions restrained to their initial positions using an harmonic constant of 1 kJ/mol.nm in each Cartesian direction, allowing free water and hydrogen movements; and ii. 5000 steps with all atoms free to move. Subsequently, the conjugated gradient algorithm was applied for further energy minimization until an energy gradient of 42 KJ/mol.nm. A preliminary MD (1 ns), with heavy atom positions restrained, was performed for achieving solvent equilibration and system heating until 298 K. In this step, the initial velocities were generated once for each simulation. Then we performed a 10 ns production MD.
We are grateful to Msc João LSG Vianez-Junior for contribution on data analysis and Dr. Paulo R Batista for contribution on analysis of data and critical reading of the manuscript. We thank FAPERJ, CNPq and CAPES for financial support.
The authors declare that they have no competing interests.
This article has been published as part of BMC Genomics Volume 11 Supplement 5, 2010: Proceedings of the 5th International Conference of the Brazilian Association for Bioinformatics and Computational Biology. The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2164/11?issue=S5.
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