Anastasia Venieraki

The Genetic Diversity of Culturable Nitrogen-Fixing Bacteria in the Rhizosphere of Wheat

A total of 17 culturable nitrogen-fixing bacterial strains associated with the roots of wheat growing in different regions of Greece were isolated and characterized for plant-growth-promoting traits such as auxin production and phosphate solubilization. The phylogenetic position of the isolates was first assessed by the analysis of the PCR-amplified 16S rRNA gene. The comparative sequence analysis and phylogenetic analysis based on 16S rRNA gene sequences show that the isolates recovered in this study are grouped with Azospirillum brasilense, Azospirillum zeae, and Pseudomonas stutzeri. The diazotrophic nature of all isolates was confirmed by amplification of partial nifH gene sequences. The phylogenetic tree based on nifH gene sequences is consistent with 16S rRNA gene phylogeny. The isolates belonging to Azospirillum species were further characterized by examining the partial dnaK gene phylogenetic tree. Furthermore, it was demonstrated that the ipdC gene was present in all Azospirillum isolates, suggesting that auxin is mainly synthesized via the indole-3-pyruvate pathway. Although members of P. stutzeri and A. zeae are known diazotrophic bacteria, to the best of our knowledge, this is the first report of isolation and characterization of strains belonging to these bacterial genera associated with wheat.

Biochemical and molecular characterization of an Azotobacter vinelandii strain with respect to its ability to grow and fix nitrogen in olive mill wastewater

Abstract The bacterial strain A belongs to a collection of nitrogen fixing bacteria isolated from soil treated with olive mill wastewater (OMW). This strain can grow in OMW showing significant nitrogen fixing capacity. The study of growth and nitrogenase activity of the above strain during its growth into the waste showed that the maximum value of total acetylene reduction activity (expressed in nmol Ethyl/24 h/ml of culture) was obtained after 24 h of incubation as well as the maximum value of bacterial population. When the above nitrogen fixing capacity was expressed in reference to the bacterial population (nmol Ethyl/24 h/μg bacterial protein) its maximum value was observed earlier, since the first 7 h of incubation. Western blot analysis of total bacterial proteins, extracted at specific time intervals showed that nitrogenase activity was induced 30 mins after the inoculation of the waste with the strain A . The respective time of the enzymes induction in chemical media (N-free) was 1 h. Southern blot analysis of total genomic DNA of strain A using as probes the three structural genes (nifH, nifD, nifK) encoding nitrogenase-1 in Azotobacter vinelandii gave hybridization patterns which are conserved between the above two bacteria. These results strongly support parallel biochemical taxonomy data indicating that strain A may belong to Azotobacter vinelandii species.

Characterization of nitrogen-fixing bacteria isolated from field-grown barley, oat, and wheat

Diazotrophic bacteria were isolated from the rhizosphere of field-grown Triticum aestivum, Hordeum vulgare, and Avena sativa grown in various regions of Greece. One isolate, with the highest nitrogen-fixation ability from each of the eleven rhizospheres, was selected for further characterisation. Diazotrophic strains were assessed for plant-growth-promoting traits such as indoleacetic acid production and phosphate solubilisation. The phylogenies of 16S rRNA gene of the selected isolates were compared with those based on dnaK and nifH genes. The constructed trees indicated that the isolates were members of the species Azospirillum brasilense, Azospirillum zeae, and Pseudomonas stutzeri. Furthermore, the ipdC gene was detected in all A. brasilence and one A. zeae isolates. The work presented here provides the first molecular genetic evidence for the presence of culturable nitrogen-fixing P. stutzeri and A. zeae associated with field-grown A. sativa and H. vulgare in Greece.

Gene Expression and Biochemical Characterization of Azotobacter vinelandii Cyclophilins and Protein Interaction Studies of the Cytoplasmic Isoform with dnaK and lpxH

The soil nitrogen-fixing bacterium Azotobacter vinelandii possesses two cyclophilins, comprising putative cytoplasmic and periplasmic isoforms, designated as AvPPIB and AvPPIA, respectively. Both recombinant cyclophilins have been purified and their peptidyl-prolyl cis/trans isomerase activity against Suc-Ala-Xaa-Pro-Phe-pNA synthetic peptides has been characterized. The substrate specificity of both cyclophilins is typical for bacterial cyclophilins, with Suc-Ala-Ala-Pro-Phe-pNA being the most rapidly catalyzed substrate. The cytoplasmic cyclophilin also displays a chaperone function in the citrate synthase thermal aggregation assay. Using real-time quantitative RT-PCR, we demonstrate that AvppiB is expressed under various physiological and growth conditions, mainly upregulated by acetate and downregulated by the stationary growth state, while AvppiA shows a tendency for downregulation under the tested conditions. Further, we identified chaperone protein dnaK and UDP-2, 3-diacylglucosamine hydrolase lpxH as probable interacting partners of AvPPIB and we demonstrate their physical interaction by coexpression studies. An increase in AvPPIB PPIase activity in the presence of AvdnaK and a decrease in the presence of AvlpxH further confirms each interaction. However, the PPIase activity does not seem to be essential for those interactions since AvPPIB active site mutants still interact with dnaK and lpxH, while their minor PPIase activity cannot be modulated by the interaction.

Cloning, characterization and transcriptional analysis of two phosphate acetyltransferase isoforms from Azotobacter vinelandii

Acetate is abundant in soil contributing to a great extent on carbon cycling in nature. Phosphate acetyltransferase (Pta, EC 2.3.1.8) catalyzes the reversible transfer of the acetyl group from acetyl-P to CoA forming acetyl-CoA and inorganic phosphate, participating to acetate assimilation/dissimilation reactions. In the present study, we demonstrate that Azotobacter vinelandii, a nitrogen-fixing, free-living, soil bacterium, possesses two class II phosphate acetyltransferase isoforms, AvPTA-1 and AvPTA-2, with different kinetic properties. At the acetyl-CoA forming direction, AvPTA-1 has lower affinity for acetyl-P and higher affinity for CoA than AvPTA-2 while at the acetyl-P forming direction; activity was measured only for AvPTA-1. Quantification of their expression patterns by RT-qPCR indicated that both genes are expressed during exponential growth on glucose or acetate and are down-regulated in the stationary phase. The ammonium availability during acetate growth resulted in up-regulation of Avpta-2 expression only. Further, the gene expression patterns of other related gene transcripts were also investigated, in order to understand the influence of each pathway in the assimilation/dissimilation of acetate.

Cyclophilin PpiB is involved in motility and biofilm formation via its functional association with certain proteins.

PpiB belongs to the superfamily of peptidyl‐prolyl cis/trans isomerases (PPIases, EC: 5.2.1.8), which catalyze the rate‐limiting protein folding step at peptidyl‐prolyl bonds and control several biological processes. In this study, we show that PpiB acts as a negative effector of motility and biofilm formation ability of Escherichia coli. We identify multicopy suppressors of each ΔppiB phenotype among putative PpiB prey proteins which upon deletion are often characterized by analogous phenotypes. Many putative preys show similar gene expression in wild‐type and ΔppiB genetic backgrounds implying possible post‐translational modifications by PpiB. We further conducted in vivo and in vitro interaction screens to determine which of them represent true preys. For DnaK, acetyl‐CoA carboxylase, biotin carboxylase subunit (AccC) and phosphate acetyltransferase (Pta) we also showed a direct role of PpiB in the functional control of these proteins because it increased the measured enzyme activity of each protein and further interfered with DnaK localization and the correct folding of AccC. Taken together, these results indicate that PpiB is involved in diverse regulatory mechanisms to negatively modulate motility and biofilm formation via its functional association with certain protein substrates.

The Nitrogen-Fixation Island Insertion Site Is Conserved in Diazotrophic Pseudomonas stutzeri and Pseudomonas sp. Isolated from Distal and Close Geographical Regions

The presence of nitrogen fixers within the genus Pseudomonas has been established and so far most isolated strains are phylogenetically affiliated to Pseudomonas stutzeri. A gene ortholog neighborhood analysis of the nitrogen fixation island (NFI) in four diazotrophic P. stutzeri strains and Pseudomonas azotifigens revealed that all are flanked by genes coding for cobalamin synthase (cobS) and glutathione peroxidise (gshP). The putative NFIs lack all the features characterizing a mobilizable genomic island. Nevertheless, bioinformatic analysis P. stutzeri DSM 4166 NFI demonstrated the presence of short inverted and/or direct repeats within both flanking regions. The other P. stutzeri strains carry only one set of repeats. The genetic diversity of eleven diazotrophic Pseudomonas isolates was also investigated. Multilocus sequence typing grouped nine isolates along with P. stutzeri and two isolates are grouped in a separate clade. A Rep-PCR fingerprinting analysis grouped the eleven isolates into four distinct genotypes. We also provided evidence that the putative NFI in our diazotrophic Pseudomonas isolates is flanked by cobS and gshP genes. Furthermore, we demonstrated that the putative NFI of Pseudomonas sp. Gr65 is flanked by inverted repeats identical to those found in P. stutzeri DSM 4166 and while the other P. stutzeri isolates harbor the repeats located in the intergenic region between cobS and glutaredoxin genes as in the case of P. stutzeri A1501. Taken together these data suggest that all putative NFIs of diazotrophic Pseudomonas isolates are anchored in an intergenic region between cobS and gshP genes and their flanking regions are designated by distinct repeats patterns. Moreover, the presence of almost identical NFIs in diazotrophic Pseudomonas strains isolated from distal geographical locations around the world suggested that this horizontal gene transfer event may have taken place early in the evolution.

Nodulin PvNOD33, a putative phosphatase whose expression is induced during Phaseolus vulgaris nodule development ☆

We have isolated a full-length cDNA clone, designated as Pvnod33, that is highly expressed during the later stages of Phaseolus vulgaris nodule development. Pvnod33 mRNA encodes a deduced polypeptide of 263 amino acids, showing similarity to a number of putative plant phosphatases-hydrolases. This hypothesis is strengthened by the presence of a conserved motif found in several bacterial and yeast phosphatases. Using reverse-transcription-polymerase chain reaction (RT-PCR) analysis, we detected that Pvnod33 gene transcripts accumulate at high levels in mature nodules of P. vulgaris, 3 weeks after infection with rhizobia. Pvnod33 is also expressed, albeit at low levels, in nonsymbiotic tissues, including roots, flowers, seedpods, leaves and stems. In situ hybridization indicated that Pvnod33 mRNA is highly abundant in infected cells of nodules 21 d post-infection, in the nodule inner cortex, as well as in the vascular bundle of the adjacent root. Detectable levels of Pvnod33 transcripts were also observed in the xylem and phloem sclerenchymatic cells of other common bean tissues, including uninfected roots, lateral roots and stems. Taking together all these data, we propose that PvNOD33 protein may belong to a novel class of phosphatases widespread in the plant kingdom, possibly involved in carbon metabolism.

Structural and functional analysis of cyclophilin PpiB mutants supports an in vivo function not limited to prolyl isomerization activity

Escherichia coli cyclophilin PpiB is a peptidyl‐prolyl cis/trans isomerase (PPIase, EC: 5.2.1.8), involved in the negative modulation of various bacterial processes, such as swimming and swarming motility and biofilm formation ability. In this study, we show that PpiB possesses also a chaperone function as it can prevent the thermal denaturation of citrate synthase even with essentially eliminated PPIase activity. We demonstrate, using active site mutations, that the PPIase activity of PpiB is required in all processes, except for the negative effect on swimming, indicating a possible isomerase‐independent function. Additionally, we show that the reduced PPIase activity of PpiB does not prevent the association with all prey proteins tested and that the PPIase active site is not involved necessarily in each association. We also used a random mutagenesis approach, to identify amino acid residues apart from the catalytic site, which are necessary for PpiB function. The combination of enzymatic studies concerning the PPIase and chaperone activities of each mutant protein, with structural analyses based on 3D models, provided further insights into the effects of the mutations on the function of PpiB and showed the importance of structural features in addition to the catalytic site, for its in vivo role.

Functional interaction of Azotobacter vinelandii cytoplasmic cyclophilin with the biotin carboxylase subunit of acetyl-CoA carboxylase.

Cyclophilins (E.C. 5.1.2.8) are protein chaperones with peptidyl-prolyl cis/trans isomerase activity (PPIase). In the present study, we demonstrate a physical interaction among AvppiB, encoding the cytoplasmic cyclophilin from the soil nitrogen-fixing bacterium Azotobacter vinelandii, and AvaccC, encoding the biotin carboxylase subunit of acetyl-CoA carboxylase, which catalyzes the committed step in long-chain fatty acid synthesis. A decrease in AvppiB PPIase activity, in the presence of AvaccC, further confirms the interaction. However, PPIase activity seems not to be essential for these interactions since a PPIase active site mutant of cyclophilin does not abolish the AvaccC binding. We further show that the presence of cyclophilin largely influences the measured ATP hydrolyzing activity of AvaccA in a way that is negatively regulated by the PPIase activity. Taken together, our data support a novel role for cyclophilin in regulating biotin carboxylase activity.