Moderate Salt Conditions Research Articles

Impact of dark septate endophytes on salt stress alleviation of tomato plants.

Fungal endophytes can improve plant tolerance to abiotic stress conditions. Dark septate endophytes (DSEs) belong to phylogenetically non-related groups of root colonizing fungi among the Ascomycota with high melanin-producing activities. They can be isolated from roots of more than 600 plant species in diverse ecosystems. Still the knowledge about their interaction with host plants and their contribution to stress alleviation is limited. The current work aimed to test the abilities of three DSEs (Periconia macrospinosa, Cadophora sp., Leptodontidium sp.) to alleviate moderate and high salt stress in tomato plants. By including an albino mutant, the role of melanin for the interaction with plants and salt stress alleviation could also be tested. P. macrospinosa and Cadophora sp. improved shoot and root growth 6 weeks after inoculation under moderate and high salt stress conditions. No matter how much salt stress was applied, macroelement (P, N, and C) contents were unaffected by DSE inoculation. The four tested DSE strains successfully colonized the roots of tomato, but the colonization level was clearly reduced in the albino mutant of Leptodontidium sp. Any difference in the effects on plant growth between the Leptodontidium sp. wild type strain and the albino mutant could, however, not be observed. These results show that particular DSEs are able to increase salt tolerance as they promote plant growth specifically under stress condition. Increased plant biomasses combined with stable nutrient contents resulted in higher P uptake in shoots of inoculated plants at moderate and high salt conditions and higher N uptake in the absence of salt stress in all inoculated plants, in P. macrospinosa-inoculated plants at moderate salt condition and in all inoculated plants except the albino mutants at high salt condition. In summary, melanin in DSEs seems to be important for the colonization process, but does not influence growth, nutrient uptake or salt tolerance of plants.

Transcriptomic analysis revealed distinctive modulations of arbuscular mycorrhizal fungi inoculation in halophyte Suaeda salsa under moderate salt conditions

As the area of soil salinization increases, the ecological niche of halophytes is important given their high salt tolerance. The physiological response of mycorrhizal halophytes is not completely consistent with that of mycorrhizal glycophytes under salt conditions. However, less information is known about the regulation of genes included by arbuscular mycorrhizal (AM) fungi in halophytes. A greenhouse pot experiment with inoculation (Funneliformis mosseae) treatments was performed to research the physiological and transcriptomic responses in the halophyte Suaeda salsa under 100 mM NaCl. The results revealed that AM symbiosis significantly increased shoot biomass, shoot height and shoot Na+ accumulation. AM fungi decreased the Na+ concentration and soluble sugar concentration in the shoots of S. salsa. Transcriptomic analysis revealed 1316 and 424 differentially expressed genes (DEGs) in shoots and roots, respectively. DEGs in shoots were involved in carbohydrate and energy metabolism; photosynthesis; amino acid metabolism; cofactors and vitamins metabolism, such as glyoxylate and dicarboxylate metabolism; carbon fixation in photosynthetic organisms; and vitamin B6 metabolism. Interestingly, the expression of DEGs related to photosynthesis was downregulated by AM fungi in S. salsa under 100 mM NaCl. DEGs of roots were enriched in starch and sucrose metabolism; and auxin transmembrane transporters. These distinctive modulations of AM fungi in genes and physiological parameters are potentially associated with the growth of halophytes under moderate salt conditions. This study will improve our understanding of the effect of AM fungi in halophytes under moderate salt conditions and suggests that the phytoextractive strategy of halophytes combined with AM fungi hold significant ecological potential in salinized ecosystems.

Comprehensive transcriptome profiling of Caragana microphylla in response to salt condition using de novo assembly.

To investigate the response of Caragana microphylla in salt condition, transcriptome analysis, differentially expressed genes (DEGs) comparison with Arabidopsis thaliana, and the chlorophyll content analysis were performed. Gene Ontology (GO) term, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of DEGs indicated that salt condition affected photosynthesis and chlorophyll in C. microphylla. The DEGs compared with salt responsive genes of A. thaliana indicated that C. microphylla's responses to salt differed greatly from those of the model plant and that the results also indicated up-regulated genes related to photosynthesis and chlorophyll in C. microphylla. Moreover, we confirmed that salt-treated C. microphylla increased chlorophyll content, and the genes of protoporphyrin IX downstream in chlorophyll biosynthesis were induced in the heatmap analysis. These results showed a similar pattern to some halophytes plants with increased chlorophyll at a certain salt concentration, and we assumed that C. microphylla also has a mechanism to adapt or tolerate moderate salt conditions.

Pararhodobacter oceanensis sp. nov., isolated from marine intertidal sediment and emended description of the genus Pararhodobacter.

A Gram-stain-negative, rod-shaped, non-motile and facultatively anaerobic bacterium, designated AM505T, was isolated from Shuangdao Bay in Weihai, China. Cells of strain AM505T were 0.4-0.8 µm wide, 1.3-3.3 µm long, catalase-positive and oxidase-positive. Strain AM505T was tolerant to moderate salt conditions. Growth occurred at 4-40 °C (optimum, 28-33 °C), pH 6.5-9.5 (pH 7.5-8.0) and with 0.5-9.0 % NaCl (w/v; 2.0-4.0 %). A phylogenetic analysis of the 16S rRNA gene indicated that strain AM505T was a member of the genus Pararhodobacter within the family Rhodobacteraceae. The most closely related neighbour was Pararhodobacter aggregans DSM 18938T (97.6 %). The average nucleotide identity value between AM505T and P. aggregans DSM 18938T was 75.3 %. The major respiratory quinone of strain AM505T was ubiquinone-10 and the predominant cellular fatty acids (>10 %) were summed feature 8 (consisting of C18 : 1ω7c and/or C18 : 1ω6c), 11-methyl C18 : 1ω7c and C18 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified aminolipid. The genomic DNA G+C content was 63.0 mol%. Based on our polyphasic taxonomic study, strain AM505T should be a novel species in the genus Pararhodobacter, for which the name Pararhodobacteroceanensis sp. nov. is proposed. The type strain is AM505T (=KCTC 62407T=MCCC 1H00289T).

Aliifodinibius halophilus sp. nov., a moderately halophilic member of the genus Aliifodinibius, and proposal of Balneolaceae fam. nov.

A novel Gram-stain-negative, rod-shaped, facultatively anaerobic, oxidase-negative and catalase-positive bacterium, designated 2W32T, was isolated from a marine solar saltern on the coast of Weihai, Shandong Province, China. Strain 2W32T was tolerant to moderate salt conditions. Optimal growth occurred at 33-37 °C (range 20-45 °C) and pH 7.5-8.0 (range pH 7.0-8.5) with 6-10 % (w/v) NaCl (range 2-18 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 2W32T shared highest similarity with Aliifodinibius sediminis YIM J21T (94.6 %), Aliifodinibius roseus YIM D15T (94.4 %), Fodinibius salinus YIM C003T (93.6 %), Gracilimonas tropica CL-CB462T (88.6 %) and Balneola vulgaris 13IX/A01/164T (86.4 %) and less than 83.0 % similarity with other species of the phylum Bacteroidetes. The isolate and closely related species formed a novel family-level clade in the phylum Bacteroidetes. The polar lipid profile of the novel isolate consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminolipid, an unidentified glycolipid and an unidentified lipid. The dominant cellular fatty acids (>10 %) were iso-C15 : 0, iso-C17 : 1ω9c and summed feature 3 (C16:1ω7c and/or iso-C15 : 0 2-OH) and the sole respiratory quinone was menaquinone 7 (MK-7). The DNA G+C content of strain 2W32T was 47.5 mol %. Comparative analysis of 16S rRNA gene sequences and characterization indicated that strain 2W32T represents a novel species within the genus Aliifodinibius, for which the name Aliifodinibius halophilus sp. nov. is proposed. The type strain is 2W32T (=KCTC 42497T=CICC 23869T). In addition, a novel family, Balneolaceae fam. nov., is proposed to accommodate the genera Fodinibius, Aliifodinibius, Gracilimonas and Balneola.

Low-density crystal packing of human protein kinase CK2 catalytic subunit in complex with resorufin or other ligands: a tool to study the unique hinge-region plasticity of the enzyme without packing bias

A low-resolution structure of the catalytic subunit CK2α of human protein kinase CK2 (formerly known as casein kinase 2) in complex with the ATP-competitive inhibitor resorufin is presented. The structure supplements previous human CK2α structures in which the interdomain hinge/helix αD region adopts a closed conformation correlating to a canonically established catalytic spine as is typical for eukaryotic protein kinases. In the corresponding crystal packing the hinge/helix αD region is nearly unaffected by crystal contacts, so that largely unbiased conformational adaptions are possible. This is documented by published human CK2α structures with the same crystal packing but with an open hinge/helix αD region, one of which has been redetermined here with a higher symmetry. An overview of all published human CK2α crystal packings serves as the basis for a discussion of the factors that determine whether the open or the closed hinge/helix αD conformation is adopted. Lyotropic salts in crystallization support the closed conformation, in which the Phe121 side chain complements the hydrophobic catalytic spine ensemble. Consequently, genuine ligand effects on the hinge/helix αD conformation can be best studied under moderate salt conditions. Ligands that stabilize either the open or the closed conformation by hydrogen bonds are known, but a general rule is not yet apparent.

DNA Condensed by Protamine: A “Short” or “Long” Polycation Behavior

Using centrifugation assay and light scattering measurements, we study the condensation of DNA by the salmon protamine, a highly basic protein carrying 21 positive charges out of 30 amino acids, in the presence of a high amount of monovalent salt. The DNA condensation is followed by a macroscopic phase separation. It occurs while a large amount of polycations remains freely diffusing in the bulk. A similar behavior was described before for small multivalent ions in diluted DNA solution in a lower salt range. Sensitivity to the salt is however amplified when increasing the charge of polycations. Indeed, a high power-law dependence is observed here with an exponent 11. This variation agrees with the power-law dependence that characterizes the binding of small polycations to DNA. In other words, we show that protamines behave like small polycations in the diluted DNA-high salt regime, while they behave like other large polycations in the diluted DNA-low salt regime as shown in a previous study. In addition, instead of the classical view where binding of polycations to DNA is supposed to trigger DNA condensation in low and moderate salt conditions, we propose that, under high salt conditions, the potential presence of a DNA dense phase triggers the binding of protamines to DNA.

Dependence of RGS9–1 Membrane Attachment on Its C-terminal Tail

RGS9-1 is a GTPase-accelerating protein (GAP) required for rapid recovery of the light response in vertebrate rod and cone photoreceptors. Similar to its phototransduction partners transducin (G(t)) and cGMP phosphodiesterase, it is a peripheral protein of the disc membranes, but it binds membranes much more tightly. It lacks the lipid modifications found on G(t) and cGMP phosphodiesterase, and the mechanism for membrane attachment is unknown. We have used limited proteolysis to generate a fragment of RGS9-1 that is readily removed from membranes under moderate salt conditions. Immunoblots reveal that this soluble fragment lacks a 3-kDa fragment from the C-terminal domain, the only domain within RGS9-1 that differs in sequence from the brain-specific isoform RGS9-2. Recombinant fragments of RGS9-1 with or without the partner subunit G beta(5L) were constructed with or without the C-terminal domain. Those lacking the C-terminal domain bound to photoreceptor membranes much less tightly than those containing it. Removal by urea of G beta(5L) from endogenous or recombinant RGS9-1 bound to rod outer segment membranes left RGS9-1 tightly membrane-bound, and recombinant RGS9-1 was urea-soluble in the absence of membranes. Thus the C-terminal domain of RGS9-1 is critical for membrane binding, whereas G beta(5L) does not play an important role in membrane attachment.

Purine N7 groups that are crucial to the interaction of Escherichia coli rnase P RNA with tRNA.

We have detected by nucleotide analog interference mapping (NAIM) purine N7 functional groups in Escherichia coli RNase P RNA that are important for tRNA binding under moderate salt conditions (0.1 M Mg2+, 0.1 M NH4+). The majority of identified positions represent highly or universally conserved nucleotides. Our assay system allowed us, for the first time, to identify c7-deaza interference effects at two G residues (G292, G306). Several c7-deazaadenine interference effects (A62, A65, A136, A249, A334, A351) have also been identified in other studies performed at very different salt concentrations, either selecting for substrate binding in the presence of 0.025 M Ca2+ and 1 M NH4+ or self-cleavage of a ptRNA-RNase P RNA conjugate in the presence of 3 M NH4+ or Na+. This indicates that these N7 functional groups play a key role in the structural organization of ribozyme-substrate and -product complexes. We further observed that a c7-deaza modification at A76 of tRNA interferes with tRNA binding to and ptRNA processing by E. coli RNase P RNA. This finding combined with the strong c7-deaza interference at G292 of RNase P RNA supports a model in which substrate and product binding to E. coli RNase P RNA involves the formation of intermolecular base triples (A258-G292-C75 and G291-G259-A76).

DNA bending due to specific p53 and p53 core domain-DNA interactions visualized by electron microscopy

We have used transmission electron microscopy to analyze the specificity and the extent of DNA bending upon binding of full-length wild-type human tumor suppressor protein p53 (p53) and the p53 core domain (p53CD) encoding amino acid residues 94–312, to linear double-stranded DNA bearing the consensus sequence 5′-AGACATGCCTAGACATGCCT-3′ (p53CON). Both proteins interacted with high specificity and efficiency with the recognition sequence in the presence of 50 mM KCl at low temperature (∼4 °C) while the p53CD also exhibits a strong and specific interaction at physiological temperature. Specific complex formation did not result in an apparent reduction of the DNA contour length. The interaction of p53 and the p53CD with p53CON induced a noticeable salt-dependent bending of the DNA axis. According to quantitative analysis with folded Gaussian distributions, the bending induced by p53 varied from ∼40 ° to 48 ° upon decreasing of the KCl concentration from 50 mM to ∼1 mM in the mounting buffer used for adsorption of the complexes to the carbon film surface. The p53CD bent DNA by 35–37 ° for all salt concentrations used in the mounting buffer. The bending angle of the p53/DNA complex under low salt conditions showed a somewhat broader distribution (σ≈39 °) than at high salt concentration (σ≈31 °) or for p53CD (σ≈24–27 °). Together, these results demonstrate that the p53CD has a dominant role in complex formation and that the complexes formed both by p53 and p53CD under moderate salt conditions are similar. However, the dependence of the bending parameters on ambient conditions suggest that the segments flanking the p53CD contribute to complex formation as well. The problems associated with the analysis of bending angles in electron microscopy experiments are discussed.

Transcription-Mediated Binding of Peptide Nucleic Acid (PNA) to Double-Stranded DNA: Sequence-Specific Suicide Transcription

Peptide nucleic acid (PNA) forms sequence-specific (PNA)2/DNA triplexes with one strand of double-stranded DNA by strand invasion. When formed with the template strand of DNA such a (PNA)2/DNA triplex can arrest transcription elongation in vitro and can thus act as an anti-gene agent. One of the major obstacles to applying PNA as an anti-gene agent in vivo is that PNA strand invasion occurs at a very slow rate under moderate salt conditions. In the present study we show that transcription can increase the rate of sequence-specific PNA binding dramatically. Such transcription-mediated PNA binding occurs three times as efficiently when the PNA target is situated on the non- template strand as compared with the template strand. Since transcription can mediate template strand-associated (PNA)2/DNA complexes which arrest further elongation, the action of RNA polymerase results in repression of its own activity, i.e. suicide transcription. These findings are highly relevant for the possible future use of PNA as an anti-gene agent.

Purification of glutathionylspermidine and trypanothione synthetases from Crithidia fasciculata.

Two enzymes involved in the biosynthesis of the trypanosomatid-specific dithiol trypanothione-glutathionylspermidine (Gsp) synthetase and trypanothione (TSH) synthetase--have been identified and purified individually from Crithidia fasciculata. The Gsp synthetase has been purified 93-fold and the TSH synthetase 52-fold to apparent homogeneity from a single DEAE fraction that contained both activities. This constitutes the first indication that the enzymatic conversion of two glutathione molecules and one spermidine to the N1,N8-bis(glutathionyl)spermidine (TSH) occurs in two discrete enzymatic steps. Gsp synthetase, which has a kcat of 600/min, shows no detectable TSH synthetase activity, whereas TSH synthetase does not make any detectable Gsp and has a kcat of 75/min. The 90-kDa Gsp synthetase and 82-kDa TSH synthetase are separable on phenyl Superose and remain separated on gel filtration columns in high salt (0.8 M NaCl). Active complexes can be formed under low to moderate salt conditions (0.0-0.15 M NaCl), consistent with a functional complex in vivo.

Purification and partial characterization of a DNA polymerase alpha species from calf thymus.

We have purified a DNA polymerase alpha species from calf thymus to near homogeneity. The enzyme sediments at 5.7 S and contains two polypeptides of 123000 and 134000 daltons in about equimolar ratio. The enzyme is inhibited by aphidicolin and N-ethylmaleimide, and retains its activity in buffers containing moderate salt conditions. Activated DNA is a better substrate than poly-(dA) . (dT) 10.