Structural basis for cytokinin receptor signaling: an evolutionary approach

Cytokinins are ubiquitous plant hormones; their signal is perceived by sensor histidine kinases—cytokinin receptors. This review focuses on recent advances on cytokinin receptor structure, in particular sensing module and adjacent domains which play an important role in hormone recognition, signal transduction and receptor subcellular localization. Principles of cytokinin binding site organization and point mutations affecting signaling are discussed. To date, more than 100 putative cytokinin receptor genes from different plant species were revealed due to the total genome sequencing. This allowed us to employ an evolutionary and bioinformatics approaches to clarify some new aspects of receptor structure and function. Non-transmembrane areas adjacent to the ligand-binding CHASE domain were characterized in detail and new conserved protein motifs were recovered. Putative mechanisms for cytokinin-triggered receptor activation were suggested.     

Putative silicon transport vesicles in the cytoplasm of the diatom Synedra acus during surge uptake of silicon

We studied the growth of the araphid pennate diatom Synedra acus subsp. radians (Kützing) Skabichevskii using a fluorescent dye N ¹,N ³-dimethyl-N ¹-(7-nitro-2,1,3-benzoxadiazol-4-yl)propane-1,3-diamine (NBD-N2), which stains growing siliceous frustules but does not stain other subcellular organelles. We used a clonal culture of S. acus that was synchronized by silicon starvation. Epifluorescence microscopy was performed in two different ways with cells stained by the addition of silicic acid and the dye. Individual cells immobilized on glass were observed during the first 15–20 min following the replenishment of silicic acid after silicon starvation. Alternatively, we examined cells of a batch culture at time intervals during 36 h after the replenishment of silicic acid using fluorescence and confocal microscopy. The addition of silicic acid and NBD-N2 resulted in the rapid (1–2 min) formation of several dozen green fluorescent submicrometer particles (GFSPs) in the cytoplasm, which was accompanied by the accumulation of fluorescent silica inside silica deposition vesicles (SDVs) along their full length. In 5–15 min, GFSPs disappeared from the cytoplasm. Mature siliceous valves were formed within the SDVs during the subsequent 14–16 h. In the next 8–10 h, GFSPs appeared again in the cytoplasm of daughter cells. The data obtained confirm observations about the two-stage mechanism of silicon assimilation, which includes rapid silicon uptake (surge uptake) followed by slow silica deposition. It is likely that the observed GFSPs are silicon transport vesicles, which were first proposed by Schmid and Schulz in (Protoplasma 100:267–288, 1979).     

The antioxidant enzymes activity in leaves of inter-varietal substitution lines of wheat (Triticum aestivum L.) with different tolerance to soil water deficit

Understanding of the genetic basis of physiological properties, which are most relevant to water-deficit tolerance would be helpful for genomic-assisted improvement of bread wheat. A set of bread wheat inter-varietal single chromosome substitution lines (ISCSLs) of variety ‘Janetzkis Probat’ (JP) in the genetic background of ‘Saratovskaya’ 29 (S29) were used to reveal the critical chromosomes in wheat genome controlling tolerance to water deficit. The same lines were involved in the identification of chromosomes associated with the activity of antioxidant enzymes that are closely related to the detoxification of H₂O₂ [catalase (CAT), ascorbate peroxidase, dehydroascorbate reductase and glutathione reductase (GR)]. The recipient cultivar S29 was highly drought tolerant while the donor JP was sensitive. Using non-metric multidimensional scaling of yield components and indices of drought tolerance/susceptibility chromosomes 2A and 4D, substitution in the genetic background of S29 was found to lead to a critical decrease of water-deficit tolerance. The drop of tolerance correlated with a sharp decline of cumulative activity of the catalase and the enzymes of ascorbate–glutathione cycle in wheat leaves. Clear evidence was obtained for the involvement of genes present on the homoeologous group 2 chromosomes in the control of GR and CAT activity. Substitution of the chromosome 4D had a significant reducing impact on the CAT activity level.     

Authigenic mineralization and detrital clay binding by freshwater biofilms: The Brahmani river,India

This study sought to understand the origin and fate of one of the bitumen mounds found on the bottom of Lake Baikal. These mounds are located at a depth of 900 m beneath oil spots detected on the surface of Lake Baikal (53° 18′24^″, 108° 23′20^″). The two mounds were sampled with a manipulator from a “MIR” deep-water manned submersible. Mature mound No. 8 was subjected to chemical and microbiological studies. Mound No. 3 was subjected only to chemical studies; we failed to perform microbiological analyses of this mound for logistic reasons. Oil spots collected from the water surface, samples of mound No. 3 and No. 8, were subjected to GC/MS analysis. The water contained aliphatic hydrocarbons with chains between C₈ and C₂₃, with the most abundant chain length being C₁₈. Mound No. 3 with the most abundant chain length being C₁₈ actively released oil droplets into the water. It contained 770 mg/g of C₁₃-C₃₂ n-alkanes, with a maximum at C₂₃ (160 mg/g). Mound No. 8 was inactive and contained 148 mg/g of aliphatic C₂₂-C₃₄ n-alkanes, with a maximum at C₂₅. Mound No. 8 also consisted of 3% inorganic matter, 48% unresolved complex mixture (UCM) and less than 1% other compounds (polyaromatic hydrocarbons, isoprenoids, carotenoids, and hopanes). The core of this sample used as inoculate, yielded Rhodococci when cultivated on oil as the only source of carbon. Cultivation of the sample on agar-containing Raymond inorganic medium with crude West Siberian oil as the only source of carbon revealed colonies of these bacteria, which all appeared identical. PCR was performed with DNA isolated from 5 colonies, using primers for 16S rRNA genes. Comparison of the sequences of the 5 PCR products over a length of 714 bp revealed that they were almost identical. Phylogenetic analysis of these homologous sequences showed that they were similar to the corresponding sequences of the genus Rhodococcus. Substrate demands, the morphology of the colonies, and SEM and TEM data confirmed that the isolates obtained could indeed be Rhodococci. All of the isolates could grow in bulk cultures with inorganic medium supplemented with crude oil. Moreover, all of the isolates degraded aliphatic hydrocarbons with lengths between C₁₁ and C₂₉. C₂₃-C₂₉ hydrocarbons were degraded completely. The isolates could grow at 4–37°C. The most unexpected finding was that of the many microorganisms capable of consuming oil, only Rhodococci exhibited this ability in the inactive bitumen mound. The possible mechanisms of how crude oil is transformed into bitumen mounds and mature bitumen are discussed.     

Abiotic Photophosphorylation Model Based on Abiogenic Flavin and Pteridine Pigments

A model for abiotic photophosphorylation of adenosine diphosphate by orthophosphate with the formation of adenosine triphosphate was studied. The model was based on the photochemical activity of the abiogenic conjugates of pigments with the polymeric material formed after thermolysis of amino acid mixtures. The pigments formed showed different fluorescence parameters depending on the composition of the mixture of amino acid precursors. Thermolysis of the mixture of glutamic acid, glycine, and lysine (8:3:1) resulted in a predominant formation of a pigment fraction which had the fluorescence maximum at 525 nm and the excitation band maxima at 260, 375, and 450 nm and was identified as flavin. When glycine in the initial mixture was replaced with alanine, a product formed whose fluorescence parameters were typical to pteridines (excitation maximum at 350 nm, emission maximum at 440 nm). When irradiated with the quasi-monochromatic light (over the range 325–525 nm), microspheres in which flavin pigments were prevailing showed a maximum photophosphorylating activity at 375 and 450 nm, and pteridine-containing chromoproteinoid microspheres were most active at 350 nm. The positions and the relative height of maxima in the action spectra correlate with those in the excitation spectra of the pigments, which point to the involvement of abiogenic flavins and pteridines in photophosphorylation.     

Folsomia of China I – fimetaria group (Collembola: Isotomidae)

An annotated list of the species of Folsomia fimetaria group recorded in China is given. The new diagnostics of Folsomia candida sensu lato and sensu stricto are proposed basing on European and Asiatic material. Folsomia postsensilis n. sp. is described from Ningxia and Qinghai Provinces. It is characterized by the combination of posterior position of medial sensilla on abdomen, presence of ocelli and short furca.     

Molecular Characterization and Evolution of Self-Incompatibility Genes in Arabidopsis thaliana: The Case of the Sc Haplotype

The switch from an outcrossing mode of mating enforced by self-incompatibility to self-fertility in the Arabidopsis thaliana lineage was associated with mutations that inactivated one or both of the two genes that comprise the self-incompatibility (SI) specificity-determining S-locus haplotype, the S-locus receptor kinase (SRK) and the S-locus cysteine-rich (SCR) genes, as well as unlinked modifier loci required for SI. All analyzed A. thaliana S-locus haplotypes belong to the SA, SB, or SC haplotypic groups. Of these three, the SC haplotype is the least well characterized. Its SRKC gene can encode a complete open-reading frame, although no functional data are available, while its SCRC sequences have not been isolated. As a result, it is not known what mutations were associated with inactivation of this haplotype. Here, we report on our analysis of the Lz-0 accession and the characterization of its highly rearranged SC haplotype. We describe the isolation of its SCRC gene as well as the subsequent isolation of SCRC sequences from other SC-containing accessions and from the A. lyrata S36 haplotype, which is the functional equivalent of the A. thaliana SC haplotype. By performing transformation experiments using chimeric SRK and SCR genes constructed with SC- and S36-derived sequences, we show that the SRKC and SCRC genes of Lz-0 and at least a few other SC-containing accessions are nonfunctional, despite SCRC encoding a functional full-length protein. We identify the probable mutations that caused the inactivation of these genes and discuss our results in the context of mechanisms of S-locus inactivation in A. thaliana.     

Holarctic genetic structure and range dynamics in the woolly mammoth

Ancient DNA analyses have provided enhanced resolution of population histories in many Pleistocene taxa. However, most studies are spatially restricted, making inference of species-level biogeographic histories difficult. Here, we analyse mitochondrial DNA (mtDNA) variation in the woolly mammoth from across its Holarctic range to reconstruct its history over the last 200 thousand years (kyr). We identify a previously undocumented major mtDNA lineage in Europe, which was replaced by another major mtDNA lineage 32–34 kyr before present (BP). Coalescent simulations provide support for demographic expansions at approximately 121 kyr BP, suggesting that the previous interglacial was an important driver for demography and intraspecific genetic divergence. Furthermore, our results suggest an expansion into Eurasia from America around 66 kyr BP, coinciding with the first exposure of the Bering Land Bridge during the Late Pleistocene. Bayesian inference indicates Late Pleistocene demographic stability until 20–15 kyr BP, when a severe population size decline occurred.