The Arabidopsis Kinome: phylogeny and evolutionary insights into functional diversification

Background

Protein kinases constitute a particularly large protein family in Arabidopsis with important functions in cellular signal transduction networks. At the same time Arabidopsis is a model plant with high frequencies of gene duplications. Here, we have conducted a systematic analysis of the Arabidopsis kinase complement, the kinome, with particular focus on gene duplication events. We matched Arabidopsis proteins to a Hidden-Markov Model of eukaryotic kinases and computed a phylogeny of 942 Arabidopsis protein kinase domains and mapped their origin by gene duplication.

Results

The phylogeny showed two major clades of receptor kinases and soluble kinases, each of which was divided into functional subclades. Based on this phylogeny, association of yet uncharacterized kinases to families was possible which extended functional annotation of unknowns. Classification of gene duplications within these protein kinases revealed that representatives of cytosolic subfamilies showed a tendency to maintain segmentally duplicated genes, while some subfamilies of the receptor kinases were enriched for tandem duplicates. Although functional diversification is observed throughout most subfamilies, some instances of functional conservation among genes transposed from the same ancestor were observed. In general, a significant enrichment of essential genes was found among genes encoding for protein kinases.

Conclusions

The inferred phylogeny allowed classification and annotation of yet uncharacterized kinases. The prediction and analysis of syntenic blocks and duplication events within gene families of interest can be used to link functional biology to insights from an evolutionary viewpoint. The approach undertaken here can be applied to any gene family in any organism with an annotated genome.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-548) contains supplementary material, which is available to authorized users.     

Linear Amplification Mediated PCR – Localization of Genetic Elements and Characterization of Unknown Flanking DNA

Linear-amplification mediated PCR (LAM-PCR) has been developed to study hematopoiesis in gene corrected cells of patients treated by gene therapy with integrating vector systems. Due to the stable integration of retroviral vectors, integration sites can be used to study the clonal fate of individual cells and their progeny. LAM- PCR for the first time provided evidence that leukemia in gene therapy treated patients originated from provirus induced overexpression of a neighboring proto-oncogene. The high sensitivity and specificity of LAM-PCR compared to existing methods like inverse PCR and ligation mediated (LM)-PCR is achieved by an initial preamplification step (linear PCR of 100 cycles) using biotinylated vector specific primers which allow subsequent reaction steps to be carried out on solid phase (magnetic beads). LAM-PCR is currently the most sensitive method available to identify unknown DNA which is located in the proximity of known DNA. Recently, a variant of LAM-PCR has been developed that circumvents restriction digest thus abrogating retrieval bias of integration sites and enables a comprehensive analysis of provirus locations in host genomes. The following protocol explains step-by-step the amplification of both 3’- and 5’- sequences adjacent to the integrated lentiviral vector.     

Isospora suis in an Epithelial Cell Culture System – An In Vitro Model for Sexual Development in Coccidia

Coccidian parasites are of major importance in animal production, public health and food safety. The most frequently used representative in basic research on this group is Toxoplasma gondii. Although this parasite is well investigated there is no adequate in vitro model for its sexual development available and knowledge on this important life cycle phase is therefore scarce. The use of Isospora suis , a sister taxon to T. gondii and the causative agent of piglet coccidiosis, could provide a solution for this. In the present study an in vitro model for neonatal porcine coccidiosis in cells representative for the in vivo situation in the piglet gut was developed and evaluated. The parasite development was investigated by light and transmission electron microscopy and optimum culture conditions were evaluated. Intestinal porcine epithelial cells (IPEC-J2) adequately representing the natural host cells supported the development of all endogenous life cycle stages of I . suis , including gametocytes and oocysts. A concentration of 5% fetal calf serum in the culture medium led to highest gametocyte densities on day 12 post infection. Low infection doses (≤1 sporozoite for 100 host cells) were best for oocyst and gametocyte development. The presented system can also be used for immunostaining with established antibodies developed against T. gondii (in our case, anti-TgIMC3 antibodies directed against the inner membrane complex 3). The complete life cycle of I . suis in a cell line representing the natural host cell type and species provides a unique model among coccidian parasites and can be used to address a wide range of topics, especially with regard to the sexual development of coccidia.     

The Role of the Epidermis in the Control of Elongation Growth in Stems and Coleoptiles

The peripheral cell wall(s) of stems and coleoptiles are 6 to 20 times thicker than the walls of the inner tissues. In coleoptiles, the outer wall of the outer epidermis shows a multilayered, helicoidal cellulose architecture, whereas the walls of the parenchyma and the outer wall of the inner epidermis are unilayered. In hypocotyls and epicotyls both the epidermal and some subepidermal walls are multilayered, helicoidal structures. The walls of the internal tissues (inner cortex, pith) are unilayered, with cellulose microfibrils oriented primarily transversely. Peeled inner tissues rapidly extend in water, whereas the outer cell layer(s) contract on isolation. This indicates that the peripheral walls limit elongation of the intact organ. Experiments with the pressure microprobe indicate that the entire organ can be viewed as a giant, turgid cell: the extensible inner tissues exert a pressure (turgor) on the peripheral wall(s), which bear the longitudinal wall stress of the epidermal and internal cells. Numerous studies have shown that auxin induces elongation of isolated, intact sections by loosening of the growth-limiting peripheral cell wall(s). Likewise, the effect of light on reduction of stem elongation and cell wall extensibility in etiolated seedlings is restricted to the peripheral cell layers of the organ. The extensible inner tissues provide the driving force (turgor pressure), whereas the rigid peripheral wall(s) limit, and hence control, the rate of organ elongation.     

Systems biology of eukaryotic superorganisms and the holobiont concept

The founders of modern biology (Jean Lamarck, Charles Darwin, August Weismann etc.) were organismic life scientists who attempted to understand the morphology and evolution of living beings as a whole (i.e., the phenotype). However, with the emergence of the study of animal and plant physiology in the nineteenth century, this “holistic view” of the living world changed and was ultimately replaced by a reductionistic perspective. Here, I summarize the history of systems biology, i.e., the modern approach to understand living beings as integrative organisms, from genotype to phenotype. It is documented that the physiologists Claude Bernard and Julius Sachs, who studied humans and plants, respectively, were early pioneers of this discipline, which was formally founded 50 years ago. In 1968, two influential monographs, authored by Ludwig von Bertalanffy and Mihajlo D. Mesarovi?, were published, wherein a “systems theory of biology” was outlined. Definitions of systems biology are presented with reference to metabolic or cell signaling networks, analyzed via genomics, proteomics, and other methods, combined with computer simulations/mathematical modeling. Then, key insights of this discipline with respect to epiphytic microbes (Methylobacterium sp.) and simple bacteria (Mycoplasma sp.) are described. The principles of homeostasis, molecular systems energetics, gnotobiology, and holobionts (i.e., complexities of host–microbiota interactions) are outlined, and the significance of systems biology for evolutionary theories is addressed. Based on the microbe—Homo sapiens—symbiosis, it is concluded that human biology and health should be interpreted in light of a view of the biomedical sciences that is based on the holobiont concept.     

Cessation of cell elongation in rye coleoptiles is accompanied by a loss of cell-wall plasticity

The mechanism by which endogenous cessation of coleoptile elongationafter emergence of the primary leaf is brought about was investigatedin rye seedlings (Secale cereale L.) that were either grownin darkness or irradiated with continuous white light. In 3-d-oldetiolated (growing) coleoptiles a turgor pressure of 0.59 MPawas measured. In 6-d-old coleoptiles, which had ceased to elongate,cell turgor was 0.51 MPa and thus only 13% lower than in therapidly growing organ. Hence, the driving force for growth (turgor)is largely maintained. Cell-wall plasticity (E_pl) and elasticity(E_Ql were determined with a constant load extensiometer bothin vivo (turgid coleoptile segments) and in vitro (frozen-thawedsamples). Cessation of coleoptile elongation was correlatedwith a 95% reduction in E_pl9 whereas E_Ql was only slightly affected.Extension kinetics were measured with living and frozen-thawedsegments cut from growing and non-growing coleoptiles. The correspondingstress-strain (load-extension) curves indicate that the cellwall of the growing coleoptile behaves like an elastic-plasticmaterial whereas that of the non-growing organ shows the behaviourof an elastic solid. These data demonstate that E_pl representsa true plastic (irreversible) deformation of the cell wall.It is concluded that cessation of coleoptile growth after emergenceof the primary leaf is attributable to a loss of cell-wall plasticity.Hence, a mechanical stiffening of the cell wall and not a lossof turgor pressure may be responsible for the deceleration ofcell elongation in the rye coleoptile. Key words: Extension growth, rye coleoptile, cell-wall extensibility, turgor pressure     

Effect of white light on meristematic activity in developing sunflower hypocotyls

Summary To determine whether hypocotyl elongation in sunflower seedlings (Helianthus annuus L.) is dependent on cell divisions (meristematic activity), we used a specific inhibitor of DNA synthesis (fluorodeoxyuridine). The seedlings were either grown for 6 days in darkness or continuous white light (WL). Under both conditions hypocotyl growth was retarded by 30–70% in the presence of the inhibitor. Because the nuclei do not become endopolyploid we conclude that hypocotyl growth is dependent on cell reproduction. In the next step an immunocytochemical method was used to detect the percentage of nuclei in S-phase (meristematic activity) in different regions and tissues of the hypocotyls. In the peripheral cell layers (epidermis, cortex) meristematic activity was much greater than in the pith of the organ. In rapidly growing (etiolated) hypocotyls meristematic activity is largely restricted to the closed apical hook of the stem. After transfer to WL the hook opens and hypocotyl elongation is inhibited. In the epidermis and cortex of the apical hook a large WL-induced enhancement in the percentage of nuclei in S-phase occurred, which was followed by a light-mediated retardation of meristematic activity. Our data show that WL exerts a transient stimulatory effect on meristematic activity during photomorphogenesis of the sunflower seedling.Abbreviations BrdUrd 5-bromo-2-deoxyuridine - D darkness - FdUrd 5-fluoro-2-deoxyuridine - TRITC tetramethyl-rhodamine-isothiocyanate - WL white light     

Two models for screening chelating agents for cadmium removal

The effectiveness of some chelating agents to mobilize cadmium from Chinese hamster ovary cells after chronic exposure (20 hr), as well as from cytosolic metallothionein, was studied. In the first protocol, the most effective substance was 2,3-dimercaptopropanol, followed by 2,3-dimercaptopropane-1-sulfonate and 2,3-dimercaptosuccinic acid, whereas CaNa₃3-diethylenetriamine pentaacetic acid × 5H₂O showed less effect. Simultaneous incubation of cells with cadmium and the chelating agent resulted in a different order of effectiveness: CaNa₃ DTPA prevented cadmium uptake almost totally, 2,3-mercaptopropanol by 75% and 2,3-dimercaptopropane-1-sulfonate by 35%. Neither CaNa₃-diethylenetriamine pentaacetic acid × 5H₂O nor 2,3-dimercaptosuccinic acid had altered the distribution of cadmium between the cytosolic protein fractions after a 2 hr incubation of cells, whereas after this period, 2,3-dimercaptopropanol had removed all cadmium from metallothionein, and 2,3-dimercaptopropane-1-sulfonate about 50%. None of the chelating agents had reduced the amount of Cd bound to high molecular weight proteins. In the cell free system, 2,3-dimercaptopropanol and 2,3-dimercaptopropane-1-sulfonate were equally effective and removed all cadmium from metallothionein within ten minutes. CaNa₃-diethylenetriamine pentaacetic acid × 5H₂O, however, even after 60 min, had removed only 50% of the cadmium. The remaining cadmium was found distributed to the high molecular weight and lower molecular weight protein fractions.Abbreviations BAL 2,3-dimercaptopropanol - CHO Chinese hamster ovary cells - DMPS 2,3-dimercaptopropane-1-sulfonate - DMSA 2,3-dimercaptosuccinic acid - DTPA CaNa₃-diethylenetriaminepentaacetic acid × 5 H₂O - HMW proteins high molecular weight proteins - MT metallothionein