Redundancy and rewiring of genetic networks following genome-wide duplication events

Polyploidy or whole-genome duplication is a frequent phenomenon within the plant kingdom and has been associated with the occurrence of evolutionary novelty and increase in biological complexity. Because genome-wide duplication events duplicate whole molecular networks it is of interest to investigate how these networks evolve subsequent to such events. Although genome duplications are generally followed by massive gene loss, at least part of the network is usually retained in duplicate and can rewire to execute novel functions. Alternatively, the network can remain largely redundant and as such confer robustness against mutations. The increasing availability of high-throughput data makes it possible to study evolution following whole genome duplication events at the network level. Here we discuss how the use of 'omics' data in network analysis can provide novel insights on network redundancy and rewiring and conclude with some directions for future research.     

Assessment of plants from the Brassicaceae family as genetic models for the study of nickel and zinc hyperaccumulation

We report on the second phase of a programme to select a relative of Arabidopsis thaliana for use in large-scale molecular genetic studies of nickel (Ni) and zinc (Zn) hyperaccumulation. We also report on the relatedness among Thlaspi caerulescens accessions and the utility of using O-acetyl-L-serine as a marker for Ni and Zn hyperaccumulation potential. Twenty-seven new accessions of metal-accumulating species collected in the Czech Republic, France, Greece, Italy, Slovenia and the USA during Spring-Summer 2002 were evaluated. The criteria established for selection were hyperaccumulation of metals (Ni and Zn); compact growth habit; reasonable time to flowering; production of > or = 1000 seeds per plant; self-fertility; compact diploid genome; high sequence similarity to A. thaliana; > or = 0.1% transformation efficiency with easy selection. We conclude that the best candidate identified in the first phase was the best candidate overall: T. caerulescens accession St Félix de Pallières.     

Footwear affects the gearing at the ankle and knee joints during running

The objective of the study was to investigate the adjustment of running mechanics by wearing five different types of running shoes on tartan compared to barefoot running on grass focusing on the gearing at the ankle and knee joints. The gear ratio, defined as the ratio of the moment arm of the ground reaction force (GRF) to the moment arm of the counteracting muscle tendon unit, is considered to be an indicator of joint loading and mechanical efficiency. Lower extremity kinematics and kinetics of 14 healthy volunteers were quantified three dimensionally and compared between running in shoes on tartan and barefoot on grass. Results showed no differences for the gear ratios and resultant joint moments for the ankle and knee joints across the five different shoes, but showed that wearing running shoes affects the gearing at the ankle and knee joints due to changes in the moment arm of the GRF. During barefoot running the ankle joint showed a higher gear ratio in early stance and a lower ratio in the late stance, while the gear ratio at the knee joint was lower during midstance compared to shod running. Because the moment arms of the counteracting muscle tendon units did not change, the determinants of the gear ratios were the moment arms of the GRF's. The results imply higher mechanical stress in shod running for the knee joint structures during midstance but also indicate an improved mechanical advantage in force generation for the ankle extensors during the push-off phase.     

DNA Is Taken Up by Root Hairs and Pollen,and Stimulates Root and Pollen Tube Growth

Phosphorus (P) enters roots as inorganic phosphate (P_i) derived from organic and inorganic P compounds in the soil. Nucleic acids can support plant growth as the sole source of P in axenic culture but are thought to be converted into P_i by plant-derived nucleases and phosphatases prior to uptake. Here, we show that a nuclease-resistant analog of DNA is taken up by plant cells. Fluorescently labeled S-DNA of 25 bp, which is protected against enzymatic breakdown by its phosphorothioate backbone, was taken up and detected in root cells including root hairs and pollen tubes. These results indicate that current views of plant P acquisition may have to be revised to include uptake of DNA into cells. We further show that addition of DNA to P_i-containing growth medium enhanced the growth of lateral roots and root hairs even though plants were P replete and had similar biomass as plants supplied with P_i only. Exogenously supplied DNA increased length growth of pollen tubes, which were studied because they have similar elongated and polarized growth as root hairs. Our results indicate that DNA is not only taken up and used as a P source by plants, but ironically and independent of P_i supply, DNA also induces morphological changes in roots similar to those observed with P limitation. This study provides, to our knowledge, first evidence that exogenous DNA could act nonspecifically as signaling molecules for root development.Phosphorus (P) is an essential macronutrient that limits plant growth in many situations due to a low availability in soils (for review, see Schachtman et al., 1998; Raghothama, 1999; Vance et al., 2003; Lambers et al., 2008). P enters plant roots as orthophosphates (P_i) via active transport across the plasma membrane (Smith et al., 2003; Park et al., 2007; Xu et al., 2007). Concentrations of P_i in soil solution are generally very low (<10 μm; Bieleski, 1973) and plants have evolved root specializations to access P from inorganic and organic sources (Raghothama, 1999; Hinsinger, 2001; López-Bucio et al., 2003; Vance et al., 2003; Lambers et al., 2008). Roots exude enzymes and chemicals to mobilize P directly from soil compounds or indirectly via enhanced activity of soil microbes, and form symbioses with P-mobilizing mycorrhizal fungi (Schachtman et al., 1998; Raghothama, 1999; Bucher, 2007).However, similar to other nutrients, notably nitrogen, research on P nutrition of plants has focused on inorganic sources although organic P (P_org) in soil can account for 40% to 80% of the total P pool of mineral and organic soils, respectively (Bower, 1945; Raghothama, 1999; Vance et al., 2003). P_org compounds in soils are derived from plant residues, soil biota, and from synthesis by soil microbes (Jencks et al., 1964). Soil P_org is composed primarily of phospholipids, nucleic acids, and phytin (Dyer and Wrenshall, 1941). Phytic acid (inositol hexaphosphate) and its salts phytate, account for a large proportion of the P_org pool of soils (Anderson, 1980). Nucleic acids (RNA, DNA) represent approximately 1% to 2% of the soil P_org pool (Dalal, 1977). It can be released from prokaryotic and eukaryotic cells after death and protected against nuclease degradation by its adsorption on soil colloids and sand particles (Pietramellara et al., 2009).Although P_org can be a substantial constituent of the soil P pool, its contribution to the P nutrition of plants is poorly understood. P_org can be converted to P_i via root-exuded enzymes (Tarafdar and Claassen, 1988; Marschner, 1995; Vance et al., 2003). Secretion of nucleolytic enzymes and breakdown of nucleic acid were considered the reason for the observed growth of axenic Arabidopsis (Arabidopsis thaliana) and wheat (Triticum aestivum) on nucleic acid substrates as the sole P source (Chen et al., 2000; Richardson et al., 2000).Whether plants take up intact DNA has not been reported. We recently showed that roots take up protein, possibly via endocytosis (Paungfoo-Lonhienne et al., 2008). We hypothesized that roots may take up DNA by a similar process and grew Arabidopsis in the presence of phosphorothioate oligonucleotides (S-DNA) labeled with Cy3-fluorescent dye. S-DNA has a sulfur backbone and cannot be digested by plant nucleases, allowing tracking DNA of known size into cells (Spitzer and Eckstein, 1988). We examined if S-DNA of 25 nucleotides in length enters root hairs and pollen tubes as both types of cells are strongly elongated and have similar polarized growth (Schiefelbein et al., 1993; Hepler et al., 2001). We also assessed if addition of DNA to the growth medium affects the morphology of roots and pollen tubes. Here, we present evidence that plants take up DNA and demonstrate that the presence of DNA in the growth medium enhances lateral branching of roots, and the length of root hairs and pollen tubes, irrespective of P_i supply.     

Polyploidy: an evolutionary and ecological force in stressful times

Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests a link with environmental conditions. Whole-genome duplications seem to correlate with periods of extinction or global change, while polyploids often thrive in harsh or disturbed environments. Evidence is also accumulating that biotic interactions, for instance, with pathogens or mutualists, affect polyploids differently than nonpolyploids. Here, we review recent findings and insights on the effect of both abiotic and biotic stress on polyploids versus nonpolyploids and propose that stress response in general is an important and even determining factor in the establishment and success of polyploidy.     

Molecular Characterization of a cDNA Encoding Functional Human CLK4 Kinase and Localization to Chromosome 4q35

Phosphorylated serine- and arginine-rich (SR) proteins play an important role in the formation of spliceosomes, possibly controlling the regulation of alternative splicing. Enzymes that phosphorylate the SR proteins belong to the family of CDC2/CDC28-like kinases (CLK). Employing nucleotide sequence comparison of human expressed sequence tag sequences to the murine counterpart, we identified, cloned, and recombinantly expressed the human orthologue to the murine CLK4 cDNA. When fused to glutathione S-transferase, the catalytically active human CLK4 is able to autophosphorylate and to phosphorylate myelin basic protein, but not histone H2B as a substrate. Inspection of mRNA accumulation demonstrated gene expression in all human tissues, with the most prominent abundance in liver, kidney, brain, and heart. Using fluorescence in situ hybridization, the human CLK4 cDNA was localized to band q35 on chromosome 4.     

Liver-specific knockdown of JNK1 up-regulates proliferator-activated receptor gamma coactivator 1 beta and increases plasma triglyceride despite reduced glucose and insulin levels in diet-induced obese mice

The c-Jun N-terminal kinases (JNKs) have been implicated in the development of insulin resistance, diabetes, and obesity. Genetic disruption of JNK1, but not JNK2, improves insulin sensitivity in diet-induced obese (DIO) mice. We applied RNA interference to investigate the specific role of hepatic JNK1 in contributing to insulin resistance in DIO mice. Adenovirus-mediated delivery of JNK1 short-hairpin RNA (Ad-shJNK1) resulted in almost complete knockdown of hepatic JNK1 protein without affecting JNK1 protein in other tissues. Liver-specific knockdown of JNK1 resulted in significant reductions in circulating insulin and glucose levels, by 57 and 16%, respectively. At the molecular level, JNK1 knockdown mice had sustained and significant increase of hepatic Akt phosphorylation. Furthermore, knockdown of JNK1 enhanced insulin signaling in vitro. Unexpectedly, plasma triglyceride levels were robustly elevated upon hepatic JNK1 knockdown. Concomitantly, expression of proliferator-activated receptor gamma coactivator 1 beta, glucokinase, and microsomal triacylglycerol transfer protein was increased. Further gene expression analysis demonstrated that knockdown of JNK1 up-regulates the hepatic expression of clusters of genes in glycolysis and several genes in triglyceride synthesis pathways. Our results demonstrate that liver-specific knockdown of JNK1 lowers circulating glucose and insulin levels but increases triglyceride levels in DIO mice.