The Role of VIN3-LIKE Genes in Environmentally Induced Epigenetic Regulation of Flowering

Given their sessile nature, it is critical for the survival of plants to adapt to their environment. Accordingly, plants have evolved the ability to sense seasonal changes to govern developmental fates such as the floral transition. Temperature and day length are among the seasonal cues that plants sense. We recently reported that VIN3-LIKE 1 (VIL1) is involved in mediating the flowering response to both cold and day length via regulation of two related genes, FLOWERING LOCUS C (FLC) and FLOWERING LOCUS M (FLM), respectively.Key Words: flowering, vernalization, photoperiod, chromatin, histone, gene expressionVernalization renders plants competent to flower after exposure to the prolonged cold of winter.^1,2 Arabidopsis exhibits facultative responses to both vernalization and photoperiod to initiate the floral transition. The facultative nature of the responses makes Arabidopsis a tractable genetic system to study these aspects of flowering time control.In Arabidopsis, vernalization creates competence to flower via silencing of the potent floral repressor, FLC, in a mitotically stable manner.^3,4 Thus, the vernalization response is an environmentally induced epigenetic switch in that exposure to cold permanently affects the plants'' developmental program. This epigenetic switch is associated with increased levels of FLC chromatin methylation on Histone H3 Lys 9 and Lys 27.^5,6 VERNALIZATION INSENSITIVE 3 (VIN3) plays an essential role in this switch since no modifications to FLC chromatin occur in vin3 mutants.⁵ Furthermore, the levels of expression of VIN3 mRNA are tightly correlated with the degree of the vernalization response.⁵ VIN3 encodes Plant HomeoDomain (PHD) finger-containing protein. PHD finger-containing proteins are often associated with protein complexes that are involved in chromatin remodeling.⁷We performed a yeast two-hybrid screen to identify potential protein partners of VIN3. VIN3-LIKE 1 (VIL1) was identified by this screen.⁸ VIL1 encodes a PHD finger-containing protein that is related to VIN3. As expected for proteins that are associated with VIN3, plants containing loss-of-function alleles of VIL1 do not respond to vernalization. Furthermore, no vernalization-mediated histone modifications occur at FLC in vil1 mutants similar to the situation in vin3 mutants. Thus, by yeast two hybrid and genetic analysis, VIL1 is a bona fide VIN3 partner that is required for vernalization-mediated histone modifications at FLC chromatin. Unlike VIN3, the expression of VIL1 does not change over the course of cold exposure. Rather, VIL1 mRNA levels are affected by photoperiod. VIL1 expression is significantly increased in non-inductive photoperiods (short days; SD). Consistent with this expression pattern, vil1 mutants in the Columbia accession exhibit a SD-specific late-flowering phenotype. Furthermore, VIL1 is required for attenuating expression of FLOWERING LOCUS M, a FLC-related gene, in a SD-specific manner. It is possible that the attenuation of FLM by VIL1 has a role in creating the facultative nature of photoperiod response in Arabidopsis since vil1 mutants tend towards an obligate photoperiod response (i.e., vil1 mutants often fail to flower in SD).In Arabidopsis, there are four VIN3-related genes, which we named as VIL1 ∼ VIL4,⁸ and which have also been called VRN5 and VEL1 ∼ VEL3.⁹ The C-terminal domain is highly conserved among these genes and was named the VIN3-Interacting Domain (VID) since it is required for protein-protein interaction between VIN3 and VIL1. The effect of cold on the expression patterns of VIN3-related genes varies. For example, VIL2 and VIL3 are induced specifically by vernalizing cold exposures whereas others such as VIL1 are, for the most part, constitutively expressed. It will be interesting to determine the functions of the remaining VIL genes.FLC is the main target for vernalization in Arabidopsis. Interestingly, FLC orthologs have not been found in vernalization-responsive varieties of cereals. However, in wheat, VRN2 appears to have a role equivalent to that of FLC in Arabidopsis.¹⁰ VRN2 encodes a ZCCT type zinc-finger protein that does not have a homolog in the Arabidopsis genome. In diploid wheat, down regulation of VRN2 is correlated with the vernalization response.¹¹ Interestingly, wheat contains three VIN3-LIKE (VIL) genes, TmVIL1, TmVIL2 and TmVIL3.¹² Furthermore, TmVIL1 is up-regulated by vernalization.¹² However, whether TmVIL1 has a direct role in the vernalization-mediated repression of VRN2 in wheat has not yet been addressed. Similar to VIL1, TmVIL3 shows elevated level of expression in SD. Furthermore, VRN2 is downregulated in SD;^13,14 thus there is a correlation between the induction of TmVIL genes and the downregulation of the floral repressor VRN2 similar to the VIN3/FLC and VIL1/FLM relationships (Fig. 1). Perhaps VIN3-related genes have similar roles both in Arabidopsis and in temperate wheat, but act on different target genes, possibly as a result of convergent evolution. Interestingly, the wheat gene TmVRN3 is homologous to FLOWERING LOCUS T (FT) of Arabidopsis, and TmVRN3 is repressed by TmVRN2 as FT is repressed by FLC,¹⁵ suggesting another similarity in the regulation of flowering time between Arabidopsis and temperate wheat (Fig. 1).Open in a separate windowFigure 1Proposed relationship of VIN3 family genes to the regulatory network controlling flowering time in response to environmental cues in Arabidopsis and diploid wheat (adapted from ref. ¹⁶).Although the PHD finger can be found in various eukaryotes, the VID is unique to plants. It is also noteworthy that VIN3-related genes can be found in various plant species, including rice, which does not have a vernalization response. It will be interesting to address whether the VIN3-related genes from various plant species are more broadly involved in relaying environmental signals to developmental programs.     

Synergistic action of the Saccharomyces cerevisiae homologous recombination factors Rad54 and Rad51 in chromatin remodeling

Rad54, a member of the Swi2/Snf2 protein family, works in concert with the RecA-like recombinase Rad51 during the early and late stages of homologous recombination. Rad51 markedly enhances the activities of Rad54, including the induction of topological changes in DNA and the remodeling of chromatin structure. Reciprocally, Rad54 promotes Rad51-mediated DNA strand invasion with either naked or chromatinized DNA. Here, using various Saccharomyces cerevisiae rad51 and rad54 mutant proteins, mechanistic aspects of Rad54/Rad51-mediated chromatin remodeling are defined. Disruption of the Rad51-Rad54 complex leads to a marked attenuation of chromatin remodeling activity. Moreover, we present evidence that assembly of the Rad51 presynaptic filament represents an obligatory step in the enhancement of the chromatin remodeling reaction. Interestingly, we find a specific interaction of the N-terminal tail of histone H3 with Rad54 and show that the H3 tail interaction domain resides within the amino terminus of Rad54. These results suggest that Rad54-mediated chromatin remodeling coincides with DNA homology search by the Rad51 presynaptic filament and that this process is facilitated by an interaction of Rad54 with histone H3.     

Transgenesis and nuclear transfer using porcine embryonic germ cells

Embryonic germ (EG) cells are undifferentiated stem cells isolated from cultured primordial germ cells (PGC). Porcine EG cell lines with capacities of both in vitro and in vivo differentiation have been established. Because EG cells can be cultured indefinitely in an undifferentiated state, they may be more suitable for nuclear donor cells in nuclear transfer (NT) than somatic cells that have limited lifespan in primary culture. Use of EG cells could be particularly advantageous to provide an inexhaustible source of transgenic cells for NT. In this study the efficiencies of transgenesis and NT using porcine fetal fibroblasts and EG cells were compared. The rate of development to the blastocyst stage was significantly higher in EG cell NT than somatic cell NT (94 of 518, 18.2% vs. 72 of 501, 14.4%). To investigate if EG cells can be used for transgenesis in pigs, green fluorescent protein (GFP) gene was introduced into porcine EG cells. Nuclear transfer embryos using transfected EG cells gave rise to blastocysts (29 of 137, 21.2%) expressing GFP based on observation under fluorescence microscope. The results obtained from the present study suggest that EG cell NT may have advantages over somatic cell NT, and transgenic pigs may be produced using EG cells.     

Role of Dnl4-Lif1 in nonhomologous end-joining repair complex assembly and suppression of homologous recombination

Nonhomologous end joining (NHEJ) eliminates DNA double-strand breaks (DSBs) in bacteria and eukaryotes. In Saccharomyces cerevisiae, there are pairwise physical interactions among the core complexes of the NHEJ pathway, namely Yku70-Yku80 (Ku), Dnl4-Lif1 and Mre11-Rad50-Xrs2 (MRX). However, MRX also has a key role in the repair of DSBs by homologous recombination (HR). Here we have examined the assembly of NHEJ complexes at DSBs biochemically and by chromatin immunoprecipitation. Ku first binds to the DNA end and then recruits Dnl4-Lif1. Notably, Dnl4-Lif1 stabilizes the binding of Ku to in vivo DSBs. Ku and Dnl4-Lif1 not only initiate formation of the nucleoprotein NHEJ complex but also attenuate HR by inhibiting DNA end resection. Therefore, Dnl4-Lif1 plays an important part in determining repair pathway choice by participating at an early stage of DSB engagement in addition to providing the DNA ligase activity that completes NHEJ.     

Exercise improves glucose homeostasis that has been impaired by a high-fat diet by potentiating pancreatic beta-cell function and mass through IRS2 in diabetic rats.

In this study, we investigated the effects of a high-fat diet and exercise on pancreatic beta-cell function and mass and its molecular mechanism in 90% pancreatectomized male rats. The pancreatectomized diabetic rats were given control diets (20% energy) or a high-fat (HF) diet (45% energy) for 12 wk. Half of each group was given regular exercise on an uphill treadmill at 20 m/min for 30 min 5 days/wk. HF diet lowered first-phase insulin secretion with glucose loading, whereas exercise training reversed this decrease. However, second-phase insulin secretion did not differ among the groups. Exercise increased pancreatic beta-cell mass. This resulted from stimulated beta-cell proliferation and reduced apoptosis, which is associated with potentiated insulin or IGF-I signaling through insulin receptor substrate-2 (IRS2) induction. Although the HF diet resulted in decreased proliferation and accelerated apoptosis by weakened insulin and IGF-I signaling from reduction of IRS2 protein, beta-cell mass was maintained in HF rats just as much as in control rats via increased individual beta-cell size and neogenesis from precursor cells. Consistent with the results of beta-cell proliferation, pancreas duodenal homeobox-1 expression increased in the islets of rats in the exercise groups, and it was reduced the most in rats fed the HF diet. In conclusion, exercise combined with a moderate fat diet is a good way to maximize beta-cell function and mass through IRS2 induction to alleviate the diabetic condition. This study suggests that dietary fat contents and exercise modulate beta-cell function and mass to overcome insulin resistance in two different pathways.     

A new sensitive and selective detection of Ga3+ by thiophene-based ‘turn-on’ fluorescent chemosensor

We designed a thiophene-based fluorescent chemosensor DHTC ((E)-2-([3,5-dichloro-2-hydroxybenzylidene]amino)thiophene-3-carboxamide) for detecting gallium (Ga³⁺). DHTC could probe Ga³⁺ using fluorescence enhancement. The limit of detection for Ga³⁺ by DHTC was 0.39 μM. The binding mode of DHTC to Ga³⁺ was determined as a 1:1 ratio from analysis by Job’s plot and electrospray ionization-mass spectrometry (ESI-MS). In addition, DHTC could selectively detect Ga³⁺ using test kits. The sensing process of Ga³⁺ by DHTC was presented using ultraviolet–visible light titration, Job’s plot, ESI-MS, ¹H nuclear magnetic resonance titration, and density functional theory calculation.     

Contrasting patterns of genetic structure and phylogeography in the marine agarophytes Gelidiophycus divaricatus and G. freshwateri (Gelidiales,Rhodophyta) from East Asia

The evolutionary and population demographic history of marine red algae in East Asia is poorly understood. Here, we reconstructed the phylogeographies of two upper intertidal species endemic to East Asia, Gelidiophycus divaricatus and G. freshwateri. Phylogenetic and phylogeographic inferences of 393 mitochondrial cox1, 128 plastid rbcL, and 342 nuclear ITS2 sequences were complemented with ecological niche models. Gelidiophycus divaricatus, a southern species adapted to warm water, is characterized by a high genetic diversity and a strong geographical population structure, characteristic of stable population sizes and sudden reduction to recent expansion. In contrast, G. freshwateri, a northern species adapted to cold temperate conditions, is genetically relatively homogeneous with a shallow population structure resulting from steady population growth and recent equilibrium. The overlap zone of the two species roughly matches summer and winter isotherms, indicating that surface seawater temperature is a key feature influencing species range. Unidirectional genetic introgression was detected at two sites on Jeju Island where G. divaricatus was rare while G. freshwateri was common, suggesting the occurrence of asymmetric natural hybrids, a rarely reported event for rhodophytes. Our results illustrate that Quaternary climate oscillations have left strong imprints on the current day genetic structure and highlight the importance of seawater temperature and sea level change in driving speciation in upper intertidal seaweed species.     

Long-term Therapeutic Effects of Extracorporeal Shock Wave-Assisted Melatonin Therapy on Mononeuropathic Pain in Rats

We evaluated the ability of extracorporeal shock wave (ECSW)-assisted melatonin (Mel) therapy to offer an additional benefit for alleviating the neuropathic pain (NP) in rats. Left sciatic nerve was subjected to chronic constriction injury (CCI) to induce NP. Animals (n?=?30) were randomized into group 1 (sham-operated control), group 2 (CCI only), group 3 (CCI?+?ECSW), group 4 (CCI?+?Mel) and group 5 (CCI?+?ECSW?+?Mel). By days 15, 22 and 29 after CCI, the thermal paw withdrawal latency (TPWL) and mechanical paw withdrawal threshold (MPWT) were highest in group 1, lowest in group 2, significantly higher in group 5 than in groups 3 and 4, but they showed no difference between the later two groups (all p?<?0.0001). The protein expressions of inflammatory (TNF-α, NF-κB, MMP-9, IL-1ß), oxidative-stress (NOXs-1, -2, -4, oxidized protein), apoptotic (cleaved-caspase3, cleaved-PARP), DNA/mitochondrial-damaged (γ-H2AX/cytosolic-cytochrome C), microglia/astrocyte activation (ox42/GFAP), and MAPKs [phosphorylated (p)-p38, p-JNK, p-ERK] biomarkers in dorsal root ganglia neurons (DRGs) and in spinal dorsal horn were exhibited an opposite pattern of TPWL among the five groups (all p?<?0.0001). Additionally, protein expressions of Nav.1.3, Nav.1.8 and Nav.1.9 in sciatic nerve exhibited an identical pattern to inflammation among the five groups (all p?<?0.0001). The numbers of cellular expressions of MAPKs (p-ERK1/2+/peripherin?+?cells, p-ERK1/2+/NF200?+?cells and p-JNK+/peripherin?+?cells, p-JNK+/NF200?+?cells) and voltage-gated sodium channels (Nav.1.8+/peripherin?+?cells, Nav.1.8+/NF200?+?cells, Nav.1.9+/peripherin?+?cells, Nav.1.9+/NF200?+?cells) in small and large DRGs displayed an identical pattern to inflammation among the five groups (all p?<?0.0001). In conclusion, the synergistic effect of combined ECSW-Mel therapy is superior to either one alone for long-term improvement of mononeuropathic pain-induced by CCI in rats.

     

Mechanical understanding of hunting waves generated by killer whales

The wave wash hunting employed by Orcinus orca, also known as killer whales, is unique in that the prey is hunted outside of the water by generating waves. To quantitatively analyze the specific mechanism of the wave wash, data were obtained using computational fluid dynamics (CFD), and wave theory was introduced as the theoretical background to clarify the mechanism. The relationships between the swimming characteristics and wave parameters are defined in this paper. The results obtained by numerical investigation revealed that the wavelength increased with the swimming speed. Additionally, the wave height increased as the swimming speed increased and the swimming depth became shallower, and subsequently converged to a maximum of 2.42 m. The success of hunting is determined by two wave parameters, which indicate the intensity of the wave wash: the wave height and force exerted on the prey. The metabolic rate and the drag force are considered to evaluate the efficiency of the locomotion, which varied according to the swimming speed (V) and swimming depth (d) of the whales. To generate hunting waves efficiently, the optimal ranges of V and d were estimated to be 3 ~ 5 m/s and 0.5 m ~ 1.1 m respectively.