Cell Migration from Baby to Mother

Fetal cells migrate into the mother during pregnancy. Fetomaternal transfer probably occurs in all pregnancies and in humans the fetal cells can persist for decades. Microchimeric fetal cells are found in various maternal tissues and organs including blood, bone marrow, skin and liver. In mice, fetal cells have also been found in the brain. The fetal cells also appear to target sites of injury. Fetomaternal microchimerism may have important implications for the immune status of women, influencing autoimmunity and tolerance to transplants. Further understanding of the ability of fetal cells to cross both the placental and blood-brain barriers, to migrate into diverse tissues, and to differentiate into multiple cell types may also advance strategies for intravenous transplantation of stem cells for cytotherapeutic repair. Here we discuss hypotheses for how fetal cells cross the placental and blood-brain barriers and the persistence and distribution of fetal cells in the mother.Key Words: fetomaternal microchimerism, stem cells, progenitor cells, placental barrier, blood-brain barrier, adhesion, migrationMicrochimerism is the presence of a small population of genetically distinct and separately derived cells within an individual. This commonly occurs following transfusion or transplantation.^1–3 Microchimerism can also occur between mother and fetus. Small numbers of cells traffic across the placenta during pregnancy. This exchange occurs both from the fetus to the mother (fetomaternal)^4–7 and from the mother to the fetus.^8–10 Similar exchange may also occur between monochorionic twins in utero.^11–13 There is increasing evidence that fetomaternal microchimerism persists lifelong in many child-bearing women.^7,14 The significance of fetomaternal microchimerism remains unclear. It could be that fetomaternal microchimerism is an epiphenomenon of pregnancy. Alternatively, it could be a mechanism by which the fetus ensures maternal fitness in order to enhance its own chances of survival. In either case, the occurrence of pregnancy-acquired microchimerism in women may have implications for graft survival and autoimmunity. More detailed understanding of the biology of microchimeric fetal cells may also advance progress towards cytotherapeutic repair via intravenous transplantation of stem or progenitor cells.Trophoblasts were the first zygote-derived cell type found to cross into the mother. In 1893, Schmorl reported the appearance of trophoblasts in the maternal pulmonary vasculature.¹⁵ Later, trophoblasts were also observed in the maternal circulation.^16–20 Subsequently various other fetal cell types derived from fetal blood were also found in the maternal circulation.^21,22 These fetal cell types included lymphocytes,²³ erythroblasts or nucleated red blood cells,^24,25 haematopoietic progenitors^7,26,27 and putative mesenchymal progenitors.^14,28 While it has been suggested that small numbers of fetal cells traffic across the placenta in every human pregnancy,^29–31 trophoblast release does not appear to occur in all pregnancies.³² Likewise, in mice, fetal cells have also been reported in maternal blood.^33,34 In the mouse, fetomaternal transfer also appears to occur during all pregnancies.³⁵     

Phototropins and chloroplast activity in plant blue light signaling

In plants, phototropins 1 (phot1) and 2 (phot2) mediate chloroplast movement to blue light (BL). A recent report showed that phototropins (phot) are required for the expression of chloroplast genes in rice. The light-induced responses of phot1a rice mutants result in H₂O₂-mediated damage to chloroplast photosystems, indicating that phot-regulated responses might be associated with the other photoreceptor, such as cryptochrome (cry) BL receptor. This suggests diversification and specialization of photoreceptor signaling in plants.Key words: blue light, blue light receptor, chloroplast, cryptochrome, H₂O₂, phototropin, signalingIn order to counteract the adverse effects of environmental ight, plants have evolved sensory mechanisms that monitor their surroundings and adapt their growth and development through the use of a complex signaling network.¹ Plants sense their environmental light conditions by using three principal families of signal-transducing photoreceptors; the red/far-red (R/FR) light-absorbing phytochromes (phy) and the UV-A/blue light (BL)-absorbing cryptochromes (cry) and phototropins (phot).² The phys are reversibly photochromic biliproteins that absorb maximally in the R and FR light regions of the spectrum. Cry and phot possess a pair of flavin derivates. Two cry and two phot family members have been identified and well characterized in Arabidopsis. Photoreceptors regulate development throughout the plant lifecycle, from seed germination through to plant maturation and the onset of reproduction. BL regulates a wide variety of photoresponses in higher plants, including chloroplast movement, inhibition of hypocotyls elongation, circadian timing, regulation of gene expression and stomatal opening.^3–5 The roles of individual photoreceptors in mediating plant development have, however, often been confounded by redundant, synergistic and in some cases mutually antagonistic mechanisms of action. The mechanisms of photoreceptor signal transduction are far from being completely elucidated, but are believed to involve both cytosolic and nuclear components. The presence of putative kinase domains within photoreceptor proteins has suggested a role for phosphorylation in light signaling. The action of cry1 and cry2 has been demonstrated to involve BL-mediated autophosphorylation.^6,7 Phot1 was originally identified as a 120 kDa-membrane associated protein displaying BL-mediated autophosphorylation.⁸ It is now well accepted that phot mediates chloroplast movement, phototropism and stomatal opening in plants in response to BL.     

Historical Overview on Plant Neurobiology

The review tracks the history of electrical long-distance signals from the first recordings of action potentials (APs) in sensitive Dionea and Mimosa plants at the end of the 19^th century to their re-discovery in common plants in the 1950''s, from the first intracellular recordings of APs in giant algal cells to the identification of the ionic mechanisms by voltage-clamp experiments. An important aspect is the comparison of plant and animal signals and the resulting theoretical implications that accompany the field from the first assignment of the term “action potential” to plants to recent discussions of terms like plant neurobiology.Key Words: action potentials, slow wave potentials, plant nerves, plant neurobiology, electrical signaling in plants and animailsFor a long time plants were thought to be living organisms whose limited ability to move and respond was appropriately matched by limited abilities of sensing.¹ Exceptions were made for plants with rapid and purposeful movements such as Mimosa pudica (also called the sensitive plant), Drosera (sundews), Dionea muscipula (flytraps) and tendrils of climbing plants. These sensitive plants attracted the attention of outstanding pioneer researchers like Pfeffer,^2,3 Burdon-Sanderson,^4,5 Darwin,⁶ Haberlandt^7–9 and Bose.^10–13 They found them not only to be equipped with various mechanoreceptors exceeding the sensitivity of a human finger but also to trigger action potentials (APs) that implemented these movements.The larger field of experimental electrophysiology started with Luigi Galvani''s discovery of “animal electricity” or contractions of isolated frog legs suspended between copper hooks and the iron grit of his balcony.¹⁴ It soon became clear that the role of the electric current was not to provide the energy for the contraction but to simulate a stimulus that existed naturally in the form of directionally transmitted electrical potentials. Studies by both Matteucci and Du Bois-Reymond¹⁵ recognized that wounding of nerve strands generated the appearance of a large voltage difference between the wounded (internal) and intact (external) site of nerves. This wound or injury potential was the first, crude measurement of what later became known as membrane or resting potential of nerve cells. It was also found that various stimuli reduced the size of the potential (in modern terms: they caused a depolarization), and to describe the propagating phenomenon novel terms such as action potential (AP) and action current were created (reviewed in refs. ¹⁵ and ¹⁶). Rather than relying on such indirect methods, the membrane theory of exicitation proposed by Bernstein in 1912¹⁷ made it desirable to directly measure the value of cell membrane potentials. Such progress soon became possible by the introduction of microelectrodes (KCl-filled glass micropipettes with a tip diameter small enough to be inserted into living cells) to record intracellular, i.e., the real membrane potentials (V_m). The new technique was simultaneously adopted for giant cells (axons) of cephalopods such as Loligo and Sepia¹⁸ and giant internodal cells of Charophytic green algae. In the 1930s Umrath and Osterhout^19–21 not only made the first reliable, intracellular measurements of membrane potentials in plant cells (reporting V_m values between −100 to −170 mV) but the first intracellular recordings of plant APs as well. When this technique was complemented with precise electronic amplifiers and voltage clamp circuits in the 1940s, one could measure ion currents (instead of voltages) and so directly monitor the activity of ion channels. The smart application of these methods led to a new, highly detailed understanding of the ionic species and mechanisms involved in V_m changes, especially APs.^22–27 Whereas the depolarizing spike in animal nerve cells is driven by an increased influx of Na⁺ ions, plant APs were found to involve influx of Ca²⁺ and/or efflux of Cl⁻¹ ions.The first extracellular recording of a plant AP was initiated by Charles Darwin and performed on leaves of the Venus flytrap (Dionea muscipula Ellis) by the animal physiologist Burdon-Sanderson in 1873.^4–6 Ever since APs have often been considered to fulfil comparable roles in plants and nerve-muscle preparations of animals. However, this was never a generally accepted view. While it is commonly assumed that the AP causes the trap closure, this had not been definitely shown (see refs. ²⁸ and ²⁹). Kunkel (1878) and Bose (1907, 1926) measured action spikes also in Mimosa plants where they preceded the visible folding movements of the leaflets.^{12–13,30–31} Dutrochet and Pfeffer^2–3 had already found before that interrupting vascular bundles by incision prevented the excitation from propagating beyond the cut and concluded that the stimulus must move through the vascular bundles, in particular the woody or hadrome part (in modern terms the xylem). Haberlandt⁷ cut or steam-killed the external, nonwoody part of the vascular bundles and concluded that the phloem strands were the path for the excitation, a notion which is confirmed by a majority of recent studies in Mimosa and other plant species. APs have their largest amplitude near and in the phloem and there again in the sieve cells.^{23–24,32–35} Moreover, APs can be recorded through the excised stylets of aphids known to be inserted in sieve tube elements.^36–37 Other studies found that AP-like signals propagate with equal rate and amplitude through all cells of the vascular bundle.³⁸ Starting studies with isolated vascular bundles (e.g., from the fern Adiantum), Bose found increasing amplitudes of heat-induced spikes by repeated stimulation (tetanisation) and incubation in 0.5 % solution of sodium carbonate.^10–13 Since the electrical behavior of isolated vascular strands was comparable to that of isolated frog nerves, Bose felt justified to refer to them as plant nerves.Although at the time a hardly noticed event, the discovery that normal plants such as pumpkins had propagating APs just as the esoteric “sensitive” plants was a scientific breakthrough with important consequences.^39–40,32 First, it corrected the long-held belief that normal plants are simply less sensitive and responsive than the so-called “sensitive plants” from Mimosa to Venus flytraps. Second, it led to the stimulating belief that so widely distributed electric signals must carry important messages.⁴¹ The ensuing studies made considerable progress in linking electrical signals with respiration and photosynthesis,^40–42 pollination,^43–44 phloem transport^{33,36–37,45} and the rapid, plant-wide deployment of plant defenses.^46–53The detailed visualization of nerve cells with silver salts by the Spanish zoologist S. Ramon y Cajal, the demonstrated existence of APs in Dionea and Mimosa as well as the discovery of plant mechanoreceptors in these and other plants⁹ at the end of the century was sufficient stimulation to start a search for structures that could facilitate the rapid propagation of these and other excitation signals. Researchers began to investigate easily stainable intracellular plasma strands that run across the lumen of many plant cells, and sometimes even continue over several cells for their potential role as nerve-like, excitation-conducting structures. Such strands were shown to occur in traumatized areas of many roots⁵⁴ and in insectivorous butterworts where they connect the glue-containing hair tips with the basal peptidase-producing glands of the Pinguicula leaves.^55–56 However, after investigating these claims, Haberlandt came to the conclusion that the only nerve-like structures of plants were situated the long phloem cells of the vascular bundles.^7–8 From that time on papers, lectures and textbooks reiterated statements that “plants have no nerves”.This unproductive expression ignores the work of Darwin, Haberlandt, Pfeffer and Bose together with the fact that in spite of their anatomical differences, nerve cell networks and vascular bundles share the analog function of conducting electrical signals. Similar anatomical differences have not been an obstacle to stating that both plants and animals consist of cells. The mechanistic similarity of excitations (consisting of a transient decline in cell input resistance) in plant and nerve cells was later elegantly demonstrated by the direct comparison of action potentials in Nitella and the giant axon of squids.^57–58 Today, consideration of nerve-like structures in plants involves increasingly more aspects of comparison. We know that many plants can efficiently produce electric signals in the form of action potentials and slow wave potentials (= variation potentials) and that the long-distance propagation of these signals proceeds in the vascular bundles. We also know that plants like Dionea can propagate APs with high efficiency and speed without the use of vascular bundles, probably because their cells are electrically coupled through plasmodesmata. Other analogies with neurobiology include vesicle-operated intercellular clefts in axial root tissues (the so-called plant synapses)⁵⁹ as well as the certain existence and operation of substances like neurotransmitters and synaptotagmins in plant cells (e.g., refs. ⁶⁰ and ⁶¹). The identification of the role(s) of these substances in plants will have important implications. Altogether, modern plant neurobiology might emerge as a coherent science.⁶²Electrophysiological and other studies of long-distance signals in plants and animals greatly contributed to our knowledge of the living world by revealing important similarities and crucial differences between plants and animals in an area that might directly relate to their different capacities to respond to environmental signals. Even at this stage the results are surprising. Rather than lacking electric signals, higher plants have developed more than just one signal type that is able to cover large distances. In addition to APs that occur also in animals and lower plants,⁶³ higher plants feature an additional, unique, hydraulically propagated type of electric signals called slow wave potentials.⁶⁴     

Why have chloroplasts developed a unique motility system?

Organelle movement in plants is dependent on actin filaments with most of the organelles being transported along the actin cables by class XI myosins. Although chloroplast movement is also actin filament-dependent, a potential role of myosin motors in this process is poorly understood. Interestingly, chloroplasts can move in any direction and change the direction within short time periods, suggesting that chloroplasts use the newly formed actin filaments rather than preexisting actin cables. Furthermore, the data on myosin gene knockouts and knockdowns in Arabidopsis and tobacco do not support myosins'' XI role in chloroplast movement. Our recent studies revealed that chloroplast movement and positioning are mediated by the short actin filaments localized at chloroplast periphery (cp-actin filaments) rather than cytoplasmic actin cables. The accumulation of cp-actin filaments depends on kinesin-like proteins, KAC1 and KAC2, as well as on a chloroplast outer membrane protein CHUP1. We propose that plants evolved a myosin XI-independent mechanism of the actin-based chloroplast movement that is distinct from the mechanism used by other organelles.Key words: actin, Arabidopsis, blue light, kinesin, myosin, organelle movement, phototropinOrganelle movement and positioning are pivotal aspects of the intracellular dynamics in most eukaryotes. Although plants are sessile organisms, their organelles are quickly repositioned in response to fluctuating environmental conditions and certain endogenous signals. By and large, plant organelle movements and positioning are dependent on actin filaments, although microtubules play certain accessory roles in organelle dynamics.^1,2 Actin inhibitors effectively retard the movements of mitochondria,^3–6 peroxisomes,^5,7–11 Golgi stacks,^12,13 endoplasmic reticulum (ER),^14,15 and nuclei.^16–18 These organelles are co-aligned and associated with actin filaments.^{5,7,8,10–12,15,18} Recent progress in this field started to reveal the molecular motility system responsible for the organelle transport in plants.¹⁹Chloroplast movement is among the most fascinating models of organelle movement in plants because it is precisely controlled by ambient light conditions.^20,21 Weak light induces chloroplast accumulation response so that chloroplasts can capture photosynthetic light efficiently (Fig. 1A). Strong light induces chloroplast avoidance response to escape from photodamage (Fig. 1B).²² The blue light-induced chloroplast movement is mediated by the blue light receptor phototropin (phot). In some cryptogam plants, the red light-induced chloroplast movement is regulated by a chimeric phytochrome/phototropin photoreceptor neochrome.^23–25 In a model plant Arabidopsis, phot1 and phot2 function redundantly to regulate the accumulation response,²⁶ whereas phot2 alone is essential for the avoidance response.^27,28 Several additional factors regulating chloroplast movement were identified by analyses of Arabidopsis mutants deficient in chloroplast photorelocation.^29–32 In particular, identification of CHUP1 (chloroplast unusual positioning 1) revealed the connection between chloroplasts and actin filaments at the molecular level.²⁹ CHUP1 is a chloroplast outer membrane protein capable of interacting with F-actin, G-actin and profilin in vitro.^29,33,34 The chup1 mutant plants are defective in both the chloroplast movement and chloroplast anchorage to the plasma membrane,^22,29,33 suggesting that CHUP1 plays an important role in linking chloroplasts to the plasma membrane through the actin filaments. However, how chloroplasts move using the actin filaments and whether chloroplast movement utilizes the actin-based motility system similar to other organelle movements remained to be determined.Open in a separate windowFigure 1Schematic distribution patterns of chloroplasts in a palisade cell under different light conditions, weak (A) and strong (B) lights. Shown as a side view of mid-part of the cell and a top view with three different levels (i.e., top, middle and bottom of the cell). The cell was irradiated from the leaf surface shown as arrows. Weak light induces chloroplast accumulation response (A) and strong light induces the avoidance response (B).Here, we review the recent findings pointing to existence of a novel actin-based mechanisms for chloroplast movement and discuss the differences between the mechanism responsible for movement of chloroplasts and other organelles.     

RALFs: Peptide regulators of plant growth

Peptide signaling regulates a variety of developmental processes and environmental responses in plants.^1–6 For example, the peptide systemin induces the systemic defense response in tomato⁷ and defensins are small cysteine-rich proteins that are involved in the innate immune system of plants.^8,9 The CLAVATA3 peptide regulates meristem size¹⁰ and the SCR peptide is the pollen self-incompatibility recognition factor in the Brassicaceae.^11,12 LURE peptides produced by synergid cells attract pollen tubes to the embryo sac.⁹ RALFs are a recently discovered family of plant peptides that play a role in plant cell growth.Key words: peptide, growth factor, alkalinization     

A new callose function: Involvement in differentiation and function of fern stomatal complexes

Callose in polypodiaceous ferns performs multiple roles during stomatal development and function. This highly dynamic (1→3)-β-D-glucan, in cooperation with the cytoskeleton, is involved in: (a) stomatal pore formation, (b) deposition of local GC wall thickenings and (c) the mechanism of stomatal pore opening and closure. This behavior of callose, among others, probably relies on the particular mechanical properties as well as on the ability to form and degrade rapidly, to create a scaffold or to serve as a matrix for deposition of other cell wall materials and to produce fibrillar deposits in the periclinal GC walls, radially arranged around the stomatal pore. The local callose deposition in closing stomata is an immediate response of the external periclinal GC walls experiencing strong mechanical forces induced by the neighboring cells. The radial callose fibrils transiently co-exist with radial cellulose microfibrils and, like the latter, seem to be oriented via cortical MTs.Key words: callose, cytoskeleton, fern stomata, guard cell wall thickening, stomatal function, stomatal pore formationCallose represents a hemicellulosic matrix cell wall component, usually of temporal appearance, which is synthesized by callose synthases, enzymes localized in the plasmalemma and degraded by (1→3)-β-glucanases.^1–4 It consists of triple helices of a linear homopolymer of (1→3)-β-glucose residues.^5–7 The plant cell is able to form and degrade callose in a short time. On the surface of the plasmolyzed protoplast a thin callose surface film may arise within seconds.⁸ Callose is the only cell wall component that is implicated in a great variety of developmental plant processes, like cell plate formation,^9–11 microspore development,^12–14 trafficking through plasmodesmata,^15,16 formation and closure of sieve pores,¹⁶ response of the plant cells to multiple biotic and abiotic stresses,^4,5 establishment of distinct “cell cortex domains”,¹⁷ etc.Despite the widespread occurrence of callose, its general function(s) is (are) not well understood (reviewed in refs. ⁴ and ⁵). It may serve as: a matrix for deposition of other cell wall materials, as in developing cell plates;⁹ a cell wall-strengthening material, as in cotton seed hairs and growing pollen tubes;¹⁸ a sealing or plugging material at the plasma membrane of pit fields, plasmodesmata and sieve plate pores;¹⁶ a mechanical obstruction to growth of fungal hyphae or a special permeability barrier, as in pollen mother cell walls and muskmelon endosperm envelopes.^4,19,20 The degree of polymerization, age and thickness of callose deposits may cause variation in its physical properties.⁵Evidence accumulated so far showed that a significant number of ferns belonging to Polypodiales and some other fern classes forms intense callose deposits in the developing GC wall thickenings.^21–28 This phenomenon has not been observed in angiosperm stomata, although callose is deposited along the whole surface of the young VW and in the VW ends of differentiating and mature stomata (our unpublished data; reviewed in refs ²⁹ and ³⁰).Stomata are specialized epidermal bicellular structures (Fig. 1A) regulating gas exchange between the aerial plant organs and the external environment. Their appearance in the first land plants was crucial for their adaptation and survival in the terrestrial environment. The constituent GCs have the ability to undergo reversible changes in shape, leading to opening and closure of the stomatal pore (stomatal movement). The mechanism by which GCs change shape is based on: (a) the particular mechanical properties of GC walls owed to their particular shape, thickening, fine structure and chemical composition and (b) the reversible changes in vacuole volume, in response to environmental factors, through fairly complicated biochemical pathways.^30–33Open in a separate windowFigure 1(A) Diagrammatic representation of an elliptical stoma. (B–E) Diagram to show the process of stomatal pore formation in angiosperms (B and C) and Polypodiales ferns (D and E). The arrows in (B) indicate the forming stomatal pore. DW, dorsal wall; EPW, external periclinal wall; GC, guard cell; IPW, internal periclinal wall; ISP, internal stomatal pore; PE polar ventral wall end; VW, ventral wall.The present review is focused on the multiple-role of callose in differentiating and functioning fern stomata, as they are substantiated by the available information, including some unpublished data, and in particular in: stomatal pore formation, deposition of GC wall thickenings and opening and closure of the stomatal pore. The mode of deposition of fibrillar callose deposits in GC walls and the mechanism of their alignment are also considered.     

Prions: En route from structural models to structures

The prion hypothesis^1–3 states that the prion and non-prion form of a protein differ only in their 3D conformation and that different strains of a prion differ by their 3D structure.^4,5 Recent technical developments have enabled solid-state NMR to address the atomic-resolution structures of full-length prions, and a first comparative study of two of them, HET-s and Ure2p, in fibrillar form, has recently appeared as a pair of companion papers.^6,7 Interestingly, the two structures are rather different: HET-s features an exceedingly well-ordered prion domain and a partially disordered globular domain. Ure2p in contrast features a very well ordered globular domain with a conserved fold, and—most probably—a partially ordered prion domain.⁶ For HET-s, the structure of the prion domain is characterized at atomic-resolution. For Ure2p, structure determination is under way, but the highly resolved spectra clearly show that information at atomic resolution should be achievable.Key words: prion, NMR, solid-state NMR, MAS, structure, Ure2p, HET-sDespite the large interest in the basic mechanisms of fibril formation and prion propagation, little is known about the molecular structure of prions at atomic resolution and the mechanism of propagation. Prions with related properties to the ones responsible for mammalian diseases were also discovered in yeast and funghi^8,9 which provide convenient model system for their studies. Prion proteins described include the mammalian prion protein PrP, Ure2p,¹⁰ Rnq1p,¹¹ Sup35,¹² Swi1,¹³ and Cyc8,¹⁴ from bakers yeast (S. cervisiae) and HET-s from the filamentous fungus P. anserina. The soluble non-prion form of the proteins characterized in vitro is a globular protein with an unfolded, dynamically disordered N- or C-terminal tail.^15–18 In the prion form, the proteins form fibrillar aggregates, in which the tail adopts a different conformation and is thought to be the dominant structural element for fibril formation.Fibrills are difficult to structurally characterize at atomic resolution, as X-ray diffraction and liquid-state NMR cannot be applied because of the non-crystallinity and the mass of the fibrils. Solid-state NMR, in contrast, is nowadays well suited for this purpose. The size of the monomer, between 230 and 685 amino-acid residues for the prions of Figure 1, and therefore the number of resonances in the spectrum—that used to be large for structure determination—is now becoming tractable by this method.Open in a separate windowFigure 1Prions identified today and characterized as consisting of a prion domain (blue) and a globular domain (red).Prion proteins characterized so far were found to be usually constituted of two domains, namely the prion domain and the globular domain (see Fig. 1). This architecture suggests a divide-and-conquer approach to structure determination, in which the globular and prion domain are investigated separately. In isolation, the latter, or fragments thereof, were found to form β-sheet rich structures (e.g., Ure2p(1-89),^6,19 Rnq1p(153-405)²⁰ and HET-s(218-289)²¹). The same conclusion was reached by investigating Sup35(1-254).²² All these fragements have been characterized as amyloids, which we define in the sense that a significant part of the protein is involved in a cross-beta motif.²³ An atomic resolution structure however is available presently only for the HET-s prion domain, and was obtained from solid-state NMR²⁴ (vide infra). It contains mainly β-sheets, which form a triangular hydrophobic core. While this cross-beta structure can be classified as an amyloid, its triangular shape does deviate significantly from amyloid-like structures of smaller peptides.²³Regarding the globular domains, structures have been determined by x-ray crystallography (Ure2p^25,26 and HET-s²⁷), as well as NMR (mammal prions^15,28–30). All reveal a protein fold rich in α-helices, and dimeric structures for the Ure2 and HET-s proteins. The Ure2p fold resembles that of the β-class glutathione S-transferases (GST), but lacks GST activity.²⁵It is a central question for the structural biology of prions if the divide-and-conquer approach imposed by limitations in current structural approaches is valid. Or in other words: can the assembly of full-length prions simply be derived from the sum of the two folds observed for the isolated domains?     

Human non-CG methylation: Are human stem cells plant-like?

Non-CG methylation is well characterized in plants where it appears to play a role in gene silencing and genomic imprinting. Although strong evidence for the presence of non-CG methylation in mammals has been available for some time, both its origin and function remain elusive. In this review we discuss available evidence on non-CG methylation in mammals in light of evidence suggesting that the human stem cell methylome contains significant levels of methylation outside the CG site.Key words: non-CG methylation, stem cells, Dnmt1, Dnmt3a, human methylomeIn plant cells non-CG sites are methylated de novo by Chromomethylase 3, DRM1 and DRM2. Chromomethylase 3, along with DRM1 and DRM2 combine in the maintenance of methylation at symmetric CpHpG as well as asymmetric DNA sites where they appear to prevent reactivation of transposons.¹ DRM1 and DRM2 modify DNA de novo primarily at asymmetric CpH and CpHpH sequences targeted by siRNA.²Much less information is available on non-CG methylation in mammals. In fact, studies on mammalian non-CG methylation form a tiny fraction of those on CG methylation, even though data for cytosine methylation in other dinucleotides, CA, CT and CC, have been available since the late 1980s.³ Strong evidence for non-CG methylation was found by examining either exogenous DNA sequences, such as plasmid and viral integrants in mouse and human cell lines,^4,5 or transposons and repetitive sequences such as the human L1 retrotransposon⁶ in a human embryonic fibroblast cell line. In the latter study, non-CG methylation observed in L1 was found to be consistent with the capacity of Dnmt1 to methylate slippage intermediates de novo.⁶Non-CG methylation has also been reported at origins of replication^7,8 and a region of the human myogenic gene Myf3.⁹ The Myf3 gene is silenced in non-muscle cell lines but it is not methylated at CGs. Instead, it carries several methylated cytosines within the sequence CCTGG. Gene-specific non-CG methylation was also reported in a study of lymphoma and myeloma cell lines not expressing many B lineage-specific genes.¹⁰ The study focused on one specific gene, B29 and found heavy CG promoter methylation of that gene in most cell lines not expressing it. However, in two other cell lines where the gene was silenced, cytosine methylation was found almost exclusively at CCWGG sites. The authors provided evidence suggesting that CCWGG methylation was sufficient for silencing the B29 promoter and that methylated probes based on B29 sequences had unique gel shift patterns compared to non-methylated but otherwise identical sequences.¹⁰ The latter finding suggests that the presence of the non-CG methylation causes changes in the proteins able to bind the promoter, which could be mechanistically related to the silencing seen with this alternate methylation.Non-CG methylation is rarely seen in DNA isolated from cancer patients. However, the p16 promoter region was reported to contain both CG and non-CG methylation in breast tumor specimens but lacked methylation at these sites in normal breast tissue obtained at mammoplasty.¹¹ Moreover, CWG methylation at the CCWGG sites in the calcitonin gene is not found in normal or leukemic lymphocyte DNA obtained from patients.¹² Further, in DNA obtained from breast cancer patients, MspI sites that are refractory to digestion by MspI and thus candidates for CHG methylation were found to carry CpG methylation.¹³ Their resistance to MspI restriction was found to be caused by an unusual secondary structure in the DNA spanning the MspI site that prevents restriction.¹³ This latter observation suggests caution in interpreting EcoRII/BstNI or EcoRII/BstOI restriction differences as due to CWG methylation, since in contrast to the 37°C incubation temperature required for full EcoRII activity, BstNI and BstOI require incubation at 60°C for full activity where many secondary structures are unstable.The recent report by Lister et al.¹⁴ confirmed a much earlier report by Ramsahoye et al.¹⁵ suggesting that non-CG methylation is prevalent in mammalian stem cell lines. Nearest neighbor analysis was used to detect non-CG methylation in the earlier study on the mouse embryonic stem (ES) cell line,¹⁵ thus global methylation patterning was assessed. Lister et al.¹⁴ extend these findings to human stem cell lines at single-base resolution with whole-genome bisulfite sequencing. They report¹⁴ that the methylome of the human H1 stem cell line and the methylome of the induced pluripotent IMR90 (iPS) cell line are stippled with non-CG methylation while that of the human IMR90 fetal fibroblast cell line is not. While the results of the two studies are complementary, the human methylome study addresses locus specific non-CG methylation. Based on that data,¹⁴ one must conclude that non-CG methylation is not carefully maintained at a given site in the human H1 cell line. The average non-CG site is picked up as methylated in about 25% of the reads whereas the average CG methylation site is picked up in 92% of the reads. Moreover, non-CG methylation is not generally present on both strands and is concentrated in the body of actively transcribed genes.¹⁴Even so, the consistent finding that non-CG methylation appears to be confined to stem cell lines,^14,15 raises the possibility that cancer stem cells¹⁶ carry non-CG methylation while their nonstem progeny in the tumor carry only CG methylation. Given the expected paucity of cancer stem cells in a tumor cell population, it is unlikely that bisulfite sequencing would detect non-CG methylation in DNA isolated from tumor cells since the stem cell population is expected to be only a very minor component of tumor DNA. Published sequences obtained by bisulfite sequencing generally report only CG methylation, and to the best of our knowledge bisulfite sequenced tumor DNA specimens have not reported non-CG methylation. On the other hand, when sequences from cell lines have been reported, bisulfite-mediated genomic sequencing⁸ or ligation mediated PCR¹⁷ methylcytosine signals outside the CG site have been observed. In a more recent study plasmid DNAs carrying the Bcl2-major breakpoint cluster¹⁸ or human breast cancer DNA¹³ treated with bisulfite under non-denaturing conditions, cytosines outside the CG side were only partially converted on only one strand¹⁸ or at a symmetrical CWG site.¹³ In the breast cancer DNA study the apparent CWG methylation was not detected when the DNA was fully denatured before bisulfite treatment.¹³In both stem cell studies, non-CG methylation was attributed to the Dnmt3a,^14,15 a DNA methyltransferase with similarities to the plant DRM methyltransferase family¹⁹ and having the capacity to methylate non-CG sites when expressed in Drosophila melanogaster.¹⁵ DRM proteins however, possess a unique permuted domain structure found exclusively in plants¹⁹ and the associated RNA-directed non-CG DNA methylation has not been reproducibly observed in mammals despite considerable published^20–23 and unpublished efforts in that area. Moreover, reports where methylation was studied often infer methylation changes from 5AzaC reactivation studies²⁴ or find that CG methylation seen in plants but not non-CG methylation is detected.^21,22,25,26 In this regard, it is of interest that the level of non-CG methylation reported in stem cells corresponds to background non-CG methylation observed in vitro with human DNA methyltransferase I,²⁷ and is consistent with the recent report that cultured stem cells are epigenetically unstable.²⁸The function of non-CG methylation remains elusive. A role in gene expression has not been ruled out, as the studies above on Myf3 and B29 suggest.^9,10 However, transgene expression of the bacterial methyltransferase M.EcoRII in a human cell line (HK293), did not affect the CG methylation state at the APC and SerpinB5 genes²⁹ even though the promoters were symmetrically de novo methylated at ^mCWGs within each CCWGG sequence in each promoter. This demonstrated that CG and non-CG methylation are not mutually exclusive as had been suggested by earlier reports.^9,10 That observation is now extended to the human stem cell line methylome where CG and non-CG methylation co-exist.¹⁴ Gene expression at the APC locus was likewise unaffected by transgene expression of M.EcoRII. In those experiments genome wide methylation of the CCWGG site was detected by restriction analysis and bisulfite sequencing,²⁹ however stem cell characteristics were not studied.Many alternative functions can be envisioned for non-CG methylation, but the existing data now constrains them to functions that involve low levels of methylation that are primarily asymmetric. Moreover, inheritance of such methylation patterns requires low fidelity methylation. If methylation were maintained with high fidelity at particular CHG sites one would expect that the spontaneous deamination of 5-methylcytosine would diminish the number of such sites, so as to confine the remaining sites to those positions performing an essential function, as is seen in CG methylation.^30–33 However, depletion of CWG sites is not observed in the human genome.³⁴ Since CWG sites account for only about 50% of the non-CG methylation observed in the stem cell methylome¹⁴ where methylated non-CG sites carry only about 25% methylation, the probability of deamination would be about 13% of that for CWG sites that are subject to maintenance methylation in the germ line. Since mutational depletion of methylated cytosines has to have its primary effect on the germ line, if the maintenance of non-CG methylation were more accurate and more widespread, one would have had to argue that stem cells in the human germ lines lack CWG methylation. As it is the data suggests that whatever function non-CG methylation may have in stem cells, it does not involve accurate somatic inheritance in the germ line.The extensive detail on non-CG methylation in the H1 methylome¹⁴ raises interesting questions about the nature of this form of methylation in human cell lines. A key finding in this report is the contrast between the presence of non-CG methylation in the H1 stem cell line and its absence in the IMR90 human fetal lung fibroblast cell line.¹⁴ This suggests that it may have a role in the origin and maintenance of the pluripotent lineage.¹⁴By analogy with the well known methylated DNA binding proteins specific for CG methylation,³⁵ methylated DNA binding proteins that selectively bind sites of non-CG methylation are expected to exist in stem cells. Currently the only protein reported to have this binding specificity is human Dnmt1.^36–38 While Dnmt1 has been proposed to function stoichiometrically³⁹ and could serve a non-CG binding role in stem cells, this possibility and the possibility that other stem-cell specific non-CG binding proteins might exist remain to be been explored.Finally, the nature of the non-CG methylation patterns in human stem cell lines present potentially difficult technical problems in methylation analysis. First, based on the data in the H1 stem cell methylome,⁴⁰ a standard MS-qPCR for non-CG methylation would be impractical because non-CG sites are infrequent, rarely clustered and are generally characterized by partial asymmetric methylation. This means that a PCR primer that senses the 3 adjacent methylation sites usually recommended for MS-qPCR primer design^41,42 cannot be reliably found. For example in the region near Oct4 (Chr6:31,246,431), a potential MS-qPCR site exists with a suboptimal set of two adjacent CHG sites both methylated on the + strand at Chr6:31,252,225 and 31,252,237.^14,40 However these sites were methylated only in 13/45 and 30/52 reads. Thus the probability that they would both be methylated on the same strand is about 17%. Moreover, reverse primer locations containing non-CG methylation sites are generally too far away for practical bisulfite mediated PCR. Considering the losses associated with bisulfite mediated PCR⁴³ the likelihood that such an MS-qPCR system would detect non-CG methylation in the H1 cell line or stem cells present in a cancer stem cell niche^44,45 is very low.The second difficulty is that methods based on the specificity of MeCP2 and similar methylated DNA binding proteins for enriching methylated DNA (e.g., MIRA,⁴⁶ COMPARE-MS⁴⁷) will discard sequences containing non-CG methylation since they require cooperative binding afforded by runs of adjacent methylated CG sites for DNA capture. This latter property of the methylated cytosine capture techniques makes it also unlikely that methods based on 5-methylcytosine antibodies (e.g., meDIP⁴⁸) will capture non-CG methylation patterns accurately since the stem cell methylome shows that adjacent methylated non-CG sites are rare in comparison to methylated CG sites.¹⁴In summary, whether or not mammalian stem cells in general or human stem cells in particular possess functional plant-like methylation patterns is likely to continue to be an interesting and challenging question. At this point we can conclude that the non-CG patterns reported in human cells appear to differ significantly from the non-CG patterns seen in plants, suggesting that they do not have a common origin or function.     

Silicon efflux transporters isolated from two pumpkin cultivars contrasting in Si uptake

The accumulation of silicon (Si) differs greatly with plant species and cultivars due to different ability of the roots to take up Si. In Si accumulating plants such as rice, barley and maize, Si uptake is mediated by the influx (Lsi1) and efflux (Lsi2) transporters. Here we report isolation and functional analysis of two Si efflux transporters (CmLsi2-1 and CmLsi2-2) from two pumpkin (Cucurbita moschata Duch.) cultivars contrasting in Si uptake. These cultivars are used for rootstocks of bloom and bloomless cucumber, respectively. Different from mutations in the Si influx transporter CmLsi1, there was no difference in the sequence of either CmLsi2 between two cultivars. Both CmLsi2-1 and CmLsi2-2 showed an efflux transport activity for Si and they were expressed in both the roots and shoots. These results confirm our previous finding that mutation in CmLsi1, but not in CmLsi2-1 and CmLsi2-2 are responsible for bloomless phenotype resulting from low Si uptake.Key words: silicon, efflux transporter, pumpkin, cucumber, bloomSilicon (Si) is the second most abundant elements in earth''s crust.¹ Therefore, all plants rooting in soils contain Si in their tissues. However Si accumulation in the shoot differs greatly among plant species, ranging for 0.1 to 10% of dry weight.^1–3 In higher plants, only Poaceae, Equisetaceae and Cyperaceae show a high Si accumulation.^2,3 Si accumulation also differs with cultivars within a species.^4,5 These differences in Si accumulation have been attributed to the ability of the roots to take up Si.^6,7Genotypic difference in Si accumulation has been used to produce bloomless cucumber (Cucumis sativus L.).⁸ Bloom (white and fine powders) on the surface of cucumber fruits is primarily composed of silica (SiO₂).⁹ However, nowadays, cucumber without bloom (bloomless cucumber) is more popular in Japan due to its more attractive and distinctly shiny appearance. Bloomless cucumber is produced by grafting cucumber on some specific pumpkin (Cucurbita moschata Duch.) cultivars. These pumpkin cultivars used for bloomless cucumber rootstocks have lower silicon accumulation compared with the rootstocks used for producing bloom cucumber.⁹Our study showed that the difference in Si accumulation between bloom and bloomless root stocks of pumpkin cultivars results from different Si uptake by the roots.¹⁰ Si uptake has been demonstrated to be mediated by two different types of transporters (Lsi1 and Lsi2) in rice, barley and maize.^11–15 Lsi1 is an influx transporter of Si, belonging to a NIP subfamily of aquaporin family.^10,11,13,14 This transporter is responsible for transport of Si from external solution to the root cells.¹¹ On the other hand, Lsi2 is an efflux transporter of Si, belonging to putative anion transporter.¹² Lsi2 releases Si from the root cells towards the xylem. Both Lsi1 and Lsi2 are required for Si uptake by the roots.^11,12 To understand the mechanism underlying genotypic difference in Si uptake, we have isolated and functionally characterized an influx Si transporter CmLsi1 from two pumpkin cultivars used for rootstocks of bloomless and bloom cucumber.¹⁰ Sequence analysis showed only two amino acids difference of CmLsi1 between two pumpkin cultivars. However, CmLsi1 from bloom rootstock [CmLsi1(B⁺)] showed transport activity for Si, whereas that from bloomless rootstock [CmLsi1(B⁻)] did not.¹⁰ Furthermore, we found that loss of Si transport activity was caused by one amino acid mutation at the position of 242 (from proline to leucine).¹⁰ This mutation resulted in failure to be localized at the plasma membrane, which is necessary for functioning as an influx transporter. The mutated protein was localized at the ER.¹⁰ Here, we report isolation and expression analysis of Si efflux transporters from two pumpkin cultivars contrasting in Si uptake and accumulation to examine whether Si efflux transporter is also involved in the bloom and bloomless phenotypes.     

Hypoxia: A novel function for VIN3

VERNALIZATION INSENSITIVE 3 (VIN3) encodes a PHD domain chromatin remodelling protein that is induced in response to cold and is required for the establishment of the vernalization response in Arabidopsis thaliana.¹ Vernalization is the acquisition of the competence to flower after exposure to prolonged low temperatures, which in Arabidopsis is associated with the epigenetic repression of the floral repressor FLOWERING LOCUS C (FLC).^2,3 During vernalization VIN3 binds to the chromatin of the FLC locus,¹ and interacts with conserved components of Polycomb-group Repressive Complex 2 (PRC2).^4,5 This complex catalyses the tri-methylation of histone H3 lysine 27 (H3K27me3),^4,6,7 a repressive chromatin mark that increases at the FLC locus as a result of vernalization.^4,7–10 In our recent paper¹¹ we found that VIN3 is also induced by hypoxic conditions, and as is the case with low temperatures, induction occurs in a quantitative manner. Our experiments indicated that VIN3 is required for the survival of Arabidopsis seedlings exposed to low oxygen conditions. We suggested that the function of VIN3 during low oxygen conditions is likely to involve the mediation of chromatin modifications at certain loci that help the survival of Arabidopsis in response to prolonged hypoxia. Here we discuss the implications of our observations and hypotheses in terms of epigenetic mechanisms controlling gene regulation in response to hypoxia.Key words: arabidopsis, VIN3, FLC, hypoxia, vernalization, chromatin remodelling, survival     

Strigolactones as mediators of plant growth responses to environmental conditions

Strigolactones (SLs) have been recently identified as a new group of plant hormones or their derivatives thereof, shown to play a role in plant development. Evolutionary forces have driven the development of mechanisms in plants that allow adaptive adjustments to a variety of different habitats by employing plasticity in shoot and root growth and development. The ability of SLs to regulate both shoot and root development suggests a role in the plant''s response to its growth environment. To play this role, SL pathways need to be responsive to plant growth conditions, and affect plant growth toward increased adaptive adjustment. Here, the effects of SLs on shoot and root development are presented, and possible feedback loops between SLs and two environmental cues, light and nutrient status, are discussed; these might suggest a role for SLs in plants'' adaptive adjustment to growth conditions.Key words: strigolactones, light, nutrient status, root, shoot, branching, lateral roots, root hairsStrigolactones (SLs) are carotenoid-derived terpenoid lactones suggested to stem from the carotenoid pathway¹ via the activity of various oxygenases.^2,3 SLs production has been demonstrated in both monocotyledons and eudicotyledons (reviewed in ref. ⁴), suggesting their presence in many plant species.⁵ SLs are synthesized mainly in the roots and in some parts of the stem and then move towards the shoot apex (reviewed ref. ⁷).^6,8,9SLs were first characterized more than 40 years ago as germination stimulants of the parasitic plants Striga and Orobanche and later, as stimulants of arbuscular mycorrhiza hyphal branching as well (reviewed in ref. ^{4, 10–13}). Recently, SLs or derivatives thereof, have been identified as a new group of plant hormones, shown to play a role in inhibition of shoot branching,^2,3,8,9 thereby affecting shoot architecture; more recently they have also been shown to affect root growth by affecting auxin efflux.¹⁴Plants have developed mechanisms that allow adaptive adjustments to a variety of different habitats by employing plasticity in their growth and development.¹⁵ Shoot architecture is affected by environmental cues, such as light quality and quantity and nutrient status.^16–19 Root-system architecture and development are affected by environmental conditions such as nutrient availability (reviewed in ref. ^{20, 21}). At the same time, plant hormones are known to be involved in the regulation of plant growth, development and architecture (reviewed in ref. ^22–24) and to be mediators of the effects of environmental cues on plant development; one classic example is auxin''s role in the plant''s shade-avoidance response (reviewed in ref. ²⁵).The ability of SLs to regulate shoot and root development suggests that these phytohormones also have a role in the plant''s growth response to its environment. To play this putative role, SL pathways need to be responsive to plant growth conditions, and affect plant growth toward enhancing its adaptive adjustment. The present review examines the SLs'' possible role in adaptive adjustment of the plant''s response to growth conditions, by discussing their effect on plant development and the possible associations and feedback loops between SLs and two environmental cues: light and nutrient status.     

Plant defensins: Defense,development and application

Plant defensins are small, highly stable, cysteine-rich peptides that constitute a part of the innate immune system primarily directed against fungal pathogens. Biological activities reported for plant defensins include antifungal activity, antibacterial activity, proteinase inhibitory activity and insect amylase inhibitory activity. Plant defensins have been shown to inhibit infectious diseases of humans and to induce apoptosis in a human pathogen. Transgenic plants overexpressing defensins are strongly resistant to fungal pathogens. Based on recent studies, some plant defensins are not merely toxic to microbes but also have roles in regulating plant growth and development.Key words: defensin, antifungal, antimicrobial peptide, development, innate immunityDefensins are diverse members of a large family of cationic host defence peptides (HDP), widely distributed throughout the plant and animal kingdoms.^1–3 Defensins and defensin-like peptides are functionally diverse, disrupting microbial membranes and acting as ligands for cellular recognition and signaling.⁴ In the early 1990s, the first members of the family of plant defensins were isolated from wheat and barley grains.^5,6 Those proteins were originally called γ-thionins because their size (∼5 kDa, 45 to 54 amino acids) and cysteine content (typically 4, 6 or 8 cysteine residues) were found to be similar to the thionins.⁷ Subsequent “γ-thionins” homologous proteins were indentified and cDNAs were cloned from various monocot or dicot seeds.⁸ Terras and his colleagues⁹ isolated two antifungal peptides, Rs-AFP1 and Rs-AFP2, noticed that the plant peptides'' structural and functional properties resemble those of insect and mammalian defensins, and therefore termed the family of peptides “plant defensins” in 1995. Sequences of more than 80 different plant defensin genes from different plant species were analyzed.¹⁰ A query of the UniProt database (www.uniprot.org/) currently reveals publications of 371 plant defensins available for review. The Arabidopsis genome alone contains more than 300 defensin-like (DEFL) peptides, 78% of which have a cysteine-stabilized α-helix β-sheet (CSαβ) motif common to plant and invertebrate defensins.¹¹ In addition, over 1,000 DEFL genes have been identified from plant EST projects.¹²Unlike the insect and mammalian defensins, which are mainly active against bacteria,^2,3,10,13 plant defensins, with a few exceptions, do not have antibacterial activity.¹⁴ Most plant defensins are involved in defense against a broad range of fungi.^2,3,10,15 They are not only active against phytopathogenic fungi (such as Fusarium culmorum and Botrytis cinerea), but also against baker''s yeast and human pathogenic fungi (such as Candida albicans).² Plant defensins have also been shown to inhibit the growth of roots and root hairs in Arabidopsis thaliana¹⁶ and alter growth of various tomato organs which can assume multiple functions related to defense and development.⁴