Crystal structure of the Legionella effector Lem22

Legionella pneumophila is a pathogen causing severe pneumonia in humans called Legionnaires’ disease. Lem22 is a previously uncharacterized effector protein conserved in multiple Legionella strains. Here, we report the crystal structure of Lem22 from the Philadelphia strain, also known as lpg2328, at 1.40 Å resolution. The structure shows an up‐and‐down three‐helical bundle with a significant structural similarity to a number of protein‐binding domains involved in apoptosis and membrane trafficking. Sequence conservation identifies a putative functional site on the interface of helices 2 and 3. The structure is an important step toward a functional characterization of Lem22.     

Spatial patterns in a two-tiered semi-arid shrubland in southeastern Spain

Abstract. Single species and bivariate distribution patterns in a semi-arid shrubland in southeastern Spain, dominated by the tall leguminous shrub Retama sphaerocarpa, were investigated by second-order spatial analysis based on Ripley's K-function. Shrubs were significantly clumped because of a strong association of dwarf shrubs, mostly Artemisia barrelieri, under the canopy of Retama. Retama shrubs were randomly distributed, but when different size-classes were analysed separately, the pattern changed from significantly clumped to random and then to regular with increasing canopy diameter, suggesting increasing intraspecific competition with shrub size. Artemisia was significantly clumped at all scales because of aggregation under the canopy of large Retama shrubs. The association between the species became stronger with increasing canopy diameter of Retama shrubs, suggesting that facilitation prevailed over interspecific competition because of niche separation in different tiers, both above and below ground. Retama shrub size thus determined both the type of pattern for its own size class and tier, and the scale and intensity of the association with its understorey shrubs.     

Callus formation and plant regeneration from tubercles of Coryphantha elephantidens (Lem.) Lem.

Summary Callus cultures were established from pith tissue of Coryphantha elephantidens (Lem.) Lem. on Murashige and Skoog (MS) basal medium supplemented with 9.05 μM 2,4-dichlorophenoxyacetic acid (2,4-D) and 2.3 μM kinetin. Highest shoot regeneration frequency was observed on a medium containing 6.9 μM kinetin and 2.3 μM 2,4-D under 30 μE m⁻² s⁻¹ light intensity with a 16-h photoperiod. Calluses retained organogenic potential throughout several passages of subculture (18 mo.). Shoots were rooted on MS medium without plant growth regulators. All (100%) plantlets transplanted to soil survived acclimatization. Regenerated plants showed good overall growth and were morphologically similar to the mother plants.     

Spatial pattern in Anthyllis cytisoides shrubland on abandoned land in southeastern Spain

Abstract. Univariate and bivariate distribution patterns of small shrubs on abandoned land in semi-arid southeastern Spain were investigated by second-order spatial analysis (Ripley's K-function). All shrubs (Anthyllis cytisoides and subdominant Artemisia barrelieri) were either randomly distributed or clumped at scales of 0.25 - 1.0 m. The pattern shown by A. cytisoides shrubs alone changed from clumped to random with decreasing density. Pattern analysis and demographic data suggest a successive replacement of A. barrelieri, which had high proportions (44 - 86 %) of dead shrubs, by the dominant A. cytisoides. In two of three plots there was a positive association between A. cytisoides and A. barrelieri at a scale of 0.25 - 0.5 m. In the third plot, believed to represent a more advanced stage of colonization, there was a negative association (repulsion) between the two species, presumably as a result of interspecific competition from A. cytisoides. Dead shrubs present in spring 1994 were randomly distributed in all plots. Living and dead A. cytisoides shrubs were positively associated at a scale of 0.5 m, suggesting that the shrubs died as a result of intraspecific competition in small clumps. The shrubland previously dominated by A. barrelieri is changing to A. cytisoides shrubland with increasing biomass and ground cover.     

Effects of pioneer shrubs on the recruitment of the fleshy‐fruited tree Olea europaea ssp. cuspidata in Afromontane savanna

Question: Is seedling recruitment of a fleshy‐fruited tree in degraded Afromontane savanna dependent on shelter from pioneer shrubs, and is shelter availability related to shrub traits? Location: Degraded montane savanna in northern Ethiopia (13°36′N, 39°21′E). Method: Nurse plants of Olea europaea ssp. cuspidata seedlings were recorded using T‐square plotless sampling and clustered according to shrub traits, using Ward's method after Principal Components Analysis. Facilitation was further examined through experimental planting and Kaplan‐Meier survival analysis. Results: Both in grazed and protected areas, Olea recruits were found exclusively under shrubs, primarily under Euclea racemosa although Acacia etbaica was more abundant. Olea recruitment is distributed randomly at landscape scale, but depends on shelter at patch scale. Shelter ability is related to shrub shape and species identity. Dense multi‐stemmed shrubs with a wide base and crown on a mulch‐rich mound are key recruitment foci. Euclea shrubs have these favoured traits and probably act as preferential perching sites for avian seed dispersers. Soil and organic matter accumulation under Euclea shrubs may also create favourable conditions for Olea germination and survival. Experimentally planted seedlings had a better chance for survival under Euclea. Conclusions: Olea regeneration is probably subject to both passive (disperser‐mediated) and active facilitation. Small changes of shrub traits can alter the suitability of a patch for Olea recruitment. Protection of shrubs can increase facilitation for seedlings, while pruning may reduce competition for saplings and thus enhance forest succession. Planting of raised Olea seedlings under Euclea shrubs in years with a good rainy season may further assist forest restoration.     

Facilitation by pioneer shrubs for the ecological restoration of riparian forests in the Central Andes of Colombia

Riparian vegetation has great functional importance in agroscapes because it establishes physical connections between natural ecosystems embedded in an agricultural matrix. Throughout the tropics, the historical demand for cropland and pastures in the lands adjacent to streams has led to the replacement of forests by exotic grasses. In order to find new methods for initiating the restoration of riparian forests, we evaluated the use of the pioneer shrubs Tithonia diversifolia and Piper auritum as nurse species for their effects on (1) competition with dominant grasses; (2) natural regeneration and the ecological facilitation of six native tree species of different successional stages; and (3) influence on microclimate. Over a period of 15 months, 4.4% coverage of P. auritum was insufficient to inhibit grasses. In contrast, 81% coverage of T. diversifolia limited the growth of dominant grasses such as Cenchrus purpureus, Paspalum paniculatum, and Cynodon plectostachyus likely by intercepting more than 90% of photosynthetically active radiation (PAR), even though other factors cannot be ruled out. T. diversifolia showed simultaneous effects of facilitation and competition by promoting higher survival of the planted native trees while slowing the growth of pioneer species and inhibiting the regeneration of native woody plants probably as a result of high light interception. This study suggests that planting T. diversifolia as a nurse shrub may facilitate early stages of restoration by inhibiting the growth of pastures, but requires pruning, both to increase light availability and promote the growth of planted trees and the recruitment of woody plants.     

The small scale spatial pattern of C3 and C4 grasses depends on shrub distribution

At micro‐site scale, the spatial pattern of a plant species depends on several factors including interactions with neighbours. It has been seen that unfavourable effects generate a negative association between plants, while beneficial effects generate a positive association. In grasslands, the presence of shrubby species promotes a particular microenvironment beneath their canopy that could affect differently the spatial distribution of plants with different tolerance to abiotic conditions. We measured photosynthetic active radiation, air temperature and wind speed under shrub canopies and in adjacent open sites and analysed the spatial distribution of four grass species (two C₃ and two C₄) in relation to shrub canopy in a grazed sub‐humid natural grassland in southern Uruguay. Radiation, air temperature and wind speed were lower under shrubs than in adjacent open sites. The spatial distribution of grasses relative to the shrub canopy varied depending on the photosynthetic metabolism of grasses. C₄ grasses showed a negative association or no correlation with the shrubs, whereas C₃ grasses showed a positive association. Our results highlight the importance of the photosynthetic metabolism of the grasses in the final outcome of interactions between grasses and shrubs. Micro‐environmental conditions generated underneath shrubs create a more suitable site for the establishment of C₃ than for C₄ grasses. These results show that facilitation could be more important than previously thought in sub‐humid grasslands.     

All in the family: evidence for four new LEM-domain proteins Lem2 (NET-25), Lem3, Lem4 and Lem5 in the human genome

LEM-domain proteins share a folded structure, the 'LEM-domain', which binds a conserved chromatin protein named BAF. Most LEM-domain proteins are found at the nuclear membrane, but some are nucleoplasmic. All characterized members of this family bind nuclear lamin filaments. We summarize the 'founding' LEM-domain proteins LAP2, emerin and MAN1 ('SANE' or 'XMAN' in Xenopus) and their emerging roles in gene regulation and nuclear assembly. These roles are placed in the context of human diseases ('laminopathies') caused by mutations in either emerin or A-type lamins. Other LEM-domain proteins might modify the phenotype or severity of human laminopathy, or cause new laminopathies. We summarize evidence that the human genome encodes at least four additional LEM-domain proteins, designated Lem2 (NET-25), Lem3, Lem4 and Lem5. Early adaptation of a consistent nomenclature, such as the "Lem" names proposed here, will facilitate rapid progress in this field. Further investigation of 'founder' and novel members of this family will be important to understand nuclear structure, and presents new opportunities to understand human disease.     

Phospholipid Flippases Lem3p-Dnf1p and Lem3p-Dnf2p Are Involved in the Sorting of the Tryptophan Permease Tat2p in Yeast

The type 4 P-type ATPases are flippases that generate phospholipid asymmetry in membranes. In budding yeast, heteromeric flippases, including Lem3p-Dnf1p and Lem3p-Dnf2p, translocate phospholipids to the cytoplasmic leaflet of membranes. Here, we report that Lem3p-Dnf1/2p are involved in transport of the tryptophan permease Tat2p to the plasma membrane. The lem3Δ mutant exhibited a tryptophan requirement due to the mislocalization of Tat2p to intracellular membranes. Tat2p was relocalized to the plasma membrane when trans-Golgi network (TGN)-to-endosome transport was inhibited. Inhibition of ubiquitination by mutations in ubiquitination machinery also rerouted Tat2p to the plasma membrane. Lem3p-Dnf1/2p are localized to endosomal/TGN membranes in addition to the plasma membrane. Endocytosis mutants, in which Lem3p-Dnf1/2p are sequestered to the plasma membrane, also exhibited the ubiquitination-dependent missorting of Tat2p. These results suggest that Tat2p is ubiquitinated at the TGN and missorted to the vacuolar pathway in the lem3Δ mutant. The NH₂-terminal cytoplasmic region of Tat2p containing ubiquitination acceptor lysines interacted with liposomes containing acidic phospholipids, including phosphatidylserine. This interaction was abrogated by alanine substitution mutations in the basic amino acids downstream of the ubiquitination sites. Interestingly, a mutant Tat2p containing these substitutions was missorted in a ubiquitination-dependent manner. We propose the following model based on these results; Tat2p is not ubiquitinated when the NH₂-terminal region is bound to membrane phospholipids, but if it dissociates from the membrane due to a low level of phosphatidylserine caused by perturbation of phospholipid asymmetry in the lem3Δ mutant, Tat2p is ubiquitinated and then transported from the TGN to the vacuole.     

Effects of ultraviolet–B irradiances on soybean

Soybean [Glycine max (L.) Merr. cv. Hardee] and wheat (Triticum aestivum L. cv. Jori) were grown from seed under four ultraviolet-B irradiances and four levels of photosynthetically active radiation in a factorial design. The effects of ultraviolet-B radiation on leaf number and area, total dry matter production, dry weight of component organs, and plant height were compared between soybean and wheat. Ultraviolet-B radiation effects were dependent upon the level of photosynthetically active radiation incident during growth. Wheat and soybeans were both affected by low ultraviolet-B radiation flux densities; however, they differed markedly in their growth responses and biomass allocation patterns. Substantial interactions between ultraviolet-B and photosynthetically active radiation indicate a need for the measurement of longer wavelength radiation when evaluating the effects of ultraviolet-B radiation on plant growth in natural conditions.     

Giant clams in shallow reefs: UV-resistance mechanisms of Tridacninae in the Red Sea

The photosymbiosis of tropical giant clams (subfamily Tridacninae) with unicellular algae (Symbiodiniaceae) restricts their distribution to the sunlit, shallow waters of the euphotic zone where organisms are additionally exposed to potentially damaging levels of solar UV radiation. Metabolic and physiological responses of Red Sea Tridacna maxima clams, including net calcification and primary production, as well as valvometry (i.e., shell gaping behavior) were assessed when exposed to simulated high radiation levels received at 3 and 5 m underwater. The two levels of radiation included exposure treatments to photosynthetically active radiation (PAR; 400–700 nm) alone and to both, PAR and ultraviolet-B radiation (UV-B; 280–315 nm). The valvometry data obtained using flexible magnetic sensors indicated that specimens under PAR + UV-B exposure significantly reduced the proportion of their exposed mantle area, a potential photo-protective mechanism which, however, reduces the overall amount of PAR received by the algal symbionts. Consequently, specimens under PAR + UV-B displayed a slight, although non-significant, reduction in primary production rates but no signs of additional oxidative stress, changes in symbiont densities, chlorophyll content, or levels of mycosporine-like amino acids. Net calcification rates of T. maxima were not affected by exposure to UV-B; however, calcification was positively correlated with incident PAR levels. UV-B exposure changes the valvometry, reducing the exposed mantle area which consequently diminishes the available PAR for the photosymbionts. Still, T. maxima maintains high rates of primary production and net calcification, even under high levels of UV-B. This provides experimental support for a recently described, effective UV-defensive mechanism in Tridacninae, in which the photonic cooperation of the associated algal symbionts and giant clam iridocytes is assumed to establish optimal conditions for the photosynthetic performance of the clams’ symbionts.

     

In vitro propagation of Agave fourcroydes Lem. (Henequen)

In vitro plant regeneration of Agave fourcroydes Lem. (Agavaceae) is described. Results suggest that the NO₃ ^-:NH₄ ⁺ balance in the culture medium is a key factor controlling callus growth and organogenesis in rhizome cultures. Stem callus showed limited organogenic capacity, but high cytokinin concentrations induced adventitious shoot formation on stem explants. When these shoots were excised and subcultured, new callus formed at their base from which new shoots arose. The shoots from stem explants and rhizome callus formed extensive root systems in vitro and were transferred to pot culture with a 90% survival rate.     

Variation in species light acquisition traits under fluctuating light regimes: implications for non‐equilibrium coexistence

Resource distribution heterogeneity offers niche opportunities for species with different functional traits to develop and potentially coexist. Available light (photosynthetically active radiation or PAR) for suspended algae (phytoplankton) may fluctuate greatly over time and space. Species‐specific light acquisition traits capture important aspects of the ecophysiology of phytoplankton and characterize species growth at either limiting or saturating daily PAR supply. Efforts have been made to explain phytoplankton coexistence using species‐specific light acquisition traits under constant light conditions, but not under fluctuating light regimes that should facilitate non‐equilibrium coexistence. In the well‐mixed, hypertrophic Lake TaiHu (China), we incubated the phytoplankton community in bottles placed either at fixed depths or moved vertically through the water column to mimic vertical mixing. Incubations at constant depths received only the diurnal changes in light, while the moving bottles received rapidly fluctuating light. Species‐specific light acquisition traits of dominant cyanobacteria (Anabaena flos‐aquae, Microcystis spp.) and diatom (Aulacoseira granulata, Cyclotella pseudostelligera) species were characterized from their growth–light relationships that could explain relative biomasses along the daily PAR gradient under both constant and fluctuating light. Our study demonstrates the importance of interspecific differences in affinities to limiting and saturating light for the coexistence of phytoplankton species in spatially heterogeneous light conditions. Furthermore, we observed strong intraspecific differences in light acquisition traits between incubation under constant and fluctuating light – leading to the reversal of light utilization strategies of species. This increased the niche space for acclimated species, precluding competitive exclusion. These observations could enhance our understanding of the mechanisms behind the Paradox of the Plankton.     

A proximal upstream sequence controls tissue-specific expression of <Emphasis Type="Italic">Lem2</Emphasis>, a salicylate-inducible barley lectin-like gene

The lemma and palea (lemma/palea), which form the husk of barley (Hordeum vulgare L.) seeds, constitutively express high levels of defense-related genes, relative to leaves [Abebe et al. (2004) Crop Sci 44:942–950]. One of these genes, Lem2, is expressed mainly in the lemma/palea and coleoptile and is strongly upregulated by salicylic acid (SA) and its functional analog 2,6-dichloroisonicotinic acid . Induction by SA was rapid, occurring within 4 h of treatment. However, Lem2 is not responsive to methyl jasmonate (MeJA) or wounding and is downregulated by drought, dehydration, and abscisic acid. These results suggest that Lem2 is involved in systemic acquired resistance. Sequence analysis showed that LEM2 is a jacalin-related lectin (JRL)-like protein with two domains. Consistent with northern and western blot data, transient expression analyses using Lem2::gfp constructs showed strong expression in lemmas and a trace expression in leaves. Successive 5 deletions of the 1,414 bp upstream region gradually weakened promoter strength, as measured by real-time PCR. Promoter deletion studies also revealed that the –75/+70 region (containing the TATA box, 5 UTR, and a SA-response element) determines tissue specificity and that the distal promoter region simply enhances expression. Southern analysis indicated that Morex barley has at least three copies of the Lem2 gene arranged in tandem on chromosome 5(1H) Bin 02, near the short arm telomere. Lem2 is not present in the barley cultivars Steptoe, Harrington, Golden Promise, and Q21861.Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U. S. Department of Agriculture     

Radiation-constrained boundaries cause nonuniform responses of the carbon uptake phenology to climatic warming in the Northern Hemisphere

Climatic warming has lengthened the photosynthetically active season in recent decades, thus affecting the functioning and biogeochemistry of ecosystems, the global carbon cycle and climate. Temperature response of carbon uptake phenology varies spatially and temporally, even within species, and daily total intensity of radiation may play a role. We empirically modelled the thresholds of temperature and radiation under which daily carbon uptake is constrained in the temperate and cold regions of the Northern Hemisphere, which include temperate forests, boreal forests, alpine and tundra biomes. The two-dimensionality of the temperature-radiation constraint was reduced to one single variable, θ, which represents the angle in a polar coordinate system for the temperature-radiation observations during the start and end of the growing season. We found that radiation will constrain the trend towards longer growing seasons with future warming but differently during the start and end of season and depending on the biome type and region. We revealed that radiation is a major factor limiting photosynthetic activity that constrains the phenology response to temperature during the end-of-season. In contrast, the start of the carbon uptake is overall highly sensitive to temperature but not constrained by radiation at the hemispheric scale. This study thus revealed that while at the end-of-season the phenology response to warming is constrained at the hemispheric scale, at the start-of-season the advance of spring onset may continue, even if it is at a slower pace.     

Evaluating a three dimensional model of diffuse photosynthetically active radiation in maize canopies

Diffuse photosynthetically active radiation (DPAR) is important during overcast days and for plant parts shaded from the direct beam radiation. Simulation of DPAR interception by individual plant parts of a canopy, separately from direct beam photosynthetically active radiation (PAR), may give important insights into plant ecology. This paper presents a model to simulate the interception of DPAR in plant canopies. A sub-model of a virtual maize canopy was reconstructed. Plant surfaces were represented as small triangular facets positioned according to three-dimensionally (3D) digitized data collected in the field. Then a second sub-model to simulate the 3D DPAR distribution in the canopy was developed by dividing the sky hemisphere into a grid of fine cells that allowed for the anisotropic distribution of DPAR over the sky hemisphere. This model, DSHP (Dividing Sky Hemisphere with Projecting), simulates which DSH (Divided Sky Hemisphere) cells are directly visible from a facet in the virtual canopy, i.e. not obscured by other facets. The DPAR reaching the center of a facet was calculated by summing the amounts of DPAR present in every DSH cell. The distribution of DPAR in a canopy was obtained from the calculated DPARs intercepted by all facets in the canopy. This DSHP model was validated against DPAR measurements made in an actual maize (Zea mays L.) canopy over selected days during the early filling stage. The simulated and measured DPAR at different canopy depths showed a good agreement with a R ² equaling 0.78 (n=120).     

Geographic variation in cone volatiles and pollinators in the thermogenic African cycad Encephalartos ghellinckii Lem

• Heat and odour production can have profound effects on pollination in cycads. It is therefore expected that these traits would co‐vary geographically with pollinator assemblages. Such intraspecific variation, may lead to the evolution of pollination ecotypes, which can be an early stage of pollinator‐mediated speciation.
• We measured cone temperatures using miniature temperature data loggers and examined the composition of cone volatile odours using headspace sampling and analysis with gas chromatography‐mass spectrometry in four populations spanning the range of the African cycad Encephalartos ghellinckii. Pollinator assemblages were also investigated in three populations.
• Male and female cones were thermogenic at pollen shed and receptive stages, respectively, but patterns of thermogenesis did not vary among populations. Scent emissions from cones in populations in the Drakensberg Mountains were characterised by cis‐β‐ocimene, β‐myrcene and (3E)‐1,3‐octadiene, while camphene and α‐pinene were characteristic of scent emissions from cones in populations closer to the coast. These differences in volatile blends corresponded with differences in insect assemblages.
• These results confirm intraspecific variation in volatile emissions of E. ghellinckii and support the predictions that intraspecific variation in volatile emissions will be associated with shifts in pollinator assemblages. While further work needs to be done to test for local adaptation in this system, this preliminary evidence is consistent with the formation of pollination ecotypes in the E. ghellinckii species complex.

     

Research note: Irradiance of photosynthetically active radiation determines ultraviolet-susceptibility of photosynthesis in Ulva lactuca L.(Chlorophyta)

The respective ratio of photosynthetically active to ultraviolet radiation is of crucial importance to results obtained in ultraviolet (UV)‐research on photoautotrophic organisms. Specimens of the green macroalga Ulva lactuca L. were exposed to a constant irradiance of UV‐radiation at increasing irradiances of photosynthetically active radiation (PAR). The effects of experimental irradiance and spectral composition on photoinhibition of photosynthesis and its recovery were monitored by chlorophyll fluorescence measurements and the activity of the xanthophyll cycle was assessed by high performance liquid chromatography‐(HPLC) based pigment analysis. Results indicate a UV‐induced delay in recovery from PAR‐induced photoinhibition and a deceleration of violaxanthin conversion within the xanthophyll cycle due to the presence of UV‐radiation. Also the concentration of the protective pigment lutein increased considerably and could be indicative of the existence of an additional light‐protective mechanism, as, for example, the lutein‐epoxid cycle in Ulva. In total, results clearly show that the extent of UV‐induced inhibition of photosynthesis to be found in UV‐exposure experiments is highly dependent on the irradiance of background photosynthetically active radiation: with increasing irradiance of PAR the UV‐effects were diminished. Exemplified by the green algae Ulva lactuca this study demonstrates the crucial importance of the ratios of PAR:UV applied in UV‐research, particularly when conducting laboratory experiments in an ecological context.     

Shrubs as ecosystem engineers in a coastal dune: influences on plant populations,communities and ecosystems

Question: How do two shrubs with contrasting life‐history characteristics influence abundance of dominant plant taxa, species richness and aboveground biomass of grasses and forbs, litter accumulation, nitrogen pools and mineralization rates? How are these shrubs – and thus their effects on populations, communities and ecosystems – distributed spatially across the landscape? Location: Coastal hind‐dune system, Bodega Head, northern California. Methods: In each of 4 years, we compared vegetation, leaf litter and soil nitrogen under canopies of two native shrubs –Ericameria ericoides and the nitrogen‐fixing Lupinus chamissonis– with those in adjacent open dunes. Results: At the population level, density and cover of the native forb Claytonia perfoliata and the exotic grass Bromus diandrus were higher under shrubs than in shrub‐free areas, whereas they were lower under shrubs for the exotic grass Vulpia bromoides. In contrast, cover of three native moss species was highest under Ericameria and equally low under Lupinus and shrub‐free areas. At community level, species richness and aboveground biomass of herbaceous dicots was lower beneath shrubs, whereas no pattern emerged for grasses. At ecosystem level, areas beneath shrubs accumulated more leaf litter and had larger pools of soil ammonium and nitrate. Rates of nitrate mineralization were higher under Lupinus, followed by Ericameria and then open dune. At landscape level, the two shrubs – and their distinctive vegetation and soils – frequently had uniform spatial distributions, and the distance separating neighbouring shrubs increased as their combined sizes increased. Conclusions: Collectively, these data suggest that both shrubs serve as ecosystem engineers in this coastal dune, having influences at multiple levels of biological organization. Our data also suggest that intraspecific competition influenced the spatial distributions of these shrubs and thus altered the distribution of their effects throughout the landscape.