Phenotypic Plasticity Contributes to Maize Adaptation and Heterosis

Plant phenotypic plasticity describes altered phenotypic performance of an individual when grown in different environments. Exploring genetic architecture underlying plant plasticity variation may help mitigate the detrimental effects of a rapidly changing climate on agriculture, but little research has been done in this area to date. In the present study, we established a population of 976 maize F₁ hybrids by crossing 488 diverse inbred lines with two elite testers. Genome-wide association study identified hundreds of quantitative trait loci associated with phenotypic plasticity variation across diverse F₁ hybrids, the majority of which contributed very little variance, in accordance with the polygenic nature of these traits. We identified several quantitative trait locus regions that may have been selected during the tropical-temperate adaptation process. We also observed heterosis in terms of phenotypic plasticity, in addition to the traditional genetic value differences measured between hybrid and inbred lines, and the pattern of which was affected by genetic background. Our results demonstrate a landscape of phenotypic plasticity in maize, which will aid in the understanding of its genetic architecture, its contribution to adaptation and heterosis, and how it may be exploited for future maize breeding in a rapidly changing environment.     

Photosynthetic and Photorespiratory Characteristics of Mutants of Hordeum vulgare L

The relationship between photosynthesis and photorespiration was determined in normal and 26 mutants of barley (Hordeum vulgare L. var. Himalaya). The rate of apparent photosynthesis ranged from 1 to 30 milligrams of CO₂ per square decimeter per hour. The variation in rate of photosynthesis was due, in some cases, to differences in chlorophyll content, in others to stomatal resistance, and in still others to unknown factors; but no single factor accounted for the variation. Photorespiratory activity, as determined by the ¹⁴CO₂/¹²CO₂ technique, CO₂ evolution into CO₂-free air, and the response of photosynthesis to low and high O₂ concentrations, was positively and significantly correlated with photosynthesis. This supports the idea that the two processes are integrally and tightly coupled. There appears to be no competition between photosynthesis and photorespiration, and the probability of finding plants with high rates of photosynthesis and low rates of photorespiration measured under natural conditions, appears to be very low.     

Dynamic Balancing of Isoprene Carbon Sources Reflects Photosynthetic and Photorespiratory Responses to Temperature Stress

The volatile gas isoprene is emitted in teragrams per annum quantities from the terrestrial biosphere and exerts a large effect on atmospheric chemistry. Isoprene is made primarily from recently fixed photosynthate; however, alternate carbon sources play an important role, particularly when photosynthate is limiting. We examined the relative contribution of these alternate carbon sources under changes in light and temperature, the two environmental conditions that have the strongest influence over isoprene emission. Using a novel real-time analytical approach that allowed us to examine dynamic changes in carbon sources, we observed that relative contributions do not change as a function of light intensity. We found that the classical uncoupling of isoprene emission from net photosynthesis at elevated leaf temperatures is associated with an increased contribution of alternate carbon. We also observed a rapid compensatory response where alternate carbon sources compensated for transient decreases in recently fixed carbon during thermal ramping, thereby maintaining overall increases in isoprene production rates at high temperatures. Photorespiration is known to contribute to the decline in net photosynthesis at high leaf temperatures. A reduction in the temperature at which the contribution of alternate carbon sources increased was observed under photorespiratory conditions, while photosynthetic conditions increased this temperature. Feeding [2-¹³C]glycine (a photorespiratory intermediate) stimulated emissions of [¹³C_1–5]isoprene and ¹³CO₂, supporting the possibility that photorespiration can provide an alternate source of carbon for isoprene synthesis. Our observations have important implications for establishing improved mechanistic predictions of isoprene emissions and primary carbon metabolism, particularly under the predicted increases in future global temperatures.Many plant species emit isoprene (2-methyl-1,3-butadiene [C₅H₈]) into the atmosphere at high rates (Sharkey and Yeh, 2001). With an estimated emission rate of 500 to 750 teragram per year by terrestrial ecosystems (Guenther et al., 2006), isoprene exerts a strong control over the oxidizing capacity of the atmosphere. Due to its high reactivity to oxidants, it fuels an array of atmospheric chemical and physical processes affecting air quality and climate, including the production of ground-level ozone in environments with elevated concentrations of nitrogen oxides (Atkinson and Arey, 2003; Pacifico et al., 2009) and the formation/growth of organic aerosols (Nguyen et al., 2011). At the plant level, isoprene provides protection from stress, through stabilizing membrane processes (Sharkey and Singsaas, 1995; Velikova et al., 2011) and/or reducing the accumulation of damaging reactive oxygen species in plant tissues under stress (Loreto et al., 2001; Vickers et al., 2009b; Velikova et al., 2012). While the mechanism(s) are still under investigation, isoprene may directly or indirectly stabilize hydrophobic interactions in membranes (Singsaas et al., 1997), minimize lipid peroxidation (Loreto and Velikova, 2001), and directly react with reactive oxygen species (Kameel et al., 2014), yielding first-order oxidation products methyl vinyl ketone and methacrolein (Jardine et al., 2012, 2013). The two main environmental drivers for global changes in isoprene fluxes are light and temperature (Guenther et al., 2006). Isoprene production is closely linked to net photosynthesis, and both isoprene emissions and net photosynthesis are controlled by light intensity (Monson and Fall, 1989). There is also a positive correlation between net photosynthesis and isoprene emissions as leaf temperatures increase up to the optimum temperature for net photosynthesis (Monson et al., 1992).Despite the close correlation between photosynthesis and isoprene emissions, plant enclosure observations and leaf-level analyses have both shown that the fraction of net photosynthesis dedicated to isoprene emissions is not constant. During stress events that decrease net photosynthetic rates, isoprene emissions are often less affected or even stimulated; this results in an increase in relative isoprene production from 1% to 2% of net photosynthesis under normal conditions to 15% to 50% under extreme stress (Goldstein et al., 1998; Fuentes et al., 1999; Kesselmeier et al., 2002; Harley et al., 2004). In severe stress conditions such as drought, isoprene emissions can even continue in the complete absence of photosynthesis (Fortunati et al., 2008). An uncoupling of isoprene emissions from net photosynthesis has also been observed in a number of other studies where the optimum temperature for isoprene emissions was found to be substantially higher than that of net photosynthesis; under the high-temperature conditions, isoprene emissions can account for more than 50% of net photosynthesis (Sharkey and Loreto, 1993; Lerdau and Keller, 1997; Harley et al., 2004; Magel et al., 2006).Analyses of carbon sources using ¹³CO₂ leaf labeling have revealed that under standard conditions (i.e. leaf temperature of 30°C and photosynthetically active radiation [PAR] levels of 1,000 µmol m^–2 s^–1), isoprene is produced primarily (70%–90%) using carbon directly derived from the Calvin cycle (Delwiche and Sharkey, 1993; Affek and Yakir, 2002; Karl et al., 2002) via the chloroplastic methylerythritol phosphate (MEP) isoprenoid pathway (Zeidler et al., 1997). The relative contributions of photosynthetic and alternate carbon sources for isoprene are now recognized as being variable under different environmental conditions. Changes in net photosynthesis rates under drought stress (Funk et al., 2004; Brilli et al., 2007), salt stress (Loreto and Delfine, 2000), and changes in ambient O₂ and CO₂ concentrations (Jones and Rasmussen, 1975; Karl et al., 2002; Trowbridge et al., 2012) alter their relative contributions. Under heat stress-induced photosynthetic limitation in Populus deltoides (a temperate species), an increase in the relative contribution of alternate carbon sources was also observed (Funk et al., 2004). However, our current understanding of the responses of isoprene carbon sources to changes in temperature and light levels is poor, and the connection(s) of these responses to changes in leaf primary carbon metabolism (e.g. photosynthesis, photorespiration, and respiration) remains to be determined.Studies over the last decade have shown or suggested that potential alternate carbon sources include refixation of respired CO₂ (Loreto et al., 2004), intermediates from the cytosolic mevalonate (MVA) isoprenoid pathway (Flügge and Gao, 2005; Lichtenthaler, 2010), and intermediates from central carbon metabolism, including pyruvate (Jardine et al., 2010), phosphoenolpyruvate (Rosenstiel et al., 2003), and Glc (Schnitzler et al., 2004). Over 40 years ago, it was also proposed that photorespiratory carbon could directly contribute to isoprene production in plants (Jones and Rasmussen, 1975); however, subsequent studies (Monson and Fall, 1989; Hewitt et al., 1990; Karl et al., 2002) have concluded that photorespiration does not contribute to isoprenoid production.In this study, we examined the carbon composition of isoprene emitted from tropical tree species under changes in light and temperature, the two key environmental variables that affect isoprene emissions. Using a novel real-time analytical approach, we were able to observe compensatory changes in carbon source contribution to isoprene during thermal ramping at high temperatures, despite the overall isoprene emissions remaining relatively stable. By conducting leaf temperature curves under variable ¹³CO₂ concentrations and applying [2-¹³C]Gly leaf labeling, we also reopen the discussion on the role of photorespiration as an alternate source of carbon for isoprenoid formation.     

The Escherichia coli Phosphotyrosine Proteome Relates to Core Pathways and Virulence

While phosphotyrosine modification is an established regulatory mechanism in eukaryotes, it is less well characterized in bacteria due to low prevalence. To gain insight into the extent and biological importance of tyrosine phosphorylation in Escherichia coli, we used immunoaffinity-based phosphotyrosine peptide enrichment combined with high resolution mass spectrometry analysis to comprehensively identify tyrosine phosphorylated proteins and accurately map phosphotyrosine sites. We identified a total of 512 unique phosphotyrosine sites on 342 proteins in E. coli K12 and the human pathogen enterohemorrhagic E. coli (EHEC) O157:H7, representing the largest phosphotyrosine proteome reported to date in bacteria. This large number of tyrosine phosphorylation sites allowed us to define five phosphotyrosine site motifs. Tyrosine phosphorylated proteins belong to various functional classes such as metabolism, gene expression and virulence. We demonstrate for the first time that proteins of a type III secretion system (T3SS), required for the attaching and effacing (A/E) lesion phenotype characteristic for intestinal colonization by certain EHEC strains, are tyrosine phosphorylated by bacterial kinases. Yet, A/E lesion and metabolic phenotypes were unaffected by the mutation of the two currently known tyrosine kinases, Etk and Wzc. Substantial residual tyrosine phosphorylation present in an etk wzc double mutant strongly indicated the presence of hitherto unknown tyrosine kinases in E. coli. We assess the functional importance of tyrosine phosphorylation and demonstrate that the phosphorylated tyrosine residue of the regulator SspA positively affects expression and secretion of T3SS proteins and formation of A/E lesions. Altogether, our study reveals that tyrosine phosphorylation in bacteria is more prevalent than previously recognized, and suggests the involvement of phosphotyrosine-mediated signaling in a broad range of cellular functions and virulence.     

Characterization of the Photosynthetic Apparatus and Proteome of Roseobacter denitrificans

The phototrophic capacity of aerobic anoxygenic phototrophic bacteria endows them with a selective advantage over other heterotrophic bacteria in the oligotrophic ocean. Here, we reported the phototrophic features and proteome of an aerobic phototrophic bacterium Roseobacter denitrificans under starvation stress. The fluorescence induction and relaxation measurements suggested that the photosynthetic capacity in R. denitrificans was preserved but was lower than in the photoautotrophic bacterium Rhodobacter sphaeroides. The existence of light-harvesting complexes (LH1 and LH2) and the reaction center (RC) in the native membrane were demonstrated through atomic force microscopy image analysis as direct evidence of their phototrophy. The homology-based LH1–RC complex structure was proposed in which RC was the Rb. sphaeroides homolog structure surrounded by the LH1. Moreover, the protein expression profiles of cells in the stationary phase under heterotrophic and mixotrophic conditions show that light enhanced or activated some proteins such as carbon monoxide dehydrogenase and NifU to cope with the low levels of amino acids and carbon sources under starvation conditions.     

AFLP标记与玉米杂种产量,产量杂种优势的预测

以１７个玉米（Ｚｅａ ｍａｙｓ Ｌ．）自交系及其按双列杂效配制的１３６个单交种为材料,研究ＡＦＬＰ分子标记与玉米杂效种产量、产量杂种优势的关系。结果表明,基于ＡＦＬＰ数据计算的遗传距离与１９９７年杂种产量、产量中优势的相关系数（ｒ）分别为０．４５０３、０．３７１４,与１９９８年杂种产量、产量杂种优势的相关系数分别为０．４３５２、０．３２５３,均达到显水平,但决定系数（ｒ＾２）都很小。当亲本材料改     

Effect of Elevated Temperatures on the Activity of Alternative Pathways of Photosynthetic Electron Transport in Intact Barley and Maize Leaves

The light-induced rise in chlorophyll fluorescence and the subsequent decay of fluorescence in darkness were measured in barley and maize leaves exposed to heat treatment. The redox conversions of the photosystem I primary donor P700, induced by far-red light, were also monitored from the absorbance changes at 830 nm. After heating of leaves at temperatures above 40°C, the ratio of variable and maximum fluorescence decreased for leaves of both plant species, indicating the inhibition of photosystem II (PSII) activity. A twofold reduction of this ratio in barley and maize leaves was observed after heating at 45.3 and 48.1°C, respectively, which suggests the higher functional resistance of PSII in maize. The amplitude of the slow phase in the dark relaxation of variable fluorescence did not change after the treatment of barley and maize leaves at temperatures up to 48°C. In leaves treated at 42 and 46°C, the slow phase of dark relaxation deviated from an exponential curve. The relaxation kinetics included a temporary increase in fluorescence to a peak about 1 s after turning off the actinic light. Unlike the slow component, the fast and intermediate phases in the dark relaxation of variable fluorescence disappeared fully or partly after the treatment of leaves at 46°C. The photooxidation of P700 in heat-treated leaves was saturated at much higher irradiances of far-red light than in untreated leaves. At the same time, the dark reduction of P700⁺ was substantially accelerated after heat treatment. The data provide evidence that the heating of leaves stimulated the alternative pathways of electron transport, i.e., cyclic transport around photosystem I and/or the donation of electrons to the plastoquinone pool from the reduced compounds located in the chloroplast stroma. The rate of alternative electron transport after the heat treatment was higher in maize leaves than in barley leaves. It is supposed that the stimulation of alternative electron transport, associated with proton pumping into the thylakoid, represents a protective mechanism that prevents the photoinhibition of PSII in leaves upon a strong suppression of linear electron transport in chloroplasts exposed to heat treatment.     

dRYBP Contributes to the Negative Regulation of the Drosophila Imd Pathway

The Drosophila humoral innate immune response fights infection by producing antimicrobial peptides (AMPs) through the microbe-specific activation of the Toll or the Imd signaling pathway. Upon systemic infection, the production of AMPs is both positively and negatively regulated to reach a balanced immune response required for survival. Here, we report the function of the dRYBP (drosophila Ring and YY1 Binding Protein) protein, which contains a ubiquitin-binding domain, in the Imd pathway. We have found that dRYBP contributes to the negative regulation of AMP production: upon systemic infection with Gram-negative bacteria, Diptericin expression is up-regulated in the absence of dRYBP and down-regulated in the presence of high levels of dRYBP. Epistatic analyses using gain and loss of function alleles of imd, Relish, or skpA and dRYBP suggest that dRYBP functions upstream or together with SKPA, a member of the SCF-E3-ubiquitin ligase complex, to repress the Imd signaling cascade. We propose that the role of dRYBP in the regulation of the Imd signaling pathway is to function as a ubiquitin adaptor protein together with SKPA to promote SCF-dependent proteasomal degradation of Relish. Beyond the identification of dRYBP as a novel component of Imd pathway regulation, our results also suggest that the evolutionarily conserved RYBP protein may be involved in the human innate immune response.     

玉米杂种优势分子基础研究进展

当今作物改良中杂种优势的广泛应用得益于杂交玉米的首先培育成功,对其分子基础的探讨已历经近一个世纪却尚未达成共识。关于杂种优势的经典解释曾聚焦于显性和超显性假说,现在看来似乎是借喻遗传学分子概念而无实际分子基础的实用性概念,籍此导致了一些研究结果的不一致是可以理解的。随着基因组时代的到来和相关分子技术的出现,文章回顾了过去的研究结果,分析了杂种优势分子机制研究的现状和问题,针对两亲本及其后代杂交后基因组构架和基因表达变化的研究趋势及方向进行了评价,并提出了由此资讯引发的SNPs单倍型用于玉米杂种优势分子基础研究的新策略。     

蛋白质组学技术在玉米杂种优势研究上的应用进展

杂种优势是生物界普遍存在的一种现象,在玉米中已经广泛应用,但其形成的分子机理仍不清楚。蛋白质组学技术是一种高通量筛选重要功能蛋白的研究手段,在玉米杂种优势的形成上进行蛋白质组学研究有利于深入解析杂种优势形成的分子机制。简单介绍了玉米杂种优势的表现,并对玉米种子胚、苗期根系、叶片和雌穗等性状上有关杂种优势形成的分子机理的蛋白质组学研究进行了综述。     

Influence of Iron Regulation on the Metabolome of Cryptococcus neoformans

Iron is an essential nutrient for virtually all organisms and acts as a cofactor for many key enzymes of major metabolic pathways. Furthermore, iron plays a critical role in pathogen-host interactions. In this study, we analyzed metabolomic changes associated with iron availability and the iron regulatory protein Cir1 in a human fungal pathogen Cryptococcus neoformans. Our metabolite analysis revealed that Cir1 influences the glycolytic pathway, ergosterol biosynthesis and inositol metabolism, which require numerous iron-dependent enzymes and play important roles in pathogenesis and antifungal sensitivity of the fungus. Moreover, we demonstrated that increased cellular iron content and altered gene expression in the cir1 mutant contributed to metabolite changes. Our study provides a new insight into iron regulation and the role of Cir1 in metabolome of C. neoformans.     

Carbon-Isotope Ratios and Photosynthetic Pathways in the Neotropical Family Rapateaceae

Abstract: The Rapateaceae is a small, mainly Neotropical family of terrestrial or occasionally epiphytic herbs that grow on mesic, nutrient-poor sites. Some recent studies suggest that the Rapateaceae may be closely related to the Bromeliaceae, one of the major families containing CAM plants. To investigate the photosynthetic pathway in Rapateaceae, the plant carbon-isotope ratio (δ¹³C) was determined for samples from dried herbarium specimens for 85 of the approximately 100 species in the family. The δ¹³C values ranged from - 37.7 to - 19.8 ‰. Most Rapateaceae showed δ¹³C values typical of C₃ plants. However, six species ( Kunhardtia rhodantha Maguire, Marahuacaea schomburgkii (Maguire) Maguire, Saxofridericia compressa Maguire, Stegolepis grandis Maguire, St. guianensis Klotzsch ex Körn. and St. squarrosa Maguire) showed δ¹³C values less negative than - 23 ‰, i.e., at the higher end of the range for C₃ plants and at the lower end of the distribution for plants exhibiting CAM. The δ¹³C values became significantly less negative with increasing altitude (regression analysis indicating a change from about - 30.7 ‰ at sea level to - 22.5 ‰ at 2500 m). Although other environmental factors and the type of tissue analysed may also influence δ¹³C values, these results suggest that some Rapateaceae may be capable of performing CAM. Further studies, including measurements of diel gas exchange patterns and leaf organic-acid fluctuations, would be needed to demonstrate CAM in Rapateaceae unequivocally, but living material of many of these enigmatic plants is difficult to obtain.     

Distinct Parietal and Temporal Pathways to the Homologues of Broca's Area in the Monkey

The homologues of the two distinct architectonic areas 44 and 45 that constitute the anterior language zone (Broca's region) in the human ventrolateral frontal lobe were recently established in the macaque monkey. Although we know that the inferior parietal lobule and the lateral temporal cortical region project to the ventrolateral frontal cortex, we do not know which of the several cortical areas found in those regions project to the homologues of Broca's region in the macaque monkey and by means of which white matter pathways. We have used the autoradiographic method, which permits the establishment of the cortical area from which axons originate (i.e., the site of injection), the precise course of the axons in the white matter, and their termination within particular cortical areas, to examine the parietal and temporal connections to area 44 and the two subdivisions of area 45 (i.e., areas 45A and 45B). The results demonstrated a ventral temporo-frontal stream of fibers that originate from various auditory, multisensory, and visual association cortical areas in the intermediate superolateral temporal region. These axons course via the extreme capsule and target most strongly area 45 with a more modest termination in area 44. By contrast, a dorsal stream of axons that originate from various cortical areas in the inferior parietal lobule and the adjacent caudal superior temporal sulcus was found to target both areas 44 and 45. These axons course in the superior longitudinal fasciculus, with some axons originating from the ventral inferior parietal lobule and the adjacent superior temporal sulcus arching and forming a simple arcuate fasciculus. The cortex of the most rostral part of the inferior parietal lobule is preferentially linked with the ventral premotor cortex (ventral area 6) that controls the orofacial musculature. The cortex of the intermediate part of the inferior parietal lobule is linked with both areas 44 and 45. These findings demonstrate the posterior parietal and temporal connections of the ventrolateral frontal areas, which, in the left hemisphere of the human brain, were adapted for various aspects of language production. These precursor circuits that are found in the nonlinguistic, nonhuman, primate brain also exist in the human brain. The possible reasons why these areas were adapted for language use in the human brain are discussed. The results throw new light on the prelinguistic precursor circuitry of Broca's region and help understand functional interactions between Broca's ventrolateral frontal region and posterior parietal and temporal association areas.     

Variation in Photosynthetic Characteristics and Leaf Area Contributes to Spathiphyllum Cultivar Differences in Biomass Production

Three genetically related Spathiphyllum cultivars, Claudia, Double Take, and Petite with similar initial sizes and biomass, were grown in a shaded greenhouse and fertilized with a constant supply of nitrogen at 200 g m^–3 using an ebb-and-flow fertigation system. Seven months later, Claudia and Double Take had plant sizes and biomasses significantly greater than Petite. Stomatal conductances of Claudia and Double Take were 30 % greater, thus net photosynthetic rates (P _N) were significantly higher than in Petite. In addition, the leaf areas (LA) of Claudia and Double Take were 60 % larger than of Petite. Since P _N was expressed per leaf surface area, the greater the LA was, the more CO₂ was fixed. Thus, the differences in plant size and biomass production of Claudia and Double Take compared to Petite are attributed to high P _N and increased LA.     

Larval Zebrafish Proteome Regulation in Response to an Environmental Challenge

Adaptation to the environment during development influences the life‐long survival of an animal. While brain‐wide proteomic changes are expected to underlie such experience‐driven physiological and behavioral flexibility, a comprehensive overview of the nature and extent of the proteomic regulation following an environmental challenge during development is currently lacking. In this study, the brain proteome of larval zebrafish is identified and it is determined how it is altered by an exposure to a natural and physical environmental challenge, namely prolonged exposure to strong water currents. A comprehensive larval zebrafish brain proteome is presented here. Furthermore, 57 proteins that are regulated by the exposure to an environmental challenge are identified, which cover multiple functions including neuronal plasticity, the stress response, axonal growth and guidance, spatial learning, and energy metabolism. These represent candidate proteins that may play crucial roles for the adaption to an environmental challenge during development.     

How Epigenomics Contributes to the Understanding of Gene Regulation in Toxoplasma gondii1

ABSTRACT. How apicomplexan parasites regulate their gene expression is poorly understood. The complex life cycle of these parasites implies tight control of gene expression to orchestrate the appropriate expression pattern at the right moment. Recently, several studies have demonstrated the role of epigenetic mechanisms for control of coordinated expression of genes. In this review, we discuss the contribution of epigenomics to the understanding of gene regulation in Toxoplasma gondii. Studying the distribution of modified histones on the genome links chromatin modifications to gene expression or gene repression. In particular, coincident trimethylated lysine 4 on histone H3 (H3K4me3), acetylated lysine 9 on histone H3 (H3K9ac), and acetylated histone H4 (H4ac) mark promoters of actively transcribed genes. However, the presence of these modified histones at some non‐expressed genes and other histone modifications at only a subset of active promoters implies the presence of other layers of regulation of chromatin structure in T. gondii. Epigenomics analysis provides a powerful tool to characterize the activation state of genomic loci of T. gondii and possibly of other Apicomplexa including Plasmodium or Cryptosporidium. Further, integration of epigenetic data with expression data and other genome‐wide datasets facilitates refinement of genome annotation based upon experimental data.