Citrus fruit bitter flavors: isolation and functional characterization of the gene Cm1,2RhaT encoding a 1,2 rhamnosyltransferase, a key enzyme in the biosynthesis of the bitter flavonoids of citrus

Species of the genus Citrus accumulate large quantities of flavanones that affect fruit flavor and have been documented to benefit human health. Bitter species, such as grapefruit and pummelo, accumulate bitter flavanone-7-O-neohesperidosides responsible, in part, for their characteristic taste. Non-bitter species, such as mandarin and orange, accumulate only tasteless flavanone-7-O-rutinosides. The key flavor-determining step of citrus flavanone-glycoside biosynthesis is catalyzed by rhamnosyltransferases; 1,2 rhamnosyltransferases (1,2RhaT) catalyze biosynthesis of the bitter neohesperidosides, while 1,6 rhamnosyltransferases (1,6RhaT) catalyze biosynthesis of the tasteless rutinosides. We report on the isolation and functional characterization of the gene Cm1,2RhaT from pummelo which encodes a citrus 1,2RhaT. Functional analysis of Cm1,2RhaT recombinant enzyme was conducted by biotransformation of the substrates using transgenic plant cell culture. Flavanones and flavones, but not flavonols, were biotransformed into 7-O-neohesperidosides by the transgenic BY2 tobacco cells expressing recombinant Cm1,2RhaT. Immunoblot analysis established that 1,2RhaT protein was expressed only in the bitter citrus species and that 1,6RhaT enzyme, whose activity was previously documented in non-bitter species, was not cross-reactive. Expression of Cm1,2RhaT at the RNA level was prominent in young fruit and leaves, but low in the corresponding mature tissue, thus correlating well with the developmental pattern of accumulation of flavanone-neohesperidosides previously established. Phylogenetic analysis of the flavonoid glycosyltransferase gene family places Cm1,2RhaT on a separate gene cluster together with the only other functionally characterized flavonoid-glucoside rhamnosyltransferase gene, suggesting a common evolutionary origin for rhamnosyltransferases specializing in glycosylation of the sugar moieties of flavonoid glucosides.     

Gall‐forming insect species richness along a non‐scleromorphic vegetation rainfall gradient in South Africa: The importance of plant community composition

Abstract Currently there is no single accepted hypothesis to explain gall‐forming insect species richness at a particular locality. Hygrothermal stress, soil nutrient availability, plant species richness, plant structural complexity, plant family or genus size, and host plant geographical range size have all been implicated in the determination of gall‐forming insect species richness. Previous studies of such richness at xeric sites have included predominantly scleromorphic vegetation, usually on nutrient‐poor soils. This study is the first to investigate gall‐forming insect species richness of xeric, non‐scleromorphic vegetation. Two habitat types were sampled at each of five localities across a rainfall gradient in the savanna biome of South Africa. The habitat types differed with respect to plant species composition and topography. Gall‐forming insect species richness did not increase with increasing hygrothermal stress or decreasing soil fertility. Rather, gall‐forming insect species richness was largely dependent on the presence of Terminalia sericea as well as other members of the Combretaceae and Mimosaceae. Plots where all these taxa were present had the highest gall‐forming insect species richness, up to 15 species, whereas plots with none of these taxa had a maximum of four galling‐insect species. Despite herb, shrub and tree strata not differing in gall‐forming insect species richness, insect galls were more common on woody than non‐woody plants. Also, stem galls were more frequent than apical or leaf galls. An alternative hypothesis to explain local gall‐forming insect species richness is suggested: galling insects may preferentially select those plant species with characteristics such as chemical toxicity, mechanical strength, degree of lignification or longevity that can be manipulated to benefit the galler. Thus plant community composition should be considered when attempting to explain gall‐forming insect species richness patterns.     

Genomic dissection of pod shattering in common bean: mutations at non‐orthologous loci at the basis of convergent phenotypic evolution under domestication of leguminous species

The complete or partial loss of shattering ability occurred independently during the domestication of several crops. Therefore, the study of this trait can provide an understanding of the link between phenotypic and molecular convergent evolution. The genetic dissection of ‘pod shattering’ in Phaseolus vulgaris is achieved here using a population of introgression lines and next‐generation sequencing techniques. The ‘occurrence’ of the indehiscent phenotype (indehiscent versus dehiscent) depends on a major locus on chromosome 5. Furthermore, at least two additional genes are associated with the ‘level’ of shattering (number of shattering pods per plant: low versus high) and the ‘mode’ of shattering (non‐twisting versus twisting pods), with all of these loci contributing to the phenotype by epistatic interactions. Comparative mapping indicates that the major gene identified on common bean chromosome 5 corresponds to one of the four quantitative trait loci for pod shattering in Vigna unguiculata. None of the loci identified comprised genes that are homologs of the known shattering genes in Glycine max. Therefore, although convergent domestication can be determined by mutations at orthologous loci, this was only partially true for P. vulgaris and V. unguiculata, which are two phylogenetically closely related crop species, and this was not the case for the more distant P. vulgaris and G. max. Conversely, comparative mapping suggests that the convergent evolution of the indehiscent phenotype arose through mutations in different genes from the same underlying gene networks that are involved in secondary cell‐wall biosynthesis and lignin deposition patterning at the pod level.     

Biological and molecular profile of fracture non‐union tissue: current insights

Delayed bone healing and non‐union occur in approximately 10% of long bone fractures. Despite intense investigations and progress in understanding the processes governing bone healing, the specific pathophysiological characteristics of the local microenvironment leading to non‐union remain obscure. The clinical findings and radiographic features remain the two important landmarks of diagnosing non‐unions and even when the diagnosis is established there is debate on the ideal timing and mode of intervention. In an attempt to understand better the pathophysiological processes involved in the development of fracture non‐union, a number of studies have endeavoured to investigate the biological profile of tissue obtained from the non‐union site and analyse any differences or similarities of tissue obtained from different types of non‐unions. In the herein study, we present the existing evidence of the biological and molecular profile of fracture non‐union tissue.     

Flying under the radar: The non‐canonical biochemistry and molecular biology of petrobactin from Bacillus anthracis

The dramatic, rapid growth of Bacillus anthracis that occurs during systemic anthrax implies a crucial requirement for the efficient acquisition of iron. While recent advances in our understanding of B. anthracis iron acquisition systems indicate the use of strategies similar to other pathogens, this review focuses on unique features of the major siderophore system, petrobactin. Ways that petrobactin differs from other siderophores include: A. unique ferric iron binding moieties that allow petrobactin to evade host immune proteins; B. a biosynthetic operon that encodes enzymes from both major siderophore biosynthesis classes; C. redundancy in membrane transport systems for acquisition of Fe‐petrobactin holo‐complexes; and, D. regulation that appears to be controlled predominately by sensing the host‐like environmental signals of temperature, CO₂ levels and oxidative stress, as opposed to canonical sensing of intracellular iron levels. We argue that these differences contribute in meaningful ways to B. anthracis pathogenesis. This review will also outline current major gaps in our understanding of the petrobactin iron acquisition system, some projected means for exploiting current knowledge, and potential future research directions.     

Eight years of ant‐exclusion from citrus canopies: effects on the arthropod assemblage and on fruit yield

• 1 Ants are important generalist predators in most terrestrial ecosystems. However, because many ant species are also hemipteran mutualists, their role in agriculture has generally been considered to be negative for plants.
• 2 In the present study, we report an experiment in ant‐exclusion from tree canopies in an organic citrus grove with two main objectives: (i) to examine whether the absence of ants increased the abundance of some beneficial arthropods and reduced the attack of some pests such as aphids and (ii) to examine whether ant‐exclusion increased the fruit yield of citrus trees.
• 3 The exclusion of ants from tree canopies had positive effects on the arthropod assemblage and on fruit yield. However, the 8‐year duration of the experiment can be divided into two periods with contrasting results. In the first period, the arthropod assemblage was only slightly affected, except for a greater density of aphids in ant‐excluded trees; in addition, fruit yield was higher in ant‐excluded trees than in the control ones. In the second period, ant‐exclusion increased the abundance of most arthropod groups, although the previous positive effect on fruit yield was no longer observed.
• 4 There are two main conclusions of the present study. First, from an applied perspective, ant‐exclusion from tree canopies is not a sound management alternative in citrus plantations in the Mediterranean. Second, the 8‐year duration of the experiment highlighted the importance of long‐term experiments in community ecology and biological control because the effects observed in the first 4 years of the experiment were very different from what occurred subsequently.

     

The molecular origin and evolution of dim‐light vision in mammals

The nocturnal origin of mammals is a longstanding hypothesis that is considered instrumental for the evolution of endothermy, a potential key innovation in this successful clade. This hypothesis is primarily based on indirect anatomical inference from fossils. Here, we reconstruct the evolutionary history of rhodopsin—the vertebrate visual pigment mediating the first step in phototransduction at low‐light levels—via codon‐based model tests for selection, combined with gene resurrection methods that allow for the study of ancient proteins. Rhodopsin coding sequences were reconstructed for three key nodes: Amniota, Mammalia, and Theria. When expressed in vitro, all sequences generated stable visual pigments with λ_MAX values similar to the well‐studied bovine rhodopsin. Retinal release rates of mammalian and therian ancestral rhodopsins, measured via fluorescence spectroscopy, were significantly slower than those of the amniote ancestor, indicating altered molecular function possibly related to nocturnality. Positive selection along the therian branch suggests adaptive evolution in rhodopsin concurrent with therian ecological diversification events during the Mesozoic that allowed for an exploration of the environment at varying light levels.     

A designed chimeric cyanovirin‐N homolog lectin: Structure and molecular basis of sucrose binding

The NMR and X‐ray structures of a designed chimeric cyanovirin‐N homolog (CVNH) protein were determined. The individual halves of the structure are similar to their counterparts in the parent proteins, with domains A and B resembling the structures of TbCVNH and NcCVNH, respectively. No significant differences between the solution and crystal conformations were observed, although details in loop conformations and distinct crystal packing‐induced features are present. Carbohydrate binding studies by NMR revealed affinity and specificity for Glcα(1‐2)Frc and Manα(1‐2)Man, and the parental half that is devoid of any sucrose affinity in NcCVNH was transformed into a genuine sucrose binding site in the context of the chimera. The atomic details of sugar recognition are seen in the crystal structure of the protein with two bound Glcα(1‐2)Frc molecules. Both sugars exhibit different conformations around the glycosidic bond and engage in unique hydrogen bonding networks in the two sites. Although the protein is able to bind two Manα(1‐2)Man molecules, a property associated with HIV‐inactivation, no anti‐HIV activity was observed for the hybrid protein. These results provide the structural basis for sugar recognition in the CVNH family and aid in deciphering the relationship between sugar binding and anti‐HIV activity. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

The genetic and functional analysis of flavor in commercial tomato: the FLORAL4 gene underlies a QTL for floral aroma volatiles in tomato fruit

Tomato (Solanum lycopersicum L.) has become a popular model for genetic studies of fruit flavor in the last two decades. In this article we present a study of tomato fruit flavor, including an analysis of the genetic, metabolic and sensorial variation of a collection of contemporary commercial glasshouse tomato cultivars, followed by a validation of the associations found by quantitative trait locus (QTL) analysis of representative biparental segregating populations. This led to the identification of the major sensorial and chemical components determining fruit flavor variation and detection of the underlying QTLs. The high representation of QTL haplotypes in the breeders’ germplasm suggests that there is great potential for applying these QTLs in current breeding programs aimed at improving tomato flavor. A QTL on chromosome 4 was found to affect the levels of the phenylalanine‐derived volatiles (PHEVs) 2‐phenylethanol, phenylacetaldehyde and 1‐nitro‐2‐phenylethane. Fruits of near‐isogenic lines contrasting for this locus and in the composition of PHEVs significantly differed in the perception of fruity and rose‐hip‐like aroma. The PHEV locus was fine mapped, which allowed for the identification of FLORAL4 as a candidate gene for PHEV regulation. Using a gene‐editing‐based (CRISPR‐CAS9) reverse‐genetics approach, FLORAL4 was demonstrated to be the key factor in this QTL affecting PHEV accumulation in tomato fruit.     

The mechanism of long non‐coding RNA MEG3 for hepatic ischemia‐reperfusion: Mediated by miR‐34a/Nrf2 signaling pathway

To investigate the function of MEG3 in hepatic ischemia‐reperfusion (HIR) progress, involving its association with the level of miR‐34a during hypoxia‐induced hypoxia re‐oxygenation (H/R) in vitro. HIR mice model in vivo was established. MEG3, miR‐34a expression, along with Nrf2 mRNA and protein level were detected in tissues and cells. Serum biochemical parameters (ALT and AST) were assessed in vivo. A potential binding region between MEG3 and miR34a was confirmed by luciferase assays. Hepatic cells HL7702 were subjected to hypoxia treatment in vitro for functional studies, including TUNEL‐positive cells detection and ROS analysis. MEG3, Nrf2 expression was significantly down‐regulated in infarction lesion from HIR mice, as opposed to increased miR‐34a production, while similar results were also observed in H/R HL7702 cells, while the above effects were reversed by MEG3 over‐expression. By using bioinformatics study and RNA pull down combined with luciferase assays, we demonstrated that MEG3 functioned as a competing endogenous RNA (ceRNA) for miR‐34a, and there was reciprocal repression between MEG3 and miR‐34a in an Argonaute 2‐dependent manner. Functional studies demonstrated that MEG3 showed positive regulation on TUNEL‐positive cells and ROS level. Further in vivo study confirmed that MEG3 over‐expression could improve hepatic function of HIR mice, and markedly decreased the expression of serum ALT and AST. MEG3 protected hepatocytes from HIR injury through down‐regulating miR‐34a expression, which could add our understanding of the molecular mechanisms in HIR injury.     

The comparative study of empathy: sympathetic concern and empathic perspective‐taking in non‐human animals

While empathy is a century‐old psychological concept, its study in non‐human animals has become the focus of much recent scientific interest, as it promises to provide the clues to understand the evolutionary origins of our social and moral nature. A review of the comparative study of empathy is thus timely to complement and constrain anthropocentric views, and to integrate current findings. However, this is not an easy task. The study of animal empathy has developed using different paradigms, different concepts of the phenomena involved, and the absence of a systematic program. Herein, we carry out a comprehensive review of the literature on complex forms of empathy in non‐human animals: sympathetic concern and empathic perspective‐taking. In particular, we focus on consolation and targeted helping, as the best examples of each category. In so doing, we try to shed light on the current debate concerning whether these phenomena are exclusively human traits. First, we try to clarify the terminology and taxonomy of forms of empathy, providing operative criteria for these phenomena that are applicable to both human and non‐human animals. Second, we discuss whether the available evidence qualifies such behaviour as empathic. Third, we aim to provide an integrative view of the field, clarifying the challenges and conditions to satisfy. We also hope to highlight the importance of the study of these processes for elucidating the evolutionary history of this capacity across the animal kingdom.     

miR‐148a inhibits early relapsed colorectal cancers and the secretion of VEGF by indirectly targeting HIF‐1α under non‐hypoxia/hypoxia conditions

Vascular endothelial growth factor (VEGF) is correlated with angiogenesis and early relapse of colorectal cancer (CRC). This study investigated the role of miR‐148a in the regulation of VEGF/angiogenesis and early relapse of CRC. We established a stable clone with miR‐148a expression in HCT116 and HT29 cell lines and created a hypoxic condition by using CoCl₂ to determine the underlying mechanism of miR‐148a. The effects of miR‐148a on the phosphoryl‐ERK (pERK)/hypoxia‐inducible factor‐1α (HIF‐1α)/VEGF pathway were evaluated through Western blotting and the inhibitory effect of miR‐148a on angiogenesis was demonstrated through a tube formation assay. Sixty‐three CRC tissues (28 early relapse and 35 non‐early relapse) were analysed to assess the relationship between miR‐148a and HIF‐1α/VEGF. The protein expression of pERK/HIF‐1α/VEGF in HCT116 and HT29 cells was significantly decreased by miR‐148a (all P < 0.05). The protein expression of VEGF/HIF‐1α was strongly inversely associated with the expression of miR‐148a in the 63 CRC tissue samples (all P < 0.05). Tube formation assay demonstrated that miR‐148a significantly obliterated angiogenesis. miR‐148a suppresses VEGF through down‐regulation of the pERK/HIF‐1α/VEGF pathway and might lead to the inhibition of angiogenesis; miR‐148a down‐regulation increased the early relapse rate of CRC. This demonstrates that miR‐148a is a potential diagnostic and therapeutic target.     

Molecular basis of the structural stability of hemochromatosis factor E: A combined molecular dynamic simulation and GdmCl‐induced denaturation study

Hemochromatosis factor E (HFE) is a member of class I MHC family and plays a significant role in the iron homeostasis. Denaturation of HFE induced by guanidinium chloride (GdmCl) was measured by monitoring changes in [θ]₂₂₂ (mean residue ellipticity at 222 nm), intrinsic fluorescence emission intensity at 346 nm (F₃₄₆) and the difference absorption coefficient at 287 nm (Δε₂₈₇) at pH 8.0 and 25°C. Coincidence of denaturation curves of these optical properties suggests that GdmCl‐induced denaturation (native (N) state ? denatured (D) state) is a two‐state process. The GdmCl‐induced denaturation was found reversible in the entire concentration range of the denaturant. All denaturation curves were analyzed for , Gibbs free energy change associated with the denaturation equilibrium (N state ? D state) in the absence of GdmCl, which is a measure of HFE stability. We further performed molecular dynamics simulation for 40 ns to see the effect of GdmCl on the structural stability of HFE. A well defined correlation was established between in vitro and in silico studies. © 2015 Wiley Periodicals, Inc. Biopolymers 105: 133–142, 2016.