Identification of resistance-associated proteins in closely-related maize lines varying in aflatoxin accumulation

Aspergillus flavus infection of maize and subsequent contamination with carcinogenic aflatoxins poses serious health concerns, especially in developing countries. Maize lines resistant to A. flavus infection have been identified; however, the development of commercially-useful aflatoxin-resistant maize lines has been hindered due to a lack of breeding markers. To identify maize resistance-associated proteins (RAPs) as potential markers for breeding, 52 BC1S4 lines developed from crosses between five African maize inbreds and five temperate aflatoxin-resistant lines were screened using the kernel screening assay. Five pairs of closely-related lines that had 75?C94% genetic similarity within each pair and which varied within each pair in aflatoxin accumulation were selected for proteomic investigation. Kernel embryo and endosperm protein profile differences within the pair and across pairs were compared using two-dimensional polyacrylamide gel electrophoresis. Differentially expressed (??1.5-fold) RAPs were sequenced through tandem mass spectrometry and were identified as antifungal, stress-related, storage or regulatory proteins. Sequence homology analysis highlighted several proteins in maize that confer resistance to A. flavus infection and/or aflatoxin production.     

The LS locus of pea encodes the gibberellin biosynthesis enzyme ent-kaurene synthase A

Gibberellins (GAs) are hormones required for several aspects of plant development, including internode elongation and seed development in pea (Pisum sativum L.). The first committed step in the GA biosynthesis pathway is the conversion of geranylgeranyl diphosphate (GGDP) to ent-kaurene via copalyl diphosphate (CDP). These two reactions are catalyzed by the cyclases ent-kaurene synthase A (KSA) and ent-kaurene synthase B (KSB), respectively. Previous genetic and biochemical analysis of the GA-responsive ls-1 mutant of pea suggested that GA levels are reduced in a developmental- and organ-specific manner due to reduced GA biosynthesis. Analysis of cell-free enzyme preparations from WT and ls-1 embryos at contact point reveals that ls-1 reduces the activity of KSA but not KSB. To characterize the ls-1 mutation in more detail, a cDNA coding for a pea KSA was cloned and shown to be encoded by the LS locus. The ls-1 mutation results from an intronic G to A substitution that causes impaired RNA splicing. To determine the activity of the KSAs encoded by the LS and ls-1 alleles, a new in vitro assay for combined KSA and KSB activity has been developed using the KSB gene of pumpkin. Using recombinant WT KSA and KSB fusion proteins, GGDP is converted to ent-kaurene in vitro. Based on the sequence of RT-PCR products, three different truncated KSA proteins are predicted to exist in ls-1 plants. The most abundant mutant KSA protein does not possess detectable activity in vitro. Nevertheless, the ls-1 allele is not null and is able to encode at least a partially functional KSA since a more severe ls allele has been identified. The ls-1 mutation has played a key role in identifying a role for GAs in pea seed development in the first few days after fertilization, but not in older seeds. KSA expression in seeds is developmentally regulated and parallels overall GA biosynthesis, suggesting that KSA expression may play an important role in the regulation of GA biosynthesis and seed development.     

Proteomic analysis of Giardia: Studies from the pre- and post-genomic era

The proteome of Giardia duodenalis has been under study for the last 25 years and has lead to the discovery of valuable information on the biology and variation of the parasite. Proteomic techniques, mainly SDS-PAGE and 2D-PAGE, have been used to investigate protein variation, cellular structure and host parasite interactions. This has allowed for the identification of assemblage and host specific proteins, structural proteins, proteins released by trophozoites upon exposure to host cell monolayers and immunoreactive proteins. These data are important in understanding the pathogenesis of G. duodenalis infections, as well as highlighting potential drug and vaccine targets. There is, however, a large amount of future work needed to fully understand the proteome of this parasite.     

Gene-for-gene interactions: bacterial avirulence proteins specify plant disease resistance

Resistance of plants to bacterial pathogens is often controlled by corresponding genes for resistance and avirulence in host and pathogen, respectively. Fifty years after discovery of the genetic basis of gene-for-gene interactions, several avirulence and plant resistance genes have been isolated and are being studied on the molecular level. Tremendous progress has been made due to a better understanding of type III secretion systems that are required for bacterial pathogenicity. We are beginning to grasp how the plant actually recognizes bacterial avirulence determinants. The current view is that the bacterium translocates avirulence proteins into the host cell by the Hrp type III secretion system and that recognition occurs in the plant cell.     

<Emphasis Type="Italic">Lactococcus lactis</Emphasis> M4, a potential host for the expression of heterologous proteins

Background  

Many plasmid-harbouring strains of Lactococcus lactis have been isolated from milk and other sources. Plasmids of Lactococcus have been shown to harbour antibiotic resistance genes and those that express some important proteins. The generally regarded as safe (GRAS) status of L. lactis also makes it an attractive host for the production of proteins that are beneficial in numerous applications such as the production of biopharmaceutical and nutraceutical. In the present work, strains of L. lactis were isolated from cow's milk, plasmids were isolated and characterised and one of the strains was identified as a potential new lactococcal host for the expression of heterologous proteins.     

New insights into protein export in malaria parasites

In order to survive and promote its virulence the malaria parasite must export hundreds of its proteins beyond an encasing vacuole and membrane into the host red blood cell. In the last few years, several major advances have been made that have significantly contributed to our understanding of this export process. These include: (i) the identification of sequences that direct protein export (a signal sequence and a motif termed PEXEL), which have allowed predictions of the exportomes of Plasmodium species that are the cause of malaria, (ii) the recognition that the fate of proteins destined for export is already decided within the parasite's endoplasmic reticulum and involves the PEXEL motif being recognized and cleaved by the aspartic protease plasmepsin V and (iii) the discovery of the Plasmodium translocon of exported proteins (PTEX) that is responsible for the passage of proteins across the vacuolar membrane. We review protein export in Plasmodium and these latest developments in the field that have now provided a new platform from which trafficking of malaria proteins can be dissected.     

Production of recombinant proteins in Mycobacterium smegmatis for structural and functional studies

Protein production using recombinant DNA technology has a fundamental impact on our understanding of biology through providing proteins for structural and functional studies. Escherichia coli (E. coli) has been traditionally used as the default expression host to over‐express and purify proteins from many different organisms. E. coli does, however, have known shortcomings for obtaining soluble, properly folded proteins suitable for downstream studies. These shortcomings are even more pronounced for the mycobacterial pathogen Mycobacterium tuberculosis, the bacterium that causes tuberculosis, with typically only one third of proteins expressed in E. coli produced as soluble proteins. Mycobacterium smegmatis (M. smegmatis) is a closely related and non‐pathogenic species that has been successfully used as an expression host for production of proteins from various mycobacterial species. In this review, we describe the early attempts to produce mycobacterial proteins in alternative expression hosts and then focus on available expression systems in M. smegmatis. The advantages of using M. smegmatis as an expression host, its application in structural biology and some practical aspects of protein production are also discussed. M. smegmatis provides an effective expression platform for enhanced understanding of mycobacterial biology and pathogenesis and for developing novel and better therapeutics and diagnostics.     

Genetic background of host—pathogen interaction betweenCucumis sativus L. andPseudomonas syringae pv.lachrymans

The interplay of plant resistance mechanisms and bacterial pathogenicity is very complex. This applies also to the interaction that takes place between the pathogenPseudomonas syringae pv.lachrymans (Smith et Bryan) and the cucumber (Cucumis sativus L.) as its host plant. Research onP. syringae pv.lachrymans has led to the discovery of specific factors produced during pathogenesis, i.e. toxins or enzymes. Similarly, studies on cucumber have identified the specific types of plant resistance expressed, namely Systemic Acquired Resistance (SAR) or Induced Systemic Resistance (ISR). This paper presents a summary of the current state of knowledge about this particular host-pathogen interaction, with reference to general information about interactions ofP. syringae pathovars with host plants.     

Differential proteomics in the search for biomarkers of radiotherapy resistance

The individualization of radiotherapy treatment would be beneficial for cancer patients; however, there are no predictive biomarkers of radiotherapy resistance in routine clinical use. This article describes the body of work in this field where comparative proteomics methods have been used for the discovery of putative biomarkers associated with radiotherapy resistance. A large number of differentially expressed proteins have been reported, mostly from the study of novel radiotherapy-resistant cell lines. Here, we have assessed these putative biomarkers through the discovery, confirmation and validation phases of the biomarker pipeline, and inform the reader on the current status of proteomics-based findings. Suggested avenues for future work are discussed.     

The ins and outs of bacterial iron metabolism

Iron is a critical nutrient for the growth and survival of most bacterial species. Accordingly, much attention has been paid to the mechanisms by which host organisms sequester iron from invading bacteria and how bacteria acquire iron from their environment. However, under oxidative stress conditions such as those encountered within phagocytic cells during the host immune response, iron is released from proteins and can act as a catalyst for Fenton chemistry to produce cytotoxic reactive oxygen species. The transitory efflux of free intracellular iron may be beneficial to bacteria under such conditions. The recent discovery of putative iron efflux transporters in Salmonella enterica serovar Typhimurium is discussed in the context of cellular iron homeostasis.     

Mass spectrometry and illicit drug testing: analytical challenges of the anti-doping laboratories

The individualization of radiotherapy treatment would be beneficial for cancer patients; however, there are no predictive biomarkers of radiotherapy resistance in routine clinical use. This article describes the body of work in this field where comparative proteomics methods have been used for the discovery of putative biomarkers associated with radiotherapy resistance. A large number of differentially expressed proteins have been reported, mostly from the study of novel radiotherapy-resistant cell lines. Here, we have assessed these putative biomarkers through the discovery, confirmation and validation phases of the biomarker pipeline, and inform the reader on the current status of proteomics-based findings. Suggested avenues for future work are discussed.     

Drug discovery in leishmaniasis using protein lipidation as a target

The leishmaniases are infectious diseases caused by a number of species of obligate intracellular protozoa of the genus Leishmania with disease manifesting as cutaneous, mucocutaneous and visceral forms. Despite being endemic in more than 80 countries and its being the cause of high morbidity and mortality, leishmaniasis remains a neglected tropical disease. Chemotherapy is the frontline treatment, but drugs in current use suffer from toxic side effects, difficulties in administration and extended treatment times — moreover, resistance is emerging. New anti-leishmanial drugs are a recognised international priority. Here, we review investigations into N-myristoyltransferase (NMT) as a potential drug target. NMT catalyses the co-translational transfer of a C₁₄ fatty acid from myristoyl-CoA onto the N-terminal glycine residue of a significant subset of proteins in eukaryotic cells. This covalent modification influences the stability and interactions of substrate proteins with lipids and partner proteins. Structure-guided development of new lead compounds emerging from high-throughput screening campaigns targeting Leishmania donovani NMT has led to the discovery of potent inhibitors which have been used to gain insights into the role of protein myristoylation in these parasites and to validate NMT as a drug target.     

Trichomes of Lycopersicon species and their hybrids: effects on pests and natural enemies

1 The cultivated tomato, Lycopersicon esculentum, is an economically important worldwide crop. Current pest management techniques rely heavily on pesticides but trichome‐based host‐plant resistance may reduce pesticide use. 2 A review of the literature is provided on trichomes of wild Lycopersicon species and the effects of trichome‐based host‐plant resistance on arthropods. Solvents have been used to remove glandular trichome exudates and the resulting dimminution of their effects quantified. Correlational approaches to assess the relationship between the different trichome types and effects on pests have also been used. 3 Most studies have focused on Lepidoptera and Hemiptera, although some work has included Coleoptera, Diptera and Acarina, and both antibiotic and antixenotic effects have been demonstrated. 4 Natural enemies are a cornerstone of international pest management and this review discusses how the compatibility of this approach with trichome‐based host‐plant resistance is uncertain because of the reported negative effects of trichomes on one dipteran, one hemipteran and several Hymenoptera. 5 For trichome‐based host‐plant resistance to be utilized as a pest management tool, trichomes of wild species need to be introgressed into the cultivated tomato. Hybrids between the cultivated tomato and the wild species Lycopersicon hirsutum f. glabratum, Lycopersicon pennellii and Lycopersicon cheesmanii f. minor have been produced and useful levels of resistance to Acarina, Diptera and Hemiptera pests have been exhibited, although these effects may be tempered by effects on natural enemies. 6 This review proposes that studies on genetic links between fruit quality and resistance, field studies to determine the compatibility of natural enemies and trichome‐based host‐plant resistance, and a strong focus on L. cheesmanii f. minor, are all priorities for further research that will help realize the potential of this natural defence mechanism in pest management.     

Trichomes of Lycopersicon species and their hybrids: effects on pests and natural enemies

1 The cultivated tomato, Lycopersicon esculentum, is an economically important worldwide crop. Current pest management techniques rely heavily on pesticides but trichome‐based host‐plant resistance may reduce pesticide use. 2 A review of the literature is provided on trichomes of wild Lycopersicon species and the effects of trichome‐based host‐plant resistance on arthropods. Solvents have been used to remove glandular trichome exudates and the resulting dimminution of their effects quantified. Correlational approaches to assess the relationship between the different trichome types and effects on pests have also been used. 3 Most studies have focused on Lepidoptera and Hemiptera, although some work has included Coleoptera, Diptera and Acarina, and both antibiotic and antixenotic effects have been demonstrated. 4 Natural enemies are a cornerstone of international pest management and this review discusses how the compatibility of this approach with trichome‐based host‐plant resistance is uncertain because of the reported negative effects of trichomes on one dipteran, one hemipteran and several Hymenoptera. 5 For trichome‐based host‐plant resistance to be utilized as a pest management tool, trichomes of wild species need to be introgressed into the cultivated tomato. Hybrids between the cultivated tomato and the wild species Lycopersicon hirsutum f. glabratum, Lycopersicon pennellii and Lycopersicon cheesmanii f. minor have been produced and useful levels of resistance to Acarina, Diptera and Hemiptera pests have been exhibited, although these effects may be tempered by effects on natural enemies. 6 This review proposes that studies on genetic links between fruit quality and resistance, field studies to determine the compatibility of natural enemies and trichome‐based host‐plant resistance, and a strong focus on L. cheesmanii f. minor, are all priorities for further research that will help realize the potential of this natural defence mechanism in pest management.     

Toll-like receptor recognition of Toxoplasma gondii

Toxoplasma gondii potently stimulates IFN-gamma production by both the innate and adaptive immune system as part of its host adaptation. This response is known to be dependent on an Myeloid Differentiation factor 88 signaling pathway used by Toll-like receptors (TLRs), a family of proteins involved in the recognition of microbial molecular patterns. In the following review, we summarise the evidence for specific TLR function in host resistance to T. gondii focusing on the recent discovery in the parasite of a profilin-like ligand that potently stimulates TLR11 and regulates the production of IL-12, a cytokine necessary for the protective IFN-gamma response. In addition, we discuss the hypothesis that TLR11 may have evolved as a general pattern recognition receptor for apicomplexan protozoa and that as highly conserved proteins associated with actin-based motility, profilins are logical ligand targets for this form of pathogen detection. Finally, we review the evidence for involvement of other TLR and TLR ligands in host resistance to T. gondii and discuss how such receptors might synergise with TLR11 in the innate response to the parasite.     

Transfer parameters for ICRP reference animals and plants collected from a forest ecosystem

The International Commission on Radiological Protection (ICRP) have suggested the identification of a series of terrestrial, marine and freshwater sites from which samples of each Reference animal and plant (RAP) could be systematically collected and analysed. We describe the first such study in which six of the eight terrestrial RAPs, and associated soil samples, were collected from a site located in a managed coniferous forestry plantation in north-west England. Adult life stages of species representing six of the terrestrial RAPs (Wild grass, Pine tree, Deer, Rat, Earthworm and Bee) were sampled and analysed to determine concentrations of 60 elements and gamma-emitting radionuclides. The resultant data have been used to derive concentration ratios (CR_wo-soil) relating element/radionuclide concentrations in the RAPs to those in soil. This paper presents the first-reported transfer parameters for a number of the RAP–element combinations. Where possible, the derived CR_wo-soil values are compared with the ICRPs-recommended values and any appreciable differences discussed.     

Genetic,physiological and molecular interactions of rice and its major dipteran pest,gall midge

The gall midge, Orseolia oryzae, is a major dipteran pest of rice affecting most rice growing regions in Asia, Southeast Asia and Africa. Chemical and other cultural methods for control of this pest are neither very effective nor environmentally safe. The gall midge problem is further compounded by the fact that there are many biotypes of this insect and new biotypes are continuously evolving. However, resistance to this pest is found in the rice germ plasm. Resistance is generally governed by single dominant genes and a number of non-allelic resistance genes that confer resistance to different biotypes have been identified. Genetic studies have revealed that there is a gene-for-gene interaction between the different biotypes of gall midge and the various resistance genes found in rice. This review discusses different aspects of the process of infestation by the rice gall midge and its interaction with its host. Identification of the gall midge biotypes by conventional methods is a long and tedious process. The review discusses the PCR-based molecular markers that have been developed recently to speed up the identification process. Similarly, molecular markers have been developed for two gall midge resistance genes in rice – Gm2 and Gm4t – and these markers are now being used for marker-assisted selection. The mapping, tagging and map-based gene cloning of one of these genes – Gm2 – has also been discussed. This revised version was published online in June 2006 with corrections to the Cover Date.     

Contemporary evolution of a Lepidopteran species,Heliothis virescens,in response to modern agricultural practices

Adaptation to human‐induced environmental change has the potential to profoundly influence the genomic architecture of affected species. This is particularly true in agricultural ecosystems, where anthropogenic selection pressure is strong. Heliothis virescens primarily feeds on cotton in its larval stages, and US populations have been declining since the widespread planting of transgenic cotton, which endogenously expresses proteins derived from Bacillus thuringiensis (Bt). No physiological adaptation to Bt toxin has been found in the field, so adaptation in this altered environment could involve (i) shifts in host plant selection mechanisms to avoid cotton, (ii) changes in detoxification mechanisms required for cotton‐feeding vs. feeding on other hosts or (iii) loss of resistance to previously used management practices including insecticides. Here, we begin to address whether such changes occurred in H. virescens populations between 1997 and 2012, as Bt‐cotton cultivation spread through the agricultural landscape. For our study, we produced an H. virescens genome assembly and used this in concert with a ddRAD‐seq‐enabled genome scan to identify loci with significant allele frequency changes over the 15‐year period. Genetic changes at a previously described H. virescens insecticide target of selection were detectable in our genome scan and increased our confidence in this methodology. Additional loci were also detected as being under selection, and we quantified the selection strength required to elicit observed allele frequency changes at each locus. Potential contributions of genes near loci under selection to adaptive phenotypes in the H. virescens cotton system are discussed.