RTM3, Which Controls Long-Distance Movement of Potyviruses,Is a Member of a New Plant Gene Family Encoding a Meprin and TRAF Homology Domain-Containing Protein

Restriction of long-distance movement of several potyviruses in Arabidopsis (Arabidopsis thaliana) is controlled by at least three dominant restricted TEV movement (RTM) genes, named RTM1, RTM2, and RTM3. RTM1 encodes a protein belonging to the jacalin family, and RTM2 encodes a protein that has similarities to small heat shock proteins. In this article, we describe the positional cloning of RTM3, which encodes a protein belonging to an undescribed protein family of 29 members that has a meprin and TRAF homology (MATH) domain in its amino-terminal region and a coiled-coil domain at its carboxy-terminal end. Involvement in the RTM resistance system is the first biological function experimentally identified for a member of this new gene family in plants. Our analyses showed that the coiled-coil domain is not only highly conserved between RTM3-homologous MATH-containing proteins but also in proteins lacking a MATH domain. The cluster organization of the RTM3 homologs in the Arabidopsis genome suggests the role of duplication events in shaping the evolutionary history of this gene family, including the possibility of deletion or duplication of one or the other domain. Protein-protein interaction experiments revealed RTM3 self-interaction as well as an RTM1-RTM3 interaction. However, no interaction has been detected involving RTM2 or the potyviral coat protein previously shown to be the determinant necessary to overcome the RTM resistance. Taken together, these observations strongly suggest the RTM proteins might form a multiprotein complex in the resistance mechanism to block the long-distance movement of potyviruses.Systemic infection of plants by viruses is the result of compatible interactions between plant and viral factors. These molecular interactions control translation and replication of the viral nucleic acid, assembly of progeny virus particles, and generalized invasion of the host through cell-to-cell and long-distance movements of viral particles or ribonucleoprotein complexes (Carrington and Whitham, 1998; Whitham and Wang, 2004). Plants have developed different mechanisms to resist viruses. Passive resistance generally results from lack of or inappropriate interactions between plant and viral factors, causing a block in one of the viral cycle steps, and is usually controlled by recessive resistance genes (Diaz-Pendon et al., 2004). Active resistance is generally triggered by the recognition of the viruses in plants and can be controlled by at least two types of mechanisms. One well-known mechanism is associated with the hypersensitive response or extreme resistance at initial infection sites and is controlled by dominant resistance genes (R genes) through a gene-for-gene relationship (Soosaar et al., 2005; Maule et al., 2007). The second mechanism concerns the general antiviral defense system of RNA interference, which recognizes and targets the viral nucleic acids (Voinnet, 2005; Maule et al., 2007).Restriction of long-distance movement of several potyviruses controlled by the dominant restricted TEV movement (RTM) genes in Arabidopsis (Arabidopsis thaliana) does not correspond to any of these known resistance mechanisms (Mahajan et al., 1998; Decroocq et al., 2006). Indeed, in this resistance process, viral replication and cell-to-cell movement in inoculated leaves appear unaffected, the hypersensitive response and systemic acquired resistance are not triggered, and salicylic acid is not involved (Mahajan et al., 1998). First identified as specific to Tobacco etch virus (TEV; Whitham et al., 2000), RTM resistance has recently been shown to be active against two other unrelated potyviruses, Lettuce mosaic virus (LMV) and Plum pox virus (PPV; Decroocq et al., 2006), showing that the RTM genes seem to be associated with a general resistance mechanism against potyviruses that blocks their long-distance movement. Whether the RTM genes are also involved in resistance mechanisms against other viral genera remains to be investigated. Genetic characterization from natural ecotype variation and chemically induced mutants has revealed that at least three dominant genes, named RTM1, RTM2, and RTM3, are involved in the restriction of long-distance movement of potyviruses in the Arabidopsis accession Columbia (Col-0; Mahajan et al., 1998; Whitham et al., 1999). Remarkably, a mutation in any of these three genes is sufficient to completely abolish the restriction of long-distance movement, suggesting that these genes act in an interdependent way to block the generalized invasion of the plant (Whitham et al., 1999). RTM1 encodes a protein belonging to the jacalin family, some members of which are involved in defense against insects and fungi (Chisholm et al., 2000). RTM2 encodes a protein that contains a transmembrane domain and has similarities to small heat shock proteins, although its expression is not heat inducible and does not contribute to thermotolerance (Whitham et al., 2000). Although it is not understood how the RTM proteins restrict long-distance movement of potyviruses, it has been shown that both RTM1 and RTM2 are expressed in phloem-associated tissues, that the corresponding proteins localize to phloem sieve elements (Chisholm et al., 2001), and that the N-terminal end of the potyviral capsid protein (CP) is involved in breaking of the RTM resistance (Decroocq et al., 2009), suggesting a direct or indirect interaction between the potyvirus CP and the RTM factors.In this article, we present the positional cloning of RTM3, which encodes a new type of protein containing a meprin and TRAF homology (MATH) domain, and show that RTM3 directly interacts with RTM1.     

DNA BARCODING IS A POWERFUL TOOL TO UNCOVER ALGAL DIVERSITY: A CASE STUDY OF THE PHYLLOPHORACEAE (GIGARTINALES,RHODOPHYTA) IN THE CANADIAN FLORA1

Previous studies have established that the 5′ end of the mitochondrial gene COI (cytochrome oxidase subunit I) is useful for rapid and reliable identification of red algal species and have demonstrated that our understanding of red algal biodiversity and biogeography is fragmentary. In this context, we are completing a thorough sampling along the Canadian coast and using the DNA barcode for the assignment of collections to genetic species to explore algal diversity in the Canadian flora. In the present study, we provide results regarding diversity of members of the red algal family Phyllophoraceae. We have analyzed 354 individuals from the Arctic, Atlantic, and Pacific coasts of Canada, as well as 26 specimens from the USA, Europe, and Australia, resolving 29 species based on the analyses of the DNA barcode. Twenty‐three of these genetic species were present in Canada where only 18 species are currently recognized, including Ceratocolax hartzii Rosenv., which was in the same genetic species group as its host Coccotylus truncatus (Pall.) M. J. Wynne et N. J. Heine and is thus transferred to Coccotylus, C. hartzii (Rosenv.) comb. nov., but retained as a distinct species owing to its unique habit and phenology. Our results revealed the presence of cryptic diversity within the genera Coccotylus, Mastocarpus, Ozophora, and Stenogramme, for which we resurrect Coccotylus brodiei (Turner) Kütz. and describe Mastocarpus pachenicus sp. nov., Ozophora lanceolata sp. nov., and Stenogramme bamfieldiensis sp. nov., leaving a multitude of unnamed Mastocarpus spp. in need of further taxonomic study. In addition, we report range extensions into British Columbia of Besa papillaeformis Setch., previously known only from its type and nearby localities in California; Gymnogongrus crenulatus (Turner) J. Agardh, recorded only from the Atlantic; and Stenogramme cf. rhodymenioides Joly et Alveal, previously only known from South America. Finally, the phylogenetic affinities of the Canadian species of Phyllophoraceae characterized in this study were investigated using LSU rDNA, RUBISCO LSU (rbcL), and combined analyses.     

Differential Specificity and Immunogenicity of Adenovirus Type 5 Neutralizing Antibodies Elicited by Natural Infection or Immunization

A recent clinical trial of a T-cell-based AIDS vaccine delivered with recombinant adenovirus type 5 (rAd5) vectors showed no efficacy in lowering viral load and was associated with increased risk of human immunodeficiency virus type 1 (HIV-1) infection. Preexisting immunity to Ad5 in humans could therefore affect both immunogenicity and vaccine efficacy. We hypothesized that vaccine-induced immunity is differentially affected, depending on whether subjects were exposed to Ad5 by natural infection or by vaccination. Serum samples from vaccine trial subjects receiving a DNA/rAd5 AIDS vaccine with or without prior immunity to Ad5 were examined for the specificity of their Ad5 neutralizing antibodies and their effect on HIV-1 immune responses. Here, we report that rAd5 neutralizing antibodies were directed to different components of the virion, depending on whether they were elicited by natural infection or vaccination in HIV vaccine trial subjects. Neutralizing antibodies elicited by natural infection were directed largely to the Ad5 fiber, while exposure to rAd5 through vaccination elicited antibodies primarily to capsid proteins other than fiber. Notably, preexisting immunity to Ad5 fiber from natural infection significantly reduced the CD4 and CD8 cell responses to HIV Gag after DNA/rAd5 vaccination. The specificity of Ad5 neutralizing antibodies therefore differs depending on the route of exposure, and natural Ad5 infection compromises Ad5 vaccine-induced immunity to weak immunogens, such as HIV-1 Gag. These results have implications for future AIDS vaccine trials and the design of next-generation gene-based vaccine vectors.Recombinant adenovirus (rAd)-based vectors are currently under investigation in a variety of gene therapy and T-cell-based vaccine clinical trials. There are more than 370 such ongoing clinical trials for broad applications, including infectious diseases and cancer therapy (http://www.wiley.co.uk/genetherapy/clinical/). Based on supportive data from nonhuman primate studies, rAd-based vectors have been developed and tested in human clinical trials to deliver human immunodeficiency virus (HIV-1) gene products that stimulate HIV-specific immune responses. Preexisting immunity to Ad serotype 5 (Ad5), from which most vectors are derived, is common in humans. Though neutralizing antibodies to Ad5 may reduce the immunogenicity of Ad5-based vectors in animal models (16), their effect on immunity in subjects with previous Ad5 infection is poorly understood. In the STEP trial, which tested a Merck rAd5 vaccine encoding HIV-1 Gag, Pol, and Nef, vaccination failed to show protection, either by lowering viral load or by decreasing acquisition of infection (3, 9, 12, 21). Furthermore, the possibility was raised that subjects with preexisting neutralizing antibodies from natural Ad5 infection may have carried an increased risk of HIV infection after vaccination. Thus, understanding the nature and immune effects of Ad5 seropositivity in humans is important to the development of vaccines against AIDS and other diseases.Ad5 is a common cause of respiratory disease and an occasional cause of gastroenteritis in humans, and exposure before adolescence is common in human populations (19). Such exposure stimulates both innate and adaptive immune responses that generate neutralizing antibodies and virus-specific T-cell responses (6). These antibodies can also synergize with each other to achieve maximum viral neutralization (7, 22). The capsid protein specificity of Ad5 neutralizing antibodies has been reported for humans following administration of rAd5 gene therapy vectors for advanced liver or lung cancer (7, 10). However, results were presented solely for antibodies induced by administration of rAd5. One report has assessed Ad5 neutralizing antibodies with a healthy human population that was Ad5 seropositive from natural exposure to the virus (18). The median titer of the population was presented, but the frequency of protein-specific neutralizing antibody has not been defined for humans.Here we describe the first report of the natural frequency and effect on immunization of neutralizing antibodies specific for different Ad capsid proteins in human subjects. We address the fundamental mechanisms of how humans generate neutralizing antibodies to a common cold virus that is in widespread use as a vector for gene therapy and vaccines. Such mechanisms may also be applicable to other nonenveloped viruses, including adeno-associated viruses and other viruses containing multiple envelope surface proteins, like influenza. To analyze the contribution of anti-capsid antibodies to neutralization by different human serum samples, wild-type and chimeric vectors were utilized. For example, a rAd type 5 (rAd5) vector with a fiber derived from Ad35 fiber (rAd5 F35) can be used to analyze the anti-Ad5 capsid response independent of fiber. Conversely, a rAd35 vector with a fiber transposed from Ad5 can determine the specificity of neutralization mediated by the Ad5 fiber. Using these vectors, we have analyzed human serum samples from two HIV vaccine clinical trials, VRC 006 and HVTN 204, in which a single-dose rAd5 vaccine alone and a three-dose DNA prime/single dose rAd5 boost vaccine encoding HIV-1 Env A,B, and C; Gag; and Pol, respectively, were administered. Thus, we sought to characterize the specificity of rAd5 neutralizing antibodies in Ad5-immune subjects and to determine their effect on immune responses elicited by vaccination.     

The genetic architecture of fitness in a seed beetle: assessing the potential for indirect genetic benefits of female choice

Background  

Quantifying the amount of standing genetic variation in fitness represents an empirical challenge. Unfortunately, the shortage of detailed studies of the genetic architecture of fitness has hampered progress in several domains of evolutionary biology. One such area is the study of sexual selection. In particular, the evolution of adaptive female choice by indirect genetic benefits relies on the presence of genetic variation for fitness. Female choice by genetic benefits fall broadly into good genes (additive) models and compatibility (non-additive) models where the strength of selection is dictated by the genetic architecture of fitness. To characterize the genetic architecture of fitness, we employed a quantitative genetic design (the diallel cross) in a population of the seed beetle Callosobruchus maculatus, which is known to exhibit post-copulatory female choice. From reciprocal crosses of inbred lines, we assayed egg production, egg-to-adult survival, and lifetime offspring production of the outbred F1 daughters (F1 productivity).     

Lettuce mosaic virus: from pathogen diversity to host interactors

TAXONOMY: Lettuce mosaic virus (LMV) belongs to the genus Potyvirus (type species Potato virus Y) in the family Potyviridae. PHYSICAL PROPERTIES: The virion is filamentous, flexuous with a length of 750 nm and a width of 15 nm. The particles are made of a genomic RNA of 10 080 nucleotides, covalently linked to a viral-encoded protein (the VPg) at the 5' end and with a 3' poly A tail, and encapsidated in a single type of capsid protein. The molecular weight of the capsid protein subunit has been estimated electrophoretically to be 34 kDa and estimated from the amino acid sequence to be 31 kDa. GENOME ORGANIZATION: The genome is expressed as a polyprotein of 3255 amino-acid residues, processed by three virus-specific proteinases into ten mature proteins. HOSTS: LMV has a worldwide distribution and a relatively broad host range among several families. Weeds and ornamentals can act as local reservoirs for lettuce crops. In particular, many species within the family Asteraceae are susceptible to LMV, including cultivated and ornamental species such as common (Lactuca sativa), prickly (L. serriola) or wild (L. virosa) lettuce, endive/escarole (Cichorium endiva), safflower (Carthamus tinctorius), starthistle (Centaurea solstitialis), Cape daisy (Osteospermum spp.) and gazania (Gazania rigens). In addition, several species within the families Brassicaceae, Cucurbitaceae, Fabaceae, Solanaceae and Chenopodiaceae are natural or experimental hosts of LMV. Genetic control of resistance to LMV: The only resistance genes currently used to protect lettuce crops worldwide are the recessive genes mo1(1) and mo1(2) corresponding to mutant alleles of the gene encoding the translation initiation factor eIF4E in lettuce. It is believed that at least one intact copy of eIF4E must be present to ensure virus accumulation. TRANSMISSION: LMV is transmitted in a non-persistent manner by a high number of aphid species. Myzus persicae and Macrosiphum euphorbiae are particularly active in disseminating this virus in the fields. LMV is also seedborne in lettuce. The effectiveness of LMV transmission depends on the cultivar and the age of the seed carrier at the inoculation time. SYMPTOMS: The characteristic symptoms on susceptible lettuce cultivars are dwarfism, mosaic, distortion and yellowing of the leaves with sometimes a much reduced heart of lettuce (failure to form heads). The differences in virus strains, cultivars and the physiological stage of the host at the moment of the attack cause different symptom severity: from a very slight discoloration of the veins to severe necrosis leading to the death of the plant.     

Anatomical and chemical characteristics of the seed coat of <i>Medicago sativa</i> L. (alfalfa) cv. Baralfa 85 seeds and their association with seed dormancy

Seeds of alfalfa (Medicago sativa L.) can exhibit seedcoat imposed dormancy, which produces hard seeds within a seed lot. These seeds do not germinate because they do not imbibe water due to a barrier to water entry in the seed coat. The aim of this work was to analyze the anatomical and chemical characteristics of the testa of alfalfa seeds with respect to water permeability levels. The anatomy of seeds of the cv. Baralfa 85 was studied and structural substances, polyphenols, tannins and cutin present in the testa of seeds of different water permeability levels were determined. The anatomical characteristics of the seed coat and the proportions of components were found to determine the permeability level of the seed coat, an aspect that is associated with the physical seed dormancy level. Anatomically, increased thickness of the testa was associated with a lower permeability level. The difference may be attributed to the variation in cuticle thickness, length of macrosclereids and thickness of the cell wall, and presence and development of osteosclereids. From the physiological and chemical points of view, the mechanism of physical dormancy of the testa is explained by a greater amount of components that repel water and cement the cell wall, such as polyphenols, lignins, condensed tannins, pectic substances, and a lower proportion of cellulose and hemicellulose.     

Coilin Shuttles between the Nucleus and Cytoplasm In Xenopus Oocytes

Coiled bodies are discrete nuclear organelles often identified by the marker protein p80-coilin. Because coilin is not detected in the cytoplasm by immunofluorescence and Western blotting, it has been considered an exclusively nuclear protein. In the Xenopus germinal vesicle (GV), most coilin actually resides in the nucleoplasm, although it is highly concentrated in 50-100 coiled bodies. When affinity-purified anti-coilin antibodies were injected into the cytoplasm of oocytes, they could be detected in coiled bodies within 2-3 h. Coiled bodies were intensely labeled after 18 h, whereas other nuclear organelles remained negative. Because the nuclear envelope does not allow passive diffusion of immunoglobulins, this observation suggests that anti-coilin antibodies are imported into the nucleus as an antigen-antibody complex with coilin. Newly synthesized coilin is not required, because cycloheximide had no effect on nuclear import and subsequent targeting of the antibodies. Additional experiments with myc-tagged coilin and myc-tagged pyruvate kinase confirmed that coilin is a shuttling protein. The shuttling of Nopp140, NO38/B23, and nucleolin was easily demonstrated by the targeting of their respective antibodies to the nucleoli, whereas anti-SC35 did not enter the germinal vesicle. We suggest that coilin, perhaps in association with Nopp140, may function as part of a transport system between the cytoplasm and the coiled bodies.     

A phase 1 clinical trial of nerve growth factor gene therapy for Alzheimer disease

Cholinergic neuron loss is a cardinal feature of Alzheimer disease. Nerve growth factor (NGF) stimulates cholinergic function, improves memory and prevents cholinergic degeneration in animal models of injury, amyloid overexpression and aging. We performed a phase 1 trial of ex vivo NGF gene delivery in eight individuals with mild Alzheimer disease, implanting autologous fibroblasts genetically modified to express human NGF into the forebrain. After mean follow-up of 22 months in six subjects, no long-term adverse effects of NGF occurred. Evaluation of the Mini-Mental Status Examination and Alzheimer Disease Assessment Scale-Cognitive subcomponent suggested improvement in the rate of cognitive decline. Serial PET scans showed significant (P < 0.05) increases in cortical 18-fluorodeoxyglucose after treatment. Brain autopsy from one subject suggested robust growth responses to NGF. Additional clinical trials of NGF for Alzheimer disease are warranted.     

Alternative splicing and protein function

Background  

Alternative splicing is a major mechanism of generating protein diversity in higher eukaryotes. Although at least half, and probably more, of mammalian genes are alternatively spliced, it was not clear, whether the frequency of alternative splicing is the same in different functional categories. The problem is obscured by uneven coverage of genes by ESTs and a large number of artifacts in the EST data.     

Preferential Incorporation of Coloured-carotenoids Occurs in the LH2 Complexes From Non-sulphur Purple Bacteria Under Carotenoid-limiting Conditions

The effect of growing Rhodopseudomonas (Rps.) acidophila and Rps. palustris in the presence of different concentrations of the carotenoid (Car) biosynthetic inhibitor diphenylamine (DPA) has been investigated. Growth with sub-maximal concentrations of DPA induces Car limitation. The exact response to DPA is species dependent. However, both Rps. acidophila and Rps. palustris respond by preferentially incorporating the limiting amount of coloured Cars into their LH2 complexes at the expense of the RC-LH1 complexes. As inhibition by DPA becomes more severe there is an increase in the percentage of Cars with reduced numbers of conjugated C=C bonds. The effect of this changed Car composition on the structure and function of the antenna complexes has been investigated using absorption, fluorescence, CD and Raman spectroscopies. The results show that although the presence of Car molecules is important for the stability of the LH2 complexes that the overall native structure can be maintained by the presence of many different Cars.