The aspartic proteinase family of three Phytophthora species

Background - Phytophthora species are oomycete plant pathogens with such major social and economic impact that genome sequences have been determined for Phytophthora infestans, P. sojae and P. ramorum. Pepsin-like aspartic proteinases (APs) are produced in a wide variety of species (from bacteria to humans) and contain conserved motifs and landmark residues. APs fulfil critical roles in infectious organisms and their host cells. Annotation of Phytophthora APs would provide invaluable information for studies into their roles in the physiology of Phytophthora species and interactions with their hosts. Results - Genomes of Phytophthora infestans, P. sojae and P. ramorum contain 11-12 genes encoding APs. Nine of the original gene models in the P. infestans database and several in P. sojae and P. ramorum (three and four, respectively) were erroneous. Gene models were corrected on the basis of EST data, consistent positioning of introns between orthologues and conservation of hallmark motifs. Phylogenetic analysis resolved the Phytophthora APs into 5 clades. Of the 12 sub-families, several contained an unconventional architecture, as they either lacked a signal peptide or a propart region. Remarkably, almost all APs are predicted to be membrane-bound. Conclusions - One of the twelve Phytophthora APs is an unprecedented fusion protein with a putative G-protein coupled receptor as the C-terminal partner. The others appear to be related to well-documented enzymes from other species, including a vacuolar enzyme that is encoded in every fungal genome sequenced to date. Unexpectedly, however, the oomycetes were found to have both active and probably-inactive forms of an AP similar to vertebrate BACE, the enzyme responsible for initiating the processing cascade that generates the Aß peptide central to Alzheimer's Disease. The oomycetes also encode enzymes similar to plasmepsin V, a membrane-bound AP that cleaves effector proteins of the malaria parasite Plasmodium falciparum during their translocation into the host red blood cell. Since the translocation of Phytophthora effector proteins is currently a topic of intense research activity, the identification in Phytophthora of potential functional homologues of plasmepsin V would appear worthy of investigation. Indeed, elucidation of the physiological roles of the APs identified here offers areas for future study. The significant revision of gene models and detailed annotation presented here should significantly facilitate experimental design

The Botrytis cinerea endopolygalacturonase gene family

C ell w all d egrading e nzyme s (CWDEs) secreted by microbial plant pathogens have been suggested to function as virulence factors. Evidence that particular bacterial CWDEs contribute to virulence has emerged in the last two decades. Targeted gene replacement of different genes encoding CWDEs resulted in mutants with reduced virulence on a number of host plants. Similar molecular genetic approaches in plant pathogenic fungi have, until recently, been unsuccessful in elucidating a role for fungal CWDEs in pathogenesis. This thesis describes molecular genetic analyses of CWDEs secreted by the necrotrophic plant pathogenic fungus Botrytis cinerea , the causal agent of gray mould.From literature it was known that B. cinerea secretes many CWDEs when grown in liquid culture. The number of CWDE encoding genes present in the B. cinerea genome was unknown and detailed expression studies were lacking. In order to fill this knowledge gap we used the following strategy:Cloning of genes encoding CWDEsStudy of the expression of CWDE genes both in liquid cultures and in plantaTargeted deletion of CWDE genes that have expression patterns that indicate a function in the infection processChapter 1 introduces the research area and gives an outline of the thesis. It describes a model of the chemical and structural composition of the plant cell wall and reviews various classes of microbial CWDEs. It summarises previously published data on the role of bacterial and fungal CWDEs in pathogenesis in general and on the CWDEs secreted by B. cinerea in particular. B. cinerea has a wide host range but prefers hosts that contain high amounts of pectin. Therefore the focus was on endo p oly g alacturonases (endoPGs), enzymes that cleave homogalacturonan, a major constituent of pectin.In order to study gene expression of B. cinereain planta , it was essential to develop a standardised inoculation procedure that enables reproducible infections both in time and space. The development of this inoculation procedure for tomato leaves is described in Chapter 2. The expression of two fungal genes and a number of plant PR-protein genes was investigated in time course experiments performed at two different incubation temperatures.Subsequently, we set out to clone the genes of interest, analysed their expression and studied the effect in pathogenesis by targeted gene replacement. The genes were isolated by hybridisation with heterologous probes. The first gene that was cloned and characterised, Bcpg 1, is constitutively expressed. Targeted replacement of this gene resulted in a mutant with reduced virulence on apple fruits and tomato (Chapter 3). Subsequently, five additional endoPG genes were isolated (Chapter 4). The gene products were compared with other fungal endoPGs and it was shown that the members of the B. cinereaBcpg gene family fall into at least three distinct monophyletic groups (Chapter 4).The members of the endoPG gene family, denoted as Bcpg 1-6, are differentially expressed in liquid cultures that differed in carbon source or pH (Chapters 4). The constitutive expression pattern of Bcpg 1, as found in Chapter 3, was further confirmed. Bcpg 2 is expressed under all circumstances tested except when B. cinerea is grown in glucose-containing medium at low pH. Bcpg 3 is expressed at low ambient pH. Bcpg 4 is induced by the pectin breakdown end-product galacturonic acid, and is repressed by glucose. Bcpg 5 expression can be induced by a yet unknown factor present in apple pectin. Bcpg 6 is, like Bcpg 4, induced by galacturonic acid but is, unlike Bcpg 4, not repressed by glucose. The expression of the endoPG gene family enables the fungus to degrade pectate in a flexible manner. It enables the fungus to respond to environmental signals like nutrient availability and pH.The expression of the endoPG gene family during infection of tomato leaf, broad bean leaf, apple fruit and courgette fruit was studied (Chapter 5). Expression of the genes in planta is differential and most expression patterns can be explained by the results of expression studies in liquid cultures. Bcpg 1 is expressed in all host tissues tested, whereas expression of Bcpg 2 is evident in tomato, broad bean and courgette. Bcpg 3 and Bcpg 5 are expressed in apple fruit. Bcpg 4 and Bcpg 6 are expressed in all host tissues tested.Chapter 6 discusses the results in a broader context. It is hypothesised that, besides Bcpg 1, additional members of the Bcpg gene family contribute to virulence, albeit likely under specific circumstances. It is suggested that fungal CWDEs can play a role in plant pathogenesis but that this role also strongly depends on the lifestyle of the fungus. It is postulated that B. cinerea depends strongly on endoPGs for successful infection. The research described in this thesis may lead to novel disease control strategies that rely on P oly G alacturonase I nhibiting P rotein (PGIP) expression in transgenic host plants.</p

The aspartic proteinase family of three Phytophthora species

Background: Phytophthora species are oomycete plant pathogens with such major social and economic impact that genome sequences have been determined for Phytophthora infestans, P. sojae and P. ramorum. Pepsin-like aspartic proteinases (APs) are produced in a wide variety of species (from bacteria to humans) and contain conserved motifs and landmark residues. APs fulfil critical roles in infectious organisms and their host cells. Annotation of Phytophthora APs would provide invaluable information for studies into their roles in the physiology of Phytophthora species and interactions with their hosts. Results: Genomes of Phytophthora infestans, P. sojae and P. ramorum contain 11-12 genes encoding APs. Nine of the original gene models in the P. infestans database and several in P. sojae and P. ramorum (three and four, respectively) were erroneous. Gene models were corrected on the basis of EST data, consistent positioning of introns between orthologues and conservation of hallmark motifs. Phylogenetic analysis resolved the Phytophthora APs into 5 clades. Of the 12 sub-families, several contained an unconventional architecture, as they either lacked a signal peptide or a propart region. Remarkably, almost all APs are predicted to be membrane-bound. Conclusions: One of the twelve Phytophthora APs is an unprecedented fusion protein with a putative G-protein coupled receptor as the C-terminal partner. The others appear to be related to well-documented enzymes from other species, including a vacuolar enzyme that is encoded in every fungal genome sequenced to date. Unexpectedly, however, the oomycetes were found to have both active and probably-inactive forms of an AP similar to vertebrate BACE, the enzyme responsible for initiating the processing cascade that generates the Aβ peptide central to Alzheimer's Disease. The oomycetes also encode enzymes similar to plasmepsin V, a membrane-bound AP that cleaves effector proteins of the malaria parasite Plasmodium falciparum during their translocation into the host red blood cell. Since the translocation of Phytophthora effector proteins is currently a topic of intense research activity, the identification in Phytophthora of potential functional homologues of plasmepsin V would appear worthy of investigation. Indeed, elucidation of the physiological roles of the APs identified here offers areas for future study. The significant revision of gene models and detailed annotation presented here should significantly facilitate experimental design.Fil: Kay, John. Cardiff University; Reino UnidoFil: Meijer, Harold J. G.. Wageningen University; Reino UnidoFil: Ten Have, Arjen. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mar del Plata. Instituto de Investigaciones Biológicas; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales; ArgentinaFil: van Kan, Jan A. L.. Wageningen University; Reino Unid

The bile duct ligated rat : a relevant model to study muscle mass loss in cirrhosis

Muscle mass loss and hepatic encephalopathy (complex neuropsychiatric disorder) are serious complications of chronic liver disease (cirrhosis) which impact negatively on clinical outcome and quality of life and increase mortality. Liver disease leads to hyperammonemia and ammonia toxicity is believed to play a major role in the pathogenesis of hepatic encephalopathy. However, the effects of ammonia are not brain-specific and therefore may also affect other organs and tissues including muscle. The precise pathophysiological mechanisms underlying muscle wasting in chronic liver disease remains to be elucidated. In the present study, we characterized body composition as well as muscle protein synthesis in cirrhotic rats with hepatic encephalopathy using the 6-week bile duct ligation (BDL) model which recapitulates the main features of cirrhosis. Compared to sham-operated control animals, BDL rats display significant decreased gain in body weight, altered body composition, decreased gastrocnemius muscle mass and circumference as well as altered muscle morphology. Muscle protein synthesis was also significantly reduced in BDL rats compared to control animals. These findings demonstrate that the 6-week BDL experimental rat is a relevant model to study liver disease-induced muscle mass loss

Genetic heterogeneity and trans regulators of gene expression

Heterogeneity poses a challenge to linkage mapping. Here, we apply a latent class extension of Haseman-Elston regression to expression phenotypes with significant evidence of linkage to trans regulators in 14 large pedigrees. We test for linkage, accounting for heterogeneity, and classify individual families as "linked" and "unlinked" on the basis of their contribution to the overall evidence of linkage

Parent-child interaction in Nigerian families: conversation analysis, context and culture

This paper uses a conversation analysis (CA) approach to explore parent child interaction (PCI) within Nigerian families. We illustrate how speech and language therapists (SLTs), by using CA, can tailor recommendations according to the interactional style of each individual family that are consonant with the family’s cultural beliefs. Three parent-child dyads were videoed playing and talking together in their home environments. The analysis uncovered a preference for instructional talk similar to that used in the classroom. Closer examination revealed that this was not inappropriate when considering the context of the activities and their perceived discourse role. Furthermore, this was not necessarily at the expense of responsivity or semantic contingency. The preference for instructional talk appeared to reflect deeply held cultural beliefs about the role of adults and children within the family and it is argued that the cultural paradigm is vitally important to consider when evaluating PCI. Given a potential risk that such young children may be vulnerable in terms of language difficulties, we offer an example of how PCI can be enhanced to encourage language development without disrupting the naturally occurring talk or the underlying purpose of the interaction

Extensive expansion of A1 family aspartic proteinases in fungi revealed by evolutionary analyses of 107 complete eukaryotic proteomes

The A1 family of eukaryotic aspartic proteinases (APs) forms one of the 16 AP families. Although one of the best characterized families, the recent increase in genome sequence data has revealed many fungal AP homologs with novel sequence characteristics. This study was performed to explore the fungal AP sequence space and to obtain an in-depth understanding of fungal AP evolution. Using a comprehensive phylogeny of approximately 700 AP sequences from the complete proteomes of 87 fungi and 20 nonfungal eukaryotes, 11 major clades of APs were defined of which clade I largely corresponds to the A1A subfamily of pepsin-archetype APs. Clade II largely corresponds to the A1B subfamily of nepenthesin-archetype APs. Remarkably, the nine other clades contain only fungal APs, thus indicating that fungal APs have undergone a large sequence diversification. The topology of the tree indicates that fungal APs have been subject to both “birth and death” evolution and “functional redundancy and diversification.” This is substantiated by coclustering of certain functional sequence characteristics. A meta-analysis toward the identification of Cluster Determining Positions (CDPs) was performed in order to investigate the structural and biochemical basis for diversification. Seven CDPs contribute to the secondary structure of the enzyme. Three other CDPs are found in the vicinity of the substrate binding cleft. Tree topology, the large sequence variation among fungal APs, and the apparent functional diversification suggest that an amendment to update the current A1 AP classification based on a comprehensive phylogenetic clustering might contribute to refinement of the classification in the MEROPS peptidase database

The design of a randomised controlled trial to evaluate the (cost-) effectiveness of the posterolateral versus the direct anterior approach for THA (POLADA - trial)

Background: Total hip arthroplasty (THA) is one of the most successful orthopaedic procedures. Because of the increasing number of THAs, a growing demand for faster recovery and a greater emphasis on cost-effectiveness, minimally invasive THAs have been introduced in the last decades. The direct anterior approach is a minimally invasive, tissue-sparing approach in which intermuscular planes are used. Theoretically, this approach should result in a faster recovery of physical functioning and higher health-related quality of life. Methods/design: A randomised controlled trial will be performed. Patients will be randomly allocated to undergo THA by means of the anterior or posterolateral approach. Both the intervention and control group will consist of two subgroups: 1) patients with a good bone stock who will receive an uncemented femoral stem, and 2) patients with a poor bone stock who will receive a cemented femoral stem. Patients between 18 and 90 years with primary or secondary osteoarthritis will be included. Physical functioning and health-related quality of life will be assessed by means of questionnaires. Additionally, performance based tests will be performed to objectively assess the physical functioning. Cost-effectiveness will be assessed by obtaining data on medical costs in and outside the hospital and other nonmedical costs. Measurements will take place preoperatively, two and six weeks, three months and one year postoperatively. Discussion: There is some evidence that the anterior approach results in reduced tissue damage and faster recovery in the direct postoperative period, compared to the posterolateral approach. However, there is still a lack of well-designed studies that have confirmed the better outcomes and cost-effectiveness of the anterior approach. Therefore, the purpose of this study is to assess the physical functioning, health related quality of life and the cost-effectiveness of the anterior approach, compared to the conventional posterolateral approach