Outer Membrane Protease/Adhesin PgtE of Salmonella enterica: Role in Salmonella-Host Interaction

Salmonella enterica serovar Typhimurium is a common cause of gastroenteritis in humans and, occasionally, also causes systemic infection. During systemic infection an important characteristic of Salmonella is its ability to survive and replicate within macrophages. The outer membrane protease PgtE of S. enterica is a member of the omptin family of outer membrane aspartate proteases, which are beta-barrel proteins with five surface-exposed loops. The main goals of this study were to characterize biological substrates and pathogenesis-associated functions of PgtE and to determine the conditions where PgtE is fully active. In this study we found that PgtE requires rough lipopolysaccharide (LPS) to be functional but is sterically inhibited by the long O-antigen side chain in smooth LPS. Salmonella isolates normally are smooth with a long oligosaccharide O-antigen, and PgtE remains functionally cryptic in wild-type Salmonella cultivated in vitro. Interestingly, our results showed that due to increased expression of PgtE and to reduced length of the LPS O-antigen chains, the wild-type Salmonella expresses highly functional PgtE when isolated from mouse macrophage-like J774A.1 cells. Salmonella is thought to be continuously released from macrophages to infect new ones, and our results suggest that PgtE is functional during these transient extracellular growth phases. Six novel host protein substrates were identified for PgtE in this work. PgtE was previously known to activate human plasminogen (Plg) to plasmin, a broad-spectrum serine protease, and in this study PgtE was shown to interfere with the Plg system by inactivating the main inhibitor of plasmin, alpha2-antiplasmin. PgtE also interferes with another important proteolytic system of mammals by activating pro-matrix metalloproteinase-9 to an active gelatinase. PgtE also directly degrades gelatin, a component of extracellular matrices. PgtE also increases bacterial resistance against complement-mediated killing in human serum and enhances survival of Salmonella within murine macrophages as well as in the liver and spleen of intraperitoneally infected mice. Taken together, the results in this study suggest that PgtE is a virulence factor of Salmonella that has adapted to interfere with host proteolytic systems and to modify extracellular matrix; these features likely assist the migration of Salmonella during systemic salmonellosis.

Comparative and functional genome analysis of fungi for development of the protein production host Trichoderma reesei

Filamentous fungi of the subphylum Pezizomycotina are well known as protein and secondary metabolite producers. Various industries take advantage of these capabilities. However, the molecular biology of yeasts, i.e. Saccharomycotina and especially that of Saccharomyces cerevisiae, the baker's yeast, is much better known. In an effort to explain fungal phenotypes through their genotypes we have compared protein coding gene contents of Pezizomycotina and Saccharomycotina. Only biomass degradation and secondary metabolism related protein families seem to have expanded recently in Pezizomycotina. Of the protein families clearly diverged between Pezizomycotina and Saccharomycotina, those related to mitochondrial functions emerge as the most prominent. However, the primary metabolism as described in S. cerevisiae is largely conserved in all fungi. Apart from the known secondary metabolism, Pezizomycotina have pathways that could link secondary metabolism to primary metabolism and a wealth of undescribed enzymes. Previous studies of individual Pezizomycotina genomes have shown that regardless of the difference in production efficiency and diversity of secreted proteins, the content of the known secretion machinery genes in Pezizomycotina and Saccharomycotina appears very similar. Genome wide analysis of gene products is therefore needed to better understand the efficient secretion of Pezizomycotina. We have developed methods applicable to transcriptome analysis of non-sequenced organisms. TRAC (Transcriptional profiling with the aid of affinity capture) has been previously developed at VTT for fast, focused transcription analysis. We introduce a version of TRAC that allows more powerful signal amplification and multiplexing. We also present computational optimisations of transcriptome analysis of non-sequenced organism and TRAC analysis in general. Trichoderma reesei is one of the most commonly used Pezizomycotina in the protein production industry. In order to understand its secretion system better and find clues for improvement of its industrial performance, we have analysed its transcriptomic response to protein secretion stress conditions. In comparison to S. cerevisiae, the response of T. reesei appears different, but still impacts on the same cellular functions. We also discovered in T. reesei interesting similarities to mammalian protein secretion stress response. Together these findings highlight targets for more detailed studies.

The viral coat protein is regulated by HSP70 and HSP40 in Potato virus A infection

Plus-stranded (plus) RNA viruses multiply within a cellular environment as tightly integrated units and rely on the genetic information carried within their genomes for multiplication and, hence, persistence. The minimal genomes of plus RNA viruses are unable to encode the molecular machineries that are required for virus multiplication. This sets requisites for the virus, which must form compatible interactions with host components during multiplication to successfully utilize primary metabolites as building blocks or metabolic energy, and to divert the protein synthesis machinery for production of viral proteins. In fact, the emerging picture of a virus-infected cell displays tight integration with the virus, from simple host and virus protein interactions through to major changes in the physiological state of the host cell. This study set out to develop a method for the identification of host components, mainly host proteins, that interact with proteins of Potato virus A (PVA; Potyvirus) during infection. This goal was approached by developing affinity-tag based methods for the purification of viral proteins complexed with associated host proteins from infected plants. Using this method, host membrane-associated viral ribonucleoprotein (RNP) complexes were obtained, and several host and viral proteins could be identified as components of these complexes. One of the host proteins identified using this strategy was a member of the heat shock protein 70 (HSP70) family, and this protein was chosen for further analysis. To enable the analysis of viral gene expression, a second method was developed based on Agrobacterium-mediated virus genome delivery into plant cells, and detection of virally expressed Renilla luciferase (RLUC) as a quantitative measure of viral gene expression. Using this method, it was observed that down-regulation of HSP70 caused a PVA coat protein (CP)-mediated defect associated with replication. Further experimentation suggested that CP can inhibit viral gene expression and that a distinct translational activity coupled to replication, referred to as replication-associated translation (RAT), exists. Unlike translation of replication-deficient viral RNA, RAT was dependent on HSP70 and its co-chaperone CPIP. HSP70 and CPIP together regulated CP turnover by promoting its modification by ubiquitin. Based on these results, an HSP70 and CPIP-driven mechanism that functions to regulate CP during viral RNA replication and/or translation is proposed, possibly to prevent premature particle assembly caused by CP association with viral RNA.

Phylogeny of a taxonomically difficult group and evolution of host location mechanism

The parasitic wasps are one of the largest insect groups and their life histories are remarkably variable. Common to all parasitic wasps is that they kill their hosts, which are usually beetles, butterflies and sometimes spiders. Hosts are often at a larval or pupal stage and live in concealed conditions, such as in plant tissue. Parasitic wasps have two main ways of finding their host. 1) They can detect chemical compounds emitted by damaged plant material or released by larvae living in plant tissue, and 2) detect the larvae by sound vibrations. Even though pupae are immobile and silent, and therefore do not cause vibration, parasitoids have, however, adapted to find passive developmental stages by producing vibration themselves by knocking the substrate with their antennae, and then detecting the echoes with their legs. This echolocation allows a parasitoid to locate its potential hosts that are deeply buried in wood. This study focuses on the relationships of the subfamily Cryptinae (Hymenoptera: Ichneumonidae) and related taxa, and the evolution of host location mechanism. There are no earlier studies of the phylogeny of the Cryptinae, and the position of related taxa are unclear. According to the earlier classification, which is entirely intuitional, the Cryptinae is divided into three tribes: Cryptini, Hemigasterini and Phygadeuontini. Further, these tribes are subdiveded into numerous subtribes. This work, based on molecular characters, shows that the cryptine tribes Cryptini, Phygadeuon¬tini and Hemigasterini come out largely as monophyletic groups, thus agreeing with the earlier classification. The earlier subtribal classification had no support. In addition, it is shown that modified antennal structures are associated with host usage of wood-boring coleopteran hosts. The cryptines have a clear modification series on their antennal tips from a simply tip to a hammer-like structure. The species with strongly modified antennae belong mostly to the tribe Cryptini and they utilise wood-boring beetles as hosts. Also, field observations on insect behaviour support this result.

Mitochondrial helicase Twinkle in mtDNA copy number regulation and a late-onset disease model

Mitochondrial diseases are caused by disturbances of the energy metabolism. The disorders range from severe childhood neurological diseases to muscle diseases of adults. Recently, mitochondrial dysfunction has also been found in Parkinson s disease, diabetes, certain types of cancer and premature aging. Mitochondria are the power plants of the cell but they also participate in the regulation of cell growth, signaling and cell death. Mitochondria have their own genetic material, mtDNA, which contains the genetic instructions for cellular respiration. Single cell may host thousands of mitochondria and several mtDNA molecules may reside inside single mitochondrion. All proteins needed for mtDNA maintenance are, however, encoded by the nuclear genome, and therefore, mutations of the corresponding genes can also cause mitochondrial disease. We have here studied the function of mitochondrial helicase Twinkle. Our research group has previously identified nuclear Twinkle gene mutations underlying an inherited adult-onset disorder, progressive external ophthalmoplegia (PEO). Characteristic for the PEO disease is the accumulation of multiple mtDNA deletions in tissues such as the muscle and brain. In this study, we have shown that Twinkle helicase is essential for mtDNA maintenance and that it is capable of regulating mtDNA copy number. Our results support the role of Twinkle as the mtDNA replication helicase. No cure is available for mitochondrial disease. Good disease models are needed for studies of the cause of disease and its progression and for treatment trials. Such disease model, which replicates the key features of the PEO disease, has been generated in this study. The model allows for careful inspection of how Twinkle mutations lead to mtDNA deletions and further causes the PEO disease. This model will be utilized in a range of studies addressing the delay of the disease onset and progression and in subsequent treatment trials. In conclusion, in this thesis fundamental knowledge of the function of the mitochondrial helicase Twinkle was gained. In addition, the first model for adult-onset mitochondrial disease was generated.

Children’s Relationship to Plants among Primary School Children in Finland

There is considerable evidence that children in modern society are losing
their contact with nature and, more precisely, with green plants. Is this also the case in Finland, a northern country famous for its forests and wild nature? This study examines the relationship of 9- to 10-year-old Finnish schoolchildren with the green environment and plants. The data were gathered by a questionnaire
comprising structured and open-ended questions. The focus of the research was on two comparisons: first, on the nature and child relationship in rural and urban neighborhoods and, second, among boys and girls. Participants in the study amounted to a total of 76 children, 42 in the Helsinki suburb area and 34 in Paltamo. The results suggested that the children in rural surroundings had closer contact with nature than their urban associates. For example, the children of Paltamo reported to know the trees better, and considered human beings to be part of nature more often (100% vs. 76% of the pupils in Helsinki, P = 0,003). Similarly, the results showed that girls in the study (N = 48) were more interested in plants than boys (N = 28). For the girls, the beauty and joy of plants was important, whereas the boys appreciated plants as the source of life. After the pre-questioning, the children of Helsinki participated in an in-class horticultural intervention and 10 days later, answered a similar questionnaire again. The results of the open-ended questions revealed that equally to children in other Western countries, Finnish children may also be in danger of losing their direct contact with the natural environment. It was common to pass free time in organized sports such as hockey or football (boys), or by just walking and talking with friends (girls). Rural children told that they still built huts, pick berries, and climb trees, whereas urban children played in parks and city groves. The results suggest that it is essential to research
further the children’s own experiences if we are to understand, and subsequently, to enhance, the crucial role of the green environment in their lives. Horticultural interventions can be effective starting points to add to children’s knowledge, affection, and interest toward greenery, but it is highly recommended that they take place outdoors rather than indoors.

Using IRAP markers for analysis of genetic variability in populations of resource and rare species of plants

Species specific LTR retrotransposons were first cloned in five rare relic species of drug plants located in the Perm’ region. Sequences of LTR retrotransposons were used for PCR analysis based on amplification of repeated sequences from LTR or other sites of retrotransposons (IRAP). Genetic diversity was studied in six populations of rare relic species of plants Adonis vernalis L. by means of the IRAP method; 125 polymorphic IRAP markers were analyzed. Parameters for DNA polymorphism and genetic diversity of A. vernalis populations were determined.

Children’s Relationship to Plants among Primary School Children in Finland

There is considerable evidence that children in modern society are losing
their contact with nature and, more precisely, with green plants. Is this also the case in Finland, a northern country famous for its forests and wild nature? This study examines the relationship of 9- to 10-year-old Finnish schoolchildren with the green environment and plants. The data were gathered by a questionnaire
comprising structured and open-ended questions. The focus of the research was on two comparisons: first, on the nature and child relationship in rural and urban neighborhoods and, second, among boys and girls. Participants in the study amounted to a total of 76 children, 42 in the Helsinki suburb area and 34 in Paltamo. The results suggested that the children in rural surroundings had closer contact with nature than their urban associates. For example, the children of Paltamo reported to know the trees better, and considered human beings to be part of nature more often (100% vs. 76% of the pupils in Helsinki, P = 0,003). Similarly, the results showed that girls in the study (N = 48) were more interested in plants than boys (N = 28). For the girls, the beauty and joy of plants was important, whereas the boys appreciated plants as the source of life. After the pre-questioning, the children of Helsinki participated in an in-class horticultural intervention and 10 days later, answered a similar questionnaire again. The results of the open-ended questions revealed that equally to children in other Western countries, Finnish children may also be in danger of losing their direct contact with the natural environment. It was common to pass free time in organized sports such as hockey or football (boys), or by just walking and talking with friends (girls). Rural children told that they still built huts, pick berries, and climb trees, whereas urban children played in parks and city groves. The results suggest that it is essential to research
further the children’s own experiences if we are to understand, and subsequently, to enhance, the crucial role of the green environment in their lives. Horticultural interventions can be effective starting points to add to children’s knowledge, affection, and interest toward greenery, but it is highly recommended that they take place outdoors rather than indoors.

Using IRAP markers for analysis of genetic variability in populations of resource and rare species of plants

Species specific LTR retrotransposons were first cloned in five rare relic species of drug plants located in the Perm’ region. Sequences of LTR retrotransposons were used for PCR analysis based on amplification of repeated sequences from LTR or other sites of retrotransposons (IRAP). Genetic diversity was studied in six populations of rare relic species of plants Adonis vernalis L. by means of the IRAP method; 125 polymorphic IRAP markers were analyzed. Parameters for DNA polymorphism and genetic diversity of A. vernalis populations were determined.

Children’s Relationship to Plants among Primary School Children in Finland

There is considerable evidence that children in modern society are losing
their contact with nature and, more precisely, with green plants. Is this also the case in Finland, a northern country famous for its forests and wild nature? This study examines the relationship of 9- to 10-year-old Finnish schoolchildren with the green environment and plants. The data were gathered by a questionnaire
comprising structured and open-ended questions. The focus of the research was on two comparisons: first, on the nature and child relationship in rural and urban neighborhoods and, second, among boys and girls. Participants in the study amounted to a total of 76 children, 42 in the Helsinki suburb area and 34 in Paltamo. The results suggested that the children in rural surroundings had closer contact with nature than their urban associates. For example, the children of Paltamo reported to know the trees better, and considered human beings to be part of nature more often (100% vs. 76% of the pupils in Helsinki, P = 0,003). Similarly, the results showed that girls in the study (N = 48) were more interested in plants than boys (N = 28). For the girls, the beauty and joy of plants was important, whereas the boys appreciated plants as the source of life. After the pre-questioning, the children of Helsinki participated in an in-class horticultural intervention and 10 days later, answered a similar questionnaire again. The results of the open-ended questions revealed that equally to children in other Western countries, Finnish children may also be in danger of losing their direct contact with the natural environment. It was common to pass free time in organized sports such as hockey or football (boys), or by just walking and talking with friends (girls). Rural children told that they still built huts, pick berries, and climb trees, whereas urban children played in parks and city groves. The results suggest that it is essential to research
further the children’s own experiences if we are to understand, and subsequently, to enhance, the crucial role of the green environment in their lives. Horticultural interventions can be effective starting points to add to children’s knowledge, affection, and interest toward greenery, but it is highly recommended that they take place outdoors rather than indoors.