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David C. Queller - One of the best experts on this subject based on the ideXlab platform.
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low base substitution mutation rate but high rate of slippage mutations in the sequence repeat rich genome of dictyostelium Discoideum
G3: Genes Genomes Genetics, 2020Co-Authors: David C. Queller, Debra A Brock, Sibel Kucukyildirim, Megan G Behringer, Way Sung, Thomas G Doak, Hatice Mergen, Joan E. StrassmannAbstract:We describe the rate and spectrum of spontaneous mutations for the social amoeba Dictyostelium Discoideum, a key model organism in molecular, cellular, evolutionary, and developmental biology. Whole-genome sequencing of 37 mutation accumulation lines of D. Discoideum after an average of 1,500 cell divisions yields a base-substitution mutation rate of 2.47 × 10−11 per site per generation, substantially lower than that of most eukaryotic and prokaryotic organisms, and of the same order of magnitude as in the ciliates Paramecium tetraurelia and Tetrahymena thermophila. Known for its high genomic AT content and abundance of simple sequence repeats, we observe that base-substitution mutations in D. Discoideum are highly A/T biased. This bias likely contributes both to the high genomic AT content and to the formation of simple sequence repeats in the AT-rich genome of Dictyostelium Discoideum. In contrast to the situation in other surveyed unicellular eukaryotes, indel rates far exceed the base-substitution mutation rate in this organism with a high proportion of 3n indels, particularly in regions without simple sequence repeats. Like ciliates, D. Discoideum has a large effective population size, reducing the power of random genetic drift, magnifying the effect of selection on replication fidelity, in principle allowing D. Discoideum to evolve an extremely low base-substitution mutation rate.
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endosymbiotic adaptations in three new bacterial species associated with dictyostelium Discoideum paraburkholderia agricolaris sp nov paraburkholderia hayleyella sp nov and paraburkholderia bonniea sp nov
PeerJ, 2020Co-Authors: Debra A Brock, Suegene Noh, Alicia N M Hubert, Tamara S Haselkorn, Susanne Disalvo, Melanie K Suess, Alexander S Bradley, Mahboubeh Tavakolinezhad, Katherine S Geist, David C. QuellerAbstract:Here we give names to three new species of Paraburkholderia that can remain in symbiosis indefinitely in the spores of a soil dwelling eukaryote, Dictyostelium Discoideum. The new species P. agricolaris sp. nov., P. hayleyella sp. nov., and P. bonniea sp. nov. are widespread across the eastern USA and were isolated as internal symbionts of wild-collected D. Discoideum. We describe these sp. nov. using several approaches. Evidence that they are each a distinct new species comes from their phylogenetic position, average nucleotide identity, genome-genome distance, carbon usage, reduced length, cooler optimal growth temperature, metabolic tests, and their previously described ability to invade D. Discoideum amoebae and form a symbiotic relationship. All three of these new species facilitate the prolonged carriage of food bacteria by D. Discoideum, though they themselves are not food. Further studies of the interactions of these three new species with D. Discoideum should be fruitful for understanding the ecology and evolution of symbioses.
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Cooperation and conflict in the social amoeba Dictyostelium Discoideum.
The International journal of developmental biology, 2019Co-Authors: James M Medina, David C. Queller, P M Shreenidhi, Tyler J Larsen, Joan E. StrassmannAbstract:The social amoeba Dictyostelium Discoideum has provided considerable insight into the evolution of cooperation and conflict. Under starvation, D. Discoideum amoebas cooperate to form a fruiting body comprised of hardy spores atop a stalk. The stalk development is altruistic because stalk cells die to aid spore dispersal. The high relatedness of cells in fruiting bodies in nature implies that this altruism often benefits relatives. However, since the fruiting body forms through aggregation there is potential for non-relatives to join the aggregate and create conflict over spore and stalk fates. Cheating is common in chimeras of social amoebas, where one genotype often takes advantage of the other and makes more spores. This social conflict is a significant force in nature as indicated by rapid rates of adaptive evolution in genes involved in cheating and its resistance. However, cheating can be prevented by high relatedness, allorecognition via tgr genes, pleiotropy and evolved resistance. Future avenues for the study of cooperation and conflict in D. Discoideum include the sexual cycle as well as the relationship between D. Discoideum and its bacterial symbionts. D. Discoideum's tractability in the laboratory as well as its uncommon mode of aggregative multicellularity have established it as a promising model for future studies of cooperation and conflict.
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whole genome sequencing of mutation accumulation lines reveals a low mutation rate in the social amoeba dictyostelium Discoideum
PLOS ONE, 2012Co-Authors: Gerda Saxer, Joan E. Strassmann, Paul Havlak, Sara A Fox, Michael Quance, Sharu Gupta, Yuriy Fofanov, David C. QuellerAbstract:Spontaneous mutations play a central role in evolution. Despite their importance, mutation rates are some of the most elusive parameters to measure in evolutionary biology. The combination of mutation accumulation (MA) experiments and whole-genome sequencing now makes it possible to estimate mutation rates by directly observing new mutations at the molecular level across the whole genome. We performed an MA experiment with the social amoeba Dictyostelium Discoideum and sequenced the genomes of three randomly chosen lines using high-throughput sequencing to estimate the spontaneous mutation rate in this model organism. The mitochondrial mutation rate of 6.76×10−9, with a Poisson confidence interval of 4.1×10−9 − 9.5×10−9, per nucleotide per generation is slightly lower than estimates for other taxa. The mutation rate estimate for the nuclear DNA of 2.9×10−11, with a Poisson confidence interval ranging from 7.4×10−13 to 1.6×10−10, is the lowest reported for any eukaryote. These results are consistent with low microsatellite mutation rates previously observed in D. Discoideum and low levels of genetic variation observed in wild D. Discoideum populations. In addition, D. Discoideum has been shown to be quite resistant to DNA damage, which suggests an efficient DNA-repair mechanism that could be an adaptation to life in soil and frequent exposure to intracellular and extracellular mutagenic compounds. The social aspect of the life cycle of D. Discoideum and a large portion of the genome under relaxed selection during vegetative growth could also select for a low mutation rate. This hypothesis is supported by a significantly lower mutation rate per cell division in multicellular eukaryotes compared with unicellular eukaryotes.
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Genetic diversity in the social amoeba Dictyostelium Discoideum: population differentiation and cryptic species.
Molecular phylogenetics and evolution, 2011Co-Authors: Tracy E. Douglas, David C. Queller, Marcus R. Kronforst, Joan E. StrassmannAbstract:The social amoeba Dictyostelium Discoideum is a commonly used model organism for the study of social evolution, multicellularity, and cell biology. But the boundaries and structure of the species have not been explored. The lack of morphological traits to distinguish D. Discoideum makes even knowing whether a given clone is D. Discoideum a challenge. We address this with a phylogeny of a widespread collection of clones from a range of locations and including clones identified previously as potential cryptic species. We sequenced portions of nuclear ribosomal DNA and mitochondrial DNA, analyzing approximately 5500 and 2500 base pairs from the two regions respectively. We compared these sequences to known reference sequences for both D. Discoideum and other closely related Dictyostelium species to create Bayesian and neighbor-joining phylogenetic trees representing the evolutionary relationships among the clones. We identified 51 unique D. Discoideum concatenated sequences based on the combined mitochondrial and ribosomal sequence data. We also identified four unique D. citrinum concatenated sequences, three of which were previously classified as D. Discoideum clones. Our analysis of the data revealed that all D. Discoideum clones form a monophyletic group, but there are several well-supported subclades and pronounced genetic differentiation among locations (F(ST)=0.242, P=0.011), suggesting the presence of geographic or other barriers between populations. Our results reveal the need for further investigation into potential tropical cryptic species.
Joan E. Strassmann - One of the best experts on this subject based on the ideXlab platform.
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low base substitution mutation rate but high rate of slippage mutations in the sequence repeat rich genome of dictyostelium Discoideum
G3: Genes Genomes Genetics, 2020Co-Authors: David C. Queller, Debra A Brock, Sibel Kucukyildirim, Megan G Behringer, Way Sung, Thomas G Doak, Hatice Mergen, Joan E. StrassmannAbstract:We describe the rate and spectrum of spontaneous mutations for the social amoeba Dictyostelium Discoideum, a key model organism in molecular, cellular, evolutionary, and developmental biology. Whole-genome sequencing of 37 mutation accumulation lines of D. Discoideum after an average of 1,500 cell divisions yields a base-substitution mutation rate of 2.47 × 10−11 per site per generation, substantially lower than that of most eukaryotic and prokaryotic organisms, and of the same order of magnitude as in the ciliates Paramecium tetraurelia and Tetrahymena thermophila. Known for its high genomic AT content and abundance of simple sequence repeats, we observe that base-substitution mutations in D. Discoideum are highly A/T biased. This bias likely contributes both to the high genomic AT content and to the formation of simple sequence repeats in the AT-rich genome of Dictyostelium Discoideum. In contrast to the situation in other surveyed unicellular eukaryotes, indel rates far exceed the base-substitution mutation rate in this organism with a high proportion of 3n indels, particularly in regions without simple sequence repeats. Like ciliates, D. Discoideum has a large effective population size, reducing the power of random genetic drift, magnifying the effect of selection on replication fidelity, in principle allowing D. Discoideum to evolve an extremely low base-substitution mutation rate.
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Cooperation and conflict in the social amoeba Dictyostelium Discoideum.
The International journal of developmental biology, 2019Co-Authors: James M Medina, David C. Queller, P M Shreenidhi, Tyler J Larsen, Joan E. StrassmannAbstract:The social amoeba Dictyostelium Discoideum has provided considerable insight into the evolution of cooperation and conflict. Under starvation, D. Discoideum amoebas cooperate to form a fruiting body comprised of hardy spores atop a stalk. The stalk development is altruistic because stalk cells die to aid spore dispersal. The high relatedness of cells in fruiting bodies in nature implies that this altruism often benefits relatives. However, since the fruiting body forms through aggregation there is potential for non-relatives to join the aggregate and create conflict over spore and stalk fates. Cheating is common in chimeras of social amoebas, where one genotype often takes advantage of the other and makes more spores. This social conflict is a significant force in nature as indicated by rapid rates of adaptive evolution in genes involved in cheating and its resistance. However, cheating can be prevented by high relatedness, allorecognition via tgr genes, pleiotropy and evolved resistance. Future avenues for the study of cooperation and conflict in D. Discoideum include the sexual cycle as well as the relationship between D. Discoideum and its bacterial symbionts. D. Discoideum's tractability in the laboratory as well as its uncommon mode of aggregative multicellularity have established it as a promising model for future studies of cooperation and conflict.
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whole genome sequencing of mutation accumulation lines reveals a low mutation rate in the social amoeba dictyostelium Discoideum
PLOS ONE, 2012Co-Authors: Gerda Saxer, Joan E. Strassmann, Paul Havlak, Sara A Fox, Michael Quance, Sharu Gupta, Yuriy Fofanov, David C. QuellerAbstract:Spontaneous mutations play a central role in evolution. Despite their importance, mutation rates are some of the most elusive parameters to measure in evolutionary biology. The combination of mutation accumulation (MA) experiments and whole-genome sequencing now makes it possible to estimate mutation rates by directly observing new mutations at the molecular level across the whole genome. We performed an MA experiment with the social amoeba Dictyostelium Discoideum and sequenced the genomes of three randomly chosen lines using high-throughput sequencing to estimate the spontaneous mutation rate in this model organism. The mitochondrial mutation rate of 6.76×10−9, with a Poisson confidence interval of 4.1×10−9 − 9.5×10−9, per nucleotide per generation is slightly lower than estimates for other taxa. The mutation rate estimate for the nuclear DNA of 2.9×10−11, with a Poisson confidence interval ranging from 7.4×10−13 to 1.6×10−10, is the lowest reported for any eukaryote. These results are consistent with low microsatellite mutation rates previously observed in D. Discoideum and low levels of genetic variation observed in wild D. Discoideum populations. In addition, D. Discoideum has been shown to be quite resistant to DNA damage, which suggests an efficient DNA-repair mechanism that could be an adaptation to life in soil and frequent exposure to intracellular and extracellular mutagenic compounds. The social aspect of the life cycle of D. Discoideum and a large portion of the genome under relaxed selection during vegetative growth could also select for a low mutation rate. This hypothesis is supported by a significantly lower mutation rate per cell division in multicellular eukaryotes compared with unicellular eukaryotes.
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Genetic diversity in the social amoeba Dictyostelium Discoideum: population differentiation and cryptic species.
Molecular phylogenetics and evolution, 2011Co-Authors: Tracy E. Douglas, David C. Queller, Marcus R. Kronforst, Joan E. StrassmannAbstract:The social amoeba Dictyostelium Discoideum is a commonly used model organism for the study of social evolution, multicellularity, and cell biology. But the boundaries and structure of the species have not been explored. The lack of morphological traits to distinguish D. Discoideum makes even knowing whether a given clone is D. Discoideum a challenge. We address this with a phylogeny of a widespread collection of clones from a range of locations and including clones identified previously as potential cryptic species. We sequenced portions of nuclear ribosomal DNA and mitochondrial DNA, analyzing approximately 5500 and 2500 base pairs from the two regions respectively. We compared these sequences to known reference sequences for both D. Discoideum and other closely related Dictyostelium species to create Bayesian and neighbor-joining phylogenetic trees representing the evolutionary relationships among the clones. We identified 51 unique D. Discoideum concatenated sequences based on the combined mitochondrial and ribosomal sequence data. We also identified four unique D. citrinum concatenated sequences, three of which were previously classified as D. Discoideum clones. Our analysis of the data revealed that all D. Discoideum clones form a monophyletic group, but there are several well-supported subclades and pronounced genetic differentiation among locations (F(ST)=0.242, P=0.011), suggesting the presence of geographic or other barriers between populations. Our results reveal the need for further investigation into potential tropical cryptic species.
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Variation, sex, and social cooperation: Molecular population genetics of the social amoeba Dictyostelium Discoideum
PLoS Genetics, 2010Co-Authors: Jonathan M. Flowers, Elizabeth A. Ostrowski, Si I. Li, Angela Stathos, Gerda Saxer, Joan E. Strassmann, David C. Queller, Michael D. PuruggananAbstract:Dictyostelium Discoideum is a eukaryotic microbial model system for multicellular development, cell-cell signaling, and social behavior. Key models of social evolution require an understanding of genetic relationships between individuals across the genome or possibly at specific genes, but the nature of variation within D. Discoideum is largely unknown. We re-sequenced 137 gene fragments in wild North American strains of D. Discoideum and examined the levels and patterns of nucleotide variation in this social microbial species. We observe surprisingly low levels of nucleotide variation in D. Discoideum across these strains, with a mean nucleotide diversity (pi) of 0.08%, and no strong population stratification among North American strains. We also do not find any clear relationship between nucleotide divergence between strains and levels of social dominance and kin discrimination. Kin discrimination experiments, however, show that strains collected from the same location show greater ability to distinguish self from non-self than do strains from different geographic areas. This suggests that a greater ability to recognize self versus non-self may arise among strains that are more likely to encounter each other in nature, which would lead to preferential formation of fruiting bodies with clonemates and may prevent the evolution of cheating behaviors within D. Discoideum populations. Finally, despite the fact that sex has rarely been observed in this species, we document a rapid decay of linkage disequilibrium between SNPs, the presence of recombinant genotypes among natural strains, and high estimates of the population recombination parameter rho. The SNP data indicate that recombination is widespread within D. Discoideum and that sex as a form of social interaction is likely to be an important aspect of the life cycle.
Pierre Cosson - One of the best experts on this subject based on the ideXlab platform.
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A New Family of Bacteriolytic Proteins in Dictyostelium Discoideum.
Frontiers in cellular and infection microbiology, 2021Co-Authors: Cyril Guilhen, Otmane Lamrabet, Wanessa Cristina Lima, Estelle Ifrid, Xenia Crespo-yañez, Pierre CossonAbstract:Phagocytic cells ingest and destroy bacteria efficiently and in doing so ensure the defense of the human body against infections. Phagocytic Dictyostelium Discoideum amoebae represent a powerful model system to study the intracellular mechanisms ensuring destruction of ingested bacteria in phagosomes. Here, we discovered the presence of a bacteriolytic activity against Klebsiella pneumoniae in cellular extracts from D. Discoideum. The bacteriolytic activity was detected only at a very acidic pH mimicking the conditions found in D. Discoideum phagosomes. It was also strongly decreased in extracts of kil1 KO cells that were previously described to kill inefficiently internalized bacteria, suggesting that the activity observed in vitro is involved in killing of bacteria in phagosomes. We purified a fraction enriched in bacteriolytic activity where only 16 proteins were detected and focused on four proteins selectively enriched in this fraction. Three of them belong to a poorly characterized family of D. Discoideum proteins exhibiting a DUF3430 domain of unknown function and were named BadA (Bacteriolytic D. Discoideum A), BadB, and BadC. We overexpressed the BadA protein in cells, and the bacteriolytic activity increased concomitantly in cell extracts. Conversely, depletion of BadA from cell extracts decreased significantly their bacteriolytic activity. Finally, in cells overexpressing BadA, bacterial killing was faster than in parental cells. Together these results identify BadA as a D. Discoideum protein required for cellular bactericidal activity. They also define a new strategy to identify and characterize bactericidal proteins in D. Discoideum cells.
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A recombinant antibody toolbox for Dictyostelium Discoideum.
BMC research notes, 2020Co-Authors: Wanessa Cristina Lima, Philippe Hammel, Pierre CossonAbstract:Objective The amoeba Dictyostelium Discoideum has been a valuable model organism to study numerous facets of eukaryotic cell biology, such as cell motility, cell adhesion, macropinocytosis and phagocytosis, host-pathogen interactions and multicellular development. However, the relative small size of the Dictyostelium community hampers the production and distribution of reagents and tools, such as antibodies, by commercial vendors. Results For the past 5 years, our laboratory has worked to promote an increased use of recombinant antibodies (rAbs) by academic laboratories. Here we report our efforts to ensure that Dictyostelium researchers have access to rAbs. Using hybridoma sequencing and phage display techniques, we generated a panel of recombinant antibodies against D. Discoideum antigens, providing a useful and reliable set of reagents for labelling and characterization of proteins and subcellular compartments in D. Discoideum, accessible to the entire Dictyostelium community.
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Transcriptional Responses of Dictyostelium Discoideum Exposed to Different Classes of Bacteria.
Frontiers in microbiology, 2020Co-Authors: Otmane Lamrabet, Thierry Soldati, Astrid Melotti, Frédéric Burdet, Nabil Hanna, Jackie Perrin, Jahn Nitschke, Marco Pagni, Hubert Hilbi, Pierre CossonAbstract:Dictyostelium Discoideum amoebae feed by ingesting bacteria, then killing them in phagosomes. Ingestion and killing of different bacteria have been shown to rely on largely different molecular mechanisms. One would thus expect that D. Discoideum adapts its ingestion and killing machinery when encountering different bacteria. In this study, we investigated by RNA sequencing if and how D. Discoideum amoebae respond to the presence of different bacteria by modifying their gene expression patterns. Each bacterial species analyzed induced a specific modification of the transcriptome. Bacteria such as Bacillus subtilis, Klebsiella pneumoniae, or Mycobacterium marinum induced a specific and different transcriptional response, while Micrococcus luteus did not trigger a significant gene regulation. Although folate has been proposed to be one of the key molecules secreted by bacteria and recognized by hunting amoebae, it elicited a very specific and restricted transcriptional signature, distinct from that triggered by any bacteria analyzed here. Our results indicate that D. Discoideum amoebae respond in a highly specific, almost non-overlapping manner to different species of bacteria. We additionally identify specific sets of genes that can be used as reporters of the response of D. Discoideum to different bacteria.
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The multifarious lysozyme arsenal of Dictyostelium Discoideum.
Developmental and comparative immunology, 2020Co-Authors: Otmane Lamrabet, Tania Jauslin, Wanessa Cristina Lima, Matthias Leippe, Pierre CossonAbstract:Dictyostelium Discoideum is a free-living soil amoeba which feeds upon bacteria. To bind, ingest, and kill bacteria, D. Discoideum uses molecular mechanisms analogous to those found in professional phagocytic cells of multicellular organisms. D. Discoideum is equipped with a large arsenal of antimicrobial peptides and proteins including amoebapore-like peptides and lysozymes. This review describes the family of lysozymes in D. Discoideum. We identified 22 genes potentially encoding four different types of lysozymes in the D. Discoideum genome. Although most of these genes are also present in the genomes of other amoebal species, no other organism is as well-equipped with lysozyme genes as D. Discoideum.
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Dictyostelium Discoideum transformation by oscillating electric field electroporation.
BioTechniques, 2003Co-Authors: Laethitia Alibaud, Pierre Cosson, Mohammed BenghezalAbstract:Dictyostelium Discoideum has been used as a genetically tractable model organism to study many biological phenomena. High-efficiency transformation is a prerequisite for successful genetic screens such as mutant complementation, identification of suppressor genes, or insertional mutagenesis. Although exponential decay electroporation is the standard transformation technique for D. Discoideum, its efficiency is relatively low and its reproducibility is weak. Here we optimized the oscillating electroporation technique for D. Discoideum transformation and compared it to the exponential decay electroporation. A 20-fold increase in the efficiency was resproducibly achieved. This alternative electroporation technique should facilitate future genetic approaches in D. Discoideum.
Camila Valenzuela - One of the best experts on this subject based on the ideXlab platform.
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sopb and sifa dependent shaping of the salmonella containing vacuole proteome in the social amoeba dictyostelium Discoideum
Cellular Microbiology, 2021Co-Authors: Camila Valenzuela, Magdalena Gil, Italo M Urrutia, Andrea Sabag, Jost Enninga, Carlos A. SantiviagoAbstract:The ability of Salmonella to survive and replicate within mammalian host cells involves the generation of a membranous compartment known as the Salmonella-containing vacuole (SCV). Salmonella employs a number of effector proteins that are injected into host cells for SCV formation using its type-3 secretion systems encoded in SPI-1 and SPI-2 (T3SS-1 and T3SS-2, respectively). Recently, we reported that S. Typhimurium requires T3SS-1 and T3SS-2 to survive in the model amoeba Dictyostelium Discoideum. Despite these findings, the involved effector proteins have not been identified yet. Therefore, we evaluated the role of two major S. Typhimurium effectors SopB and SifA during D. Discoideum intracellular niche formation. First, we established that S. Typhimurium resides in a vacuolar compartment within D. Discoideum. Next, we isolated SCVs from amoebae infected with wild type or the ΔsopB and ΔsifA mutant strains of S. Typhimurium, and we characterised the composition of this compartment by quantitative proteomics. This comparative analysis suggests that S. Typhimurium requires SopB and SifA to modify the SCV proteome in order to generate a suitable intracellular niche in D. Discoideum. Accordingly, we observed that SopB and SifA are needed for intracellular survival of S. Typhimurium in this organism. Thus, our results provide insight into the mechanisms employed by Salmonella to survive intracellularly in phagocytic amoebae.
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Inorganic Polyphosphate Is Essential for Salmonella Typhimurium Virulence and Survival in Dictyostelium Discoideum
Frontiers in cellular and infection microbiology, 2018Co-Authors: Macarena A Varas, Sebastián Riquelme-barrios, Camila Valenzuela, Andrés E. Marcoleta, Camilo Berríos-pastén, Carlos A. Santiviago, Francisco P. ChávezAbstract:Inorganic polyphosphate (polyP) deficiency in enteric bacterial pathogens reduces their ability to invade and establish systemic infections in different hosts. For instance, inactivation of the polyphosphate kinase gene (ppk) encoding the enzyme responsible for polyP biosynthesis reduces invasiveness and intracellular survival of Salmonella enterica serovar Typhimurium (S. Typhimurium) in epithelial cells and macrophages in vitro. In addition, the virulence in vivo of a S. Typhimurium Δppk mutant is significantly reduced in a murine infection model. In spite of these observations, the role played by polyP during the Salmonella-host interaction is not well understood. The social amoeba Dictyostelium Discoideum has proven to be a useful model for studying relevant aspects of the host-pathogen interaction. In fact, many intracellular pathogens can survive within D. Discoideum cells using molecular mechanisms also required to survive within macrophages. Recently, we established that S. Typhimurium is able to survive intracellularly in D. Discoideum and identified relevant genes linked to virulence that are crucial for this process. The aim of this study was to determine the effect of a polyP deficiency in S. Typhimurium during its interaction with D. Discoideum. To do this, we evaluated the intracellular survival of wild-type and Δppk strains of S. Typhimurium in D. Discoideum and the ability of these strains to delay the social development of the amoeba. In contrast to the wild-type strain, the Δppk mutant was unable to survive intracellularly in D. Discoideum and enabled the social development of the amoeba. Both phenotypes were complemented using a plasmid carrying a copy of the ppk gene. Next, we simultaneously evaluated the proteomic response of both S. Typhimurium and D. Discoideum during host-pathogen interaction via global proteomic profiling. The analysis of our results allowed the identification of novel molecular signatures that give insight into Salmonella-Dictyostelium interaction. Altogether, our results indicate that inorganic polyP is essential for S. Typhimurium virulence and survival in D. Discoideum. In addition, we have validated the use of global proteomic analyses to simultaneously evaluate the host-pathogen interaction of S. Typhimurium and D. Discoideum. Furthermore, our infection assays using these organisms can be exploited to screen for novel anti-virulence
Debra A Brock - One of the best experts on this subject based on the ideXlab platform.
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low base substitution mutation rate but high rate of slippage mutations in the sequence repeat rich genome of dictyostelium Discoideum
G3: Genes Genomes Genetics, 2020Co-Authors: David C. Queller, Debra A Brock, Sibel Kucukyildirim, Megan G Behringer, Way Sung, Thomas G Doak, Hatice Mergen, Joan E. StrassmannAbstract:We describe the rate and spectrum of spontaneous mutations for the social amoeba Dictyostelium Discoideum, a key model organism in molecular, cellular, evolutionary, and developmental biology. Whole-genome sequencing of 37 mutation accumulation lines of D. Discoideum after an average of 1,500 cell divisions yields a base-substitution mutation rate of 2.47 × 10−11 per site per generation, substantially lower than that of most eukaryotic and prokaryotic organisms, and of the same order of magnitude as in the ciliates Paramecium tetraurelia and Tetrahymena thermophila. Known for its high genomic AT content and abundance of simple sequence repeats, we observe that base-substitution mutations in D. Discoideum are highly A/T biased. This bias likely contributes both to the high genomic AT content and to the formation of simple sequence repeats in the AT-rich genome of Dictyostelium Discoideum. In contrast to the situation in other surveyed unicellular eukaryotes, indel rates far exceed the base-substitution mutation rate in this organism with a high proportion of 3n indels, particularly in regions without simple sequence repeats. Like ciliates, D. Discoideum has a large effective population size, reducing the power of random genetic drift, magnifying the effect of selection on replication fidelity, in principle allowing D. Discoideum to evolve an extremely low base-substitution mutation rate.
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endosymbiotic adaptations in three new bacterial species associated with dictyostelium Discoideum paraburkholderia agricolaris sp nov paraburkholderia hayleyella sp nov and paraburkholderia bonniea sp nov
PeerJ, 2020Co-Authors: Debra A Brock, Suegene Noh, Alicia N M Hubert, Tamara S Haselkorn, Susanne Disalvo, Melanie K Suess, Alexander S Bradley, Mahboubeh Tavakolinezhad, Katherine S Geist, David C. QuellerAbstract:Here we give names to three new species of Paraburkholderia that can remain in symbiosis indefinitely in the spores of a soil dwelling eukaryote, Dictyostelium Discoideum. The new species P. agricolaris sp. nov., P. hayleyella sp. nov., and P. bonniea sp. nov. are widespread across the eastern USA and were isolated as internal symbionts of wild-collected D. Discoideum. We describe these sp. nov. using several approaches. Evidence that they are each a distinct new species comes from their phylogenetic position, average nucleotide identity, genome-genome distance, carbon usage, reduced length, cooler optimal growth temperature, metabolic tests, and their previously described ability to invade D. Discoideum amoebae and form a symbiotic relationship. All three of these new species facilitate the prolonged carriage of food bacteria by D. Discoideum, though they themselves are not food. Further studies of the interactions of these three new species with D. Discoideum should be fruitful for understanding the ecology and evolution of symbioses.