cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23660550.v1
title: Identification of <i>Staphylococcus aureus</i> virulence-modulating RNA from transcriptomics data with machine learning

description: The virulence factors of <i>Staphylococcus aureus</i> are tightly controlled by two-component systems (TCSs) and small RNA (sRNA). TCSs have been well studied over the past several decades, but our understanding of sRNA functions lags far behind that of TCS functions. Here, we studied the biological role of sRNA from 506 <i>S. aureus</i> RNA-seq datasets using independent component analysis (ICA). We found that a previously neglected sRNA, Sau-41, functions in the Agr system. Sau-41 is located within the PSMα operon and controlled by the Agr system. It was predicted to share 22-base complementarity with RNAIII, a major regulator of <i>S. aureus</i> virulence. The EMSA results demonstrated that Sau-41 directly binds to RNAIII. Furthermore, our results found that Sau-41 is capable of repressing <i>S. aureus</i> haemolysin activity by downregulating α-haemolysin and δ-toxin. The repression of α-haemolysin was attributed to the competition between the 5’ UTR of <i>hla</i> and Sau-41 for binding RNAIII. We observed that Sau-41 mitigated <i>S. aureus</i> virulence in an orthopaedic implant infection mouse model and alleviated osteolysis. Together, our results indicate that Sau-41 is a virulence-regulating RNA and suggest that Sau-41 might be involved in a negative feedback mechanism to control the Agr system. This work is a demonstration of using ICA in sRNA identification by mining high-throughput data and could be extended to other organisms as well.
DOI: 10.6084/m9.figshare.22116635
title: <i>Mycobacterium tuberculosis</i> protein MoxR1 enhances virulence by inhibiting host cell death pathways and disrupting cellular bioenergetics

description: <i>Mycobacterium tuberculosis</i> (<i>M. tb</i>) utilizes the multifunctionality of its protein factors to deceive the host. The unabated global incidence and prevalence of tuberculosis (TB) and the emergence of multidrug-resistant strains warrant the discovery of novel drug targets that can be exploited to manage TB. This study reports the role of <i>M. tb</i> AAA+ family protein MoxR1 in regulating host-pathogen interaction and immune system functions. We report that MoxR1 binds to TLR4 in macrophage cells and further reveal how this signal the release of proinflammatory cytokines. We show that MoxR1 activates the PI3K-AKT-MTOR signalling cascade by inhibiting the autophagy-regulating kinase ULK1 by potentiating its phosphorylation at serine 757, leading to its suppression. Using autophagy-activating and repressing agents such as rapamycin and bafilomycin A1 suggested that MoxR1 inhibits autophagy flux by inhibiting autophagy initiation. MoxR1 also inhibits apoptosis by suppressing the expression of MAPK JNK1/2 and cFOS, which play critical roles in apoptosis induction. Intriguingly, MoxR1 also induced robust disruption of cellular bioenergetics by metabolic reprogramming to rewire the citric acid cycle intermediates, as evidenced by the lower levels of citric acid and electron transport chain enzymes (ETC) to dampen host defence. These results point to a multifunctional role of <i>M. tb</i> MoxR1 in dampening host defences by inhibiting autophagy, apoptosis, and inducing metabolic reprogramming. These mechanistic insights can be utilized to devise strategies to combat TB and better understand survival tactics by intracellular pathogens.
DOI: 10.6084/m9.figshare.22116635.v2
title: <i>Mycobacterium tuberculosis</i> protein MoxR1 enhances virulence by inhibiting host cell death pathways and disrupting cellular bioenergetics

description: <i>Mycobacterium tuberculosis</i> (<i>M. tb</i>) utilizes the multifunctionality of its protein factors to deceive the host. The unabated global incidence and prevalence of tuberculosis (TB) and the emergence of multidrug-resistant strains warrant the discovery of novel drug targets that can be exploited to manage TB. This study reports the role of <i>M. tb</i> AAA+ family protein MoxR1 in regulating host-pathogen interaction and immune system functions. We report that MoxR1 binds to TLR4 in macrophage cells and further reveal how this signal the release of proinflammatory cytokines. We show that MoxR1 activates the PI3K-AKT-MTOR signalling cascade by inhibiting the autophagy-regulating kinase ULK1 by potentiating its phosphorylation at serine 757, leading to its suppression. Using autophagy-activating and repressing agents such as rapamycin and bafilomycin A1 suggested that MoxR1 inhibits autophagy flux by inhibiting autophagy initiation. MoxR1 also inhibits apoptosis by suppressing the expression of MAPK JNK1/2 and cFOS, which play critical roles in apoptosis induction. Intriguingly, MoxR1 also induced robust disruption of cellular bioenergetics by metabolic reprogramming to rewire the citric acid cycle intermediates, as evidenced by the lower levels of citric acid and electron transport chain enzymes (ETC) to dampen host defence. These results point to a multifunctional role of <i>M. tb</i> MoxR1 in dampening host defences by inhibiting autophagy, apoptosis, and inducing metabolic reprogramming. These mechanistic insights can be utilized to devise strategies to combat TB and better understand survival tactics by intracellular pathogens.
DOI: 10.6084/m9.figshare.22116635.v1
title: <i>Mycobacterium tuberculosis</i> protein MoxR1 enhances virulence by inhibiting host cell death pathways and disrupting cellular bioenergetics

description: <i>Mycobacterium tuberculosis</i> (<i>M. tb</i>) utilizes the multifunctionality of its protein factors to deceive the host. The unabated global incidence and prevalence of tuberculosis (TB) and the emergence of multidrug-resistant strains warrant the discovery of novel drug targets that can be exploited to manage TB. This study reports the role of <i>M. tb</i> AAA+ family protein MoxR1 in regulating host-pathogen interaction and immune system functions. We report that MoxR1 binds to TLR4 in macrophage cells and further reveal how this signal the release of proinflammatory cytokines. We show that MoxR1 activates the PI3K-AKT-MTOR signaling cascade by inhibiting the autophagy-regulating kinase ULK1 by potentiating its phosphorylation at serine 757, leading to its suppression. Using autophagy-activating and repressing agents such as rapamycin and bafilomycin A1 suggested that MoxR1 inhibits autophagy flux by inhibiting autophagy initiation. MoxR1 also inhibits apoptosis by suppressing the expression of MAPK JNK1/2 and cFOS, which play critical roles in apoptosis induction. Intriguingly, MoxR1 also induced robust disruption of cellular bioenergetics by metabolic reprogramming to rewire the citric acid cycle intermediates, as evidenced by the lower levels of citric acid and electron transport chain enzymes (ETC) to dampen host defense. These results point to a multifunctional role of <i>M. tb</i> MoxR1 in dampening host defenses by inhibiting autophagy, apoptosis, and inducing metabolic reprogramming. These mechanistic insights can be utilized to devise strategies to combat TB and better understand survival tactics by intracellular pathogens.
DOI: 10.6084/m9.figshare.24592216.v1
title: A <i>Drosophila melanogaster</i> model shows that fast growing <i>Metarhizium</i> species are the deadliest despite eliciting a strong immune response

description: We used <i>Drosophila melanogaster</i> to investigate how differences between <i>Metarhizium</i> species in growth rate and mechanisms of pathogenesis influence the outcome of infection. We found that the most rapid germinators and growers <i>in vitro</i> and on fly cuticle were the fastest killers, suggesting that pre-penetration competence is key to <i>Metarhizium</i> success. Virulent strains also induced the largest immune response, which did not depend on profuse growth within hosts as virulent toxin-producing strains only proliferated post-mortem while slow-killing strains that were specialized to other insects grew profusely pre-mortem. <i>Metarhizium</i> strains have apparently evolved resistance to widely distributed defenses such as the defensin Toll product drosomycin, but they were inhibited by Bomanins only found in <i>Drosophila</i> spp. Disrupting a gene (<i>Dif</i>), that mediates Toll immunity has little impact on the lethality of most <i>Metarhizium</i> strains (an exception being the early diverged <i>M. frigidum</i> and another insect pathogen <i>Beauveria bassiana</i>). However, disrupting the sensor of fungal proteases (<i>Persephone</i>) allowed rapid proliferation of strains within hosts (with the exception of <i>M. album</i>), and flies succumbed rapidly. Persephone also mediates gender differences in immune responses that determine whether male or female flies die sooner. We conclude that some strain differences in growth within hosts depend on immune-mediated interactions but intrinsic differences in pathogenic mechanisms are more important. Thus, <i>Drosophila</i> varies greatly in tolerance to different <i>Metarhizium</i> strains, in part because some of them produce toxins. Our results further develop <i>D. melanogaster</i> as a tractable model system for understanding insect-<i>Metarhizium</i> interactions.
DOI: 10.6084/m9.figshare.22350339
title: Longitudinal temperature measurement can determine humane endpoints in BALB/c mouse models of ESKAPEE infection

description: Antimicrobial resistance (AMR) is a worldwide problem, which is driving more preclinical research to find new treatments and countermeasures for drug-resistant bacteria. However, translational models in the preclinical space have remained static for years. To improve animal use ethical considerations, we assessed novel methods to evaluate survival after lethal infection with ESKAPEE pathogens (<i>Enterococcus faecium, Staphylococcus aureus</i>, <i>Klebsiella pneumoniae</i>, <i>Acinetobacter baumannii</i>, <i>Pseudomonas aeruginosa</i>, <i>Enterobacter cloacae</i>, and <i>Escherichia coli</i>) in pulmonary models of infection. Consistent with published lung infection models often used for novel antimicrobial development, BALB/c mice were immunosuppressed with cyclophosphamide and inoculated intranasally with individual ESKAPEE pathogens or sterile saline. Observations were recorded at frequent intervals to determine predictive thresholds for humane endpoint decision-making. Internal temperature was measured via implanted IPTT300 microchips, and external temperature was measured using a non-contact, infrared thermometer. Additionally, clinical scores were evaluated based on animal appearance, behaviour, hydration status, respiration, and body weight. Internal temperature differences between survivors and non-survivors were statistically significant for <i>E. faecium, S. aureus</i>, <i>K. pneumoniae</i>, <i>A. baumannii</i>, <i>E. cloacae</i>, and <i>E. coli</i>, and external temperature differences were statistically significant for <i>S. aureus</i>, <i>K. pneumoniae</i>, <i>E. cloacae</i>, and <i>E. coli</i>. Internal temperature more precisely predicted mortality compared to external temperature, indicating that a threshold of 85ºF (29.4ºC) was 86.0% predictive of mortality and 98.7% predictive of survival. Based on our findings, we recommend future studies involving BALB/c mice ESKAPEE pathogen infection use temperature monitoring as a humane endpoint threshold.
DOI: 10.6084/m9.figshare.22350339.v1
title: Longitudinal temperature measurement can determine humane endpoints in BALB/c mouse models of ESKAPEE infection

description: Antimicrobial resistance (AMR) is a worldwide problem, which is driving more preclinical research to find new treatments and countermeasures for drug-resistant bacteria. However, translational models in the preclinical space have remained static for years. To improve animal use ethical considerations, we assessed novel methods to evaluate survival after lethal infection with ESKAPEE pathogens (<i>Enterococcus faecium, Staphylococcus aureus</i>, <i>Klebsiella pneumoniae</i>, <i>Acinetobacter baumannii</i>, <i>Pseudomonas aeruginosa</i>, <i>Enterobacter cloacae</i>, and <i>Escherichia coli</i>) in pulmonary models of infection. Consistent with published lung infection models often used for novel antimicrobial development, BALB/c mice were immunosuppressed with cyclophosphamide and inoculated intranasally with individual ESKAPEE pathogens or sterile saline. Observations were recorded at frequent intervals to determine predictive thresholds for humane endpoint decision-making. Internal temperature was measured via implanted IPTT300 microchips, and external temperature was measured using a non-contact, infrared thermometer. Additionally, clinical scores were evaluated based on animal appearance, behaviour, hydration status, respiration, and body weight. Internal temperature differences between survivors and non-survivors were statistically significant for <i>E. faecium, S. aureus</i>, <i>K. pneumoniae</i>, <i>A. baumannii</i>, <i>E. cloacae</i>, and <i>E. coli</i>, and external temperature differences were statistically significant for <i>S. aureus</i>, <i>K. pneumoniae</i>, <i>E. cloacae</i>, and <i>E. coli</i>. Internal temperature more precisely predicted mortality compared to external temperature, indicating that a threshold of 85ºF (29.4ºC) was 86.0% predictive of mortality and 98.7% predictive of survival. Based on our findings, we recommend future studies involving BALB/c mice ESKAPEE pathogen infection use temperature monitoring as a humane endpoint threshold.
DOI: 10.6084/m9.figshare.24220663
title: Influenza enhances host susceptibility to non-pulmonary invasive <i>Streptococcus pyogenes</i> infections

description: <i>Streptococcus pyogenes</i> (group A streptococcus; GAS) causes a variety of invasive diseases (iGAS) such as bacteremia, toxic shock syndrome, and pneumonia, which are associated with high mortality despite the susceptibility of the bacteria to penicillin <i>ex vivo</i>. Epidemiologic studies indicate that respiratory influenza virus infection is associated with an increase in the frequency of iGAS diseases, including those not directly involving the lung. We modified a murine model of influenza A (IAV)-GAS superinfection to determine if viral pneumonia increased the susceptibility of mice subsequently infected with GAS in the peritoneum. The results showed that respiratory IAV infection increased the morbidity (weight loss) of mice infected intraperitoneally (i.p.) with GAS 3, 5, and 10 d after the initial viral infection. Mortality was also significantly increased when mice were infected with GAS 3 and 5 d after pulmonary IAV infection. Increased mortality among mice infected with virus 5 d prior to bacterial infection correlated with increased dissemination of GAS from the peritoneum to the blood, spleen, and lungs. The interval was also associated with a significant increase in the pro-inflammatory cytokines IFN-γ, IL-12, TNF-α, MCP-1 and IL-27 in sera. We conclude, using a murine model, that respiratory influenza virus infection increases the likelihood and severity of systemic iGAS disease, even when GAS infection does not originate in the respiratory tract.
DOI: 10.6084/m9.figshare.24220663.v1
title: Influenza enhances host susceptibility to non-pulmonary invasive <i>Streptococcus pyogenes</i> infections

description: <i>Streptococcus pyogenes</i> (group A streptococcus; GAS) causes a variety of invasive diseases (iGAS) such as bacteremia, toxic shock syndrome, and pneumonia, which are associated with high mortality despite the susceptibility of the bacteria to penicillin <i>ex vivo</i>. Epidemiologic studies indicate that respiratory influenza virus infection is associated with an increase in the frequency of iGAS diseases, including those not directly involving the lung. We modified a murine model of influenza A (IAV)-GAS superinfection to determine if viral pneumonia increased the susceptibility of mice subsequently infected with GAS in the peritoneum. The results showed that respiratory IAV infection increased the morbidity (weight loss) of mice infected intraperitoneally (i.p.) with GAS 3, 5, and 10 d after the initial viral infection. Mortality was also significantly increased when mice were infected with GAS 3 and 5 d after pulmonary IAV infection. Increased mortality among mice infected with virus 5 d prior to bacterial infection correlated with increased dissemination of GAS from the peritoneum to the blood, spleen, and lungs. The interval was also associated with a significant increase in the pro-inflammatory cytokines IFN-γ, IL-12, TNF-α, MCP-1 and IL-27 in sera. We conclude, using a murine model, that respiratory influenza virus infection increases the likelihood and severity of systemic iGAS disease, even when GAS infection does not originate in the respiratory tract.
DOI: 10.6084/m9.figshare.24592216
title: A <i>Drosophila melanogaster</i> model shows that fast growing <i>Metarhizium</i> species are the deadliest despite eliciting a strong immune response

description: We used <i>Drosophila melanogaster</i> to investigate how differences between <i>Metarhizium</i> species in growth rate and mechanisms of pathogenesis influence the outcome of infection. We found that the most rapid germinators and growers <i>in vitro</i> and on fly cuticle were the fastest killers, suggesting that pre-penetration competence is key to <i>Metarhizium</i> success. Virulent strains also induced the largest immune response, which did not depend on profuse growth within hosts as virulent toxin-producing strains only proliferated post-mortem while slow-killing strains that were specialized to other insects grew profusely pre-mortem. <i>Metarhizium</i> strains have apparently evolved resistance to widely distributed defenses such as the defensin Toll product drosomycin, but they were inhibited by Bomanins only found in <i>Drosophila</i> spp. Disrupting a gene (<i>Dif</i>), that mediates Toll immunity has little impact on the lethality of most <i>Metarhizium</i> strains (an exception being the early diverged <i>M. frigidum</i> and another insect pathogen <i>Beauveria bassiana</i>). However, disrupting the sensor of fungal proteases (<i>Persephone</i>) allowed rapid proliferation of strains within hosts (with the exception of <i>M. album</i>), and flies succumbed rapidly. Persephone also mediates gender differences in immune responses that determine whether male or female flies die sooner. We conclude that some strain differences in growth within hosts depend on immune-mediated interactions but intrinsic differences in pathogenic mechanisms are more important. Thus, <i>Drosophila</i> varies greatly in tolerance to different <i>Metarhizium</i> strains, in part because some of them produce toxins. Our results further develop <i>D. melanogaster</i> as a tractable model system for understanding insect-<i>Metarhizium</i> interactions.
DOI: 10.6084/m9.figshare.23903761
title: Integrated morphological and transcriptome profiles reveal a highly-developed extrusome system associated to virulence in the notorious fish parasite, <i>Ichthyophthirius multifiliis</i>

description: <i>Ichthyophthirius multifiliis</i> is an obligate parasitic ciliate that causes severe economic damage in aquaculture. The parasite contains numerous extrusive organelles (extrusomes) that assist in its pathogenesis and reproduction. However, the structure of these extrusomes and the molecular profiles involved in exocytosis remain unclear. In the present study, through comparative ultrastructural observations across the life cycle of <i>I. multifiliis</i>, we demonstrated that all three of its life stages (theront, trophont, and tomont) exhibited an abundance of extrusomes. In addition, two different types of extrusomes were identified according to their unique structures. Type I extrusomes (mucocysts) are crystalline, oval-shaped, 0.7–1.4 × 0.6–1.1 μm, and distributed as “rosettes” below the trophont membrane. Type II extrusomes, 2.0–3.0 × 0.2–0.3 μm, are rod-shaped with tubular cores and identified as toxicysts, the aggregation of which in the anterior part of the theront and cortex of the trophont revealed their potential roles in <i>I. multifiliis</i> invasion. This was confirmed by our transcriptome investigations of the three stages of <i>I. multifiliis</i>, which revealed that a set of genes involved in proteolysis and DNA/protein biogenesis was highly expressed in the theront and trophont. Furthermore, to map the molecular mechanisms of extrusome release, we characterized 25 Rab family genes in <i>I. multifiliis</i> and determined their expression profiles across the life cycle, reflecting the distribution patterns of the two extrusomes. Collectively, our data revealed that a highly developed extrusome system could play a potential role in the virulence of <i>I. multifiliis</i>, which facilitates a better understanding of the parasite’s development.
DOI: 10.6084/m9.figshare.23903761.v1
title: Integrated morphological and transcriptome profiles reveal a highly-developed extrusome system associated to virulence in the notorious fish parasite, <i>Ichthyophthirius multifiliis</i>

description: <i>Ichthyophthirius multifiliis</i> is an obligate parasitic ciliate that causes severe economic damage in aquaculture. The parasite contains numerous extrusive organelles (extrusomes) that assist in its pathogenesis and reproduction. However, the structure of these extrusomes and the molecular profiles involved in exocytosis remain unclear. In the present study, through comparative ultrastructural observations across the life cycle of <i>I. multifiliis</i>, we demonstrated that all three of its life stages (theront, trophont, and tomont) exhibited an abundance of extrusomes. In addition, two different types of extrusomes were identified according to their unique structures. Type I extrusomes (mucocysts) are crystalline, oval-shaped, 0.7–1.4 × 0.6–1.1 μm, and distributed as “rosettes” below the trophont membrane. Type II extrusomes, 2.0–3.0 × 0.2–0.3 μm, are rod-shaped with tubular cores and identified as toxicysts, the aggregation of which in the anterior part of the theront and cortex of the trophont revealed their potential roles in <i>I. multifiliis</i> invasion. This was confirmed by our transcriptome investigations of the three stages of <i>I. multifiliis</i>, which revealed that a set of genes involved in proteolysis and DNA/protein biogenesis was highly expressed in the theront and trophont. Furthermore, to map the molecular mechanisms of extrusome release, we characterized 25 Rab family genes in <i>I. multifiliis</i> and determined their expression profiles across the life cycle, reflecting the distribution patterns of the two extrusomes. Collectively, our data revealed that a highly developed extrusome system could play a potential role in the virulence of <i>I. multifiliis</i>, which facilitates a better understanding of the parasite’s development.