Biology subjects

Raftery, M. J.

Publications and source records attributed to Raftery, M. J..

3 recordsLinked to original sources

bioRxiv2024

Proteomic comparison of epidemic Australian Bordetella pertussis biofilm cells

Bordetella pertussis causes whooping cough, a severe respiratory infectious disease. Studies have compared the currently dominant single nucleotide polymorphism (SNP) cluster I (pertussis toxin promoter allele, ptxP3) and previously dominant SNP cluster II (ptxP1) strains as planktonic cells. Since biofilm formation is linked with B. pertussis pathogenesis in vivo, this study compared the biofilm formation capabilities of representative strains of cluster I and cluster II. Confocal laser scanning microscopy found that the cluster I strain had a denser biofilm structure compared to the cluster II strain. Differences in protein expression of the biofilm cells were then compared using Tandem Mass Tagging (TMT) and high-resolution multiple reaction monitoring (MRM-hr). In total, 1453 proteins were identified of which 40 proteins had significant differential expression between the two strains in biofilm conditions. Of particular interest was a large increase in expression of energy metabolism proteins (cytochrome proteins PetABC and BP3650) in the cluster I strain. When the expression of these proteins was compared between 6 additional strains from each cluster, it was found that the protein expression varied between all strains. These findings suggest that there are large levels of individual proteomic diversity between B. pertussis strains in biofilm conditions despite the highly conserved genome of the species. Overall, this study revealed visual differences in biofilm structure between B. pertussis strains and highlighted strain specific variation in protein expression that dominate potential cluster specific changes that may be linked with the dominance of cluster I strains. ImportanceBordetella pertussis causes whooping cough. The currently circulating cluster I strains have taken over previously dominant cluster II strains. It is important to understand the reasons behind the evolution to develop new strategies against the pathogen. Recent studies have shown that B. pertussis can form biofilms during infection. This study compared the biofilm formation capabilities of a cluster I and a cluster II strain and identified visual differences in the biofilms. The protein expression between these strains grown in biofilms were compared and proteins identified with varied expression were measured with additional strains from each cluster. It was found that despite the highly conserved genetics of the species, there was varied protein expression between the additional strains. This study highlights that strain specific variation in protein expression during biofilm conditions that may dominate the cluster specific changes that may be linked to the dominance of cluster I strains.

microbiology↗

bioRxiv2022

In depth characterization of an archaeal virus-host system reveals numerous virus exclusion mechanisms

Archaeal head-tailed viruses appear, at first sight, very closely related to head-tailed bacteriophages simply due to morphological similarities and similar life cycles. However, they encounter host cells that are very different from bacteria and share characteristics, that greatly influence virus life cycles, with eukaryotes. Here we present an in-depth characterization of the archaeal head-tailed virus, HRTV-Dl1, isolated from Deep Lake, Antarctica. The host Halorubrum lacusprofundi exhibits a large arsenal of virus exclusion mechanisms, indicating a long ongoing arms race with viruses. However, we uncover that the majority of this arsenal was lost spontaneously in a strain grown under non-challenging laboratory conditions. By challenging both the parental strain and the sensitive strain with HRTV-DL1, we discovered a number of putative virus exclusion mechanisms that are only activated in the sensitive strain upon the lack of defense systems present in the parental strain. We identify virus exclusion mechanisms that are also common in bacteria, mechanisms that are unique to archaea, and a potential mechanisms involving the archaeal homolog of the eukaryotic ORC1 and CDC6. We identify one of two S-layer proteins as primary receptor for HRTV-DL1, demonstrating that the presence of two different S-layer proteins in one strain provides a strong advantage in the arms race with viruses. Our results clearly reflect the differences between bacterial and archaeal head-tailed viruses. Finally, we observed that our intention to isolate a clean and stable model virus-host system led to the generation of a virus-host pair with reduced genomes. This model system is great to study in the laboratory, but barely reflects the entire spectrum of virus-host interactions as they would occur in the environment, emphasizing the importance of combining wet lab data with environmental data.

microbiology↗

bioRxiv2022

Integrating proteomic data with metabolic modelling provides insight into key pathways of Bordetella pertussis biofilms

Pertussis, commonly known as whooping cough is a severe respiratory disease caused by the bacterium, Bordetella pertussis. Despite widespread vaccination, pertussis resurgence has been observed globally. The development of the current acellular vaccine (ACV) has been based on planktonic studies. However, recent studies have shown that B. pertussis readily forms biofilms. A better understanding of B. pertussis biofilms is important for developing novel vaccines that can target all aspects of B. pertussis infection. This study compared the proteomic expression of biofilm and planktonic B. pertussis cells to identify key changes between the conditions. Major differences were identified in virulence factors including an upregulation of toxins (adenylate cyclase toxin and dermonecrotic toxin) and downregulation of pertactin and type III secretion system proteins in biofilm cells. To further dissect metabolic pathways that are altered during the biofilm lifestyle, the proteomic data was then incorporated into a genome scale metabolic model using the integrative metabolic analysis tool (iMAT). The analysis revealed that planktonic cells utilised the glyoxylate shunt while biofilm cells completed the full tricarboxylic acid cycle. Differences in processing aspartate, arginine and alanine were identified as well as unique export of valine out of biofilm cells which may have a role in inter-bacterial communication and regulation. Finally, increased polyhydroxybutyrate accumulation and superoxide dismutase activity in biofilm cells may contribute to increased persistence during infection. Taken together, this study modelled major proteomic and metabolic changes that occur in biofilm cells which helps lay the groundwork for further understanding B. pertussis pathogenesis.

microbiology↗