Biology subjects

Shafeeq, S.

Publications and source records attributed to Shafeeq, S..

3 recordsLinked to original sources

bioRxiv2023

Epigenetics and chromatin structure regulate var2csa expression and the placental binding phenotype in Plasmodium falciparum

Plasmodium falciparum is responsible for what appears to be a never-ending public health issue in the developing world. With repeated infections, a gradual semi-immunity to severe malaria can be acquired but this is disrupted when women become pregnant as the parasite cytoadheres in the placenta to prevent splenic clearance. This change in tissue tropism is due to specific transcription of the antigenically variable adhesin VAR2CSA. To better understand the molecular mechanisms activating var2csa and antigenic variation overall, we used a combination of phenotypic and systems biology assays. We first established phenotypically homogenous populations of VAR2CSA expressing and placenta binding parasites that were shown to exclusively transcribe var2csa while all other var genes remained silenced. We also confirmed that the transcriptional activation was strongly associated with distinct depletion of repressive H3K9me3 marks. Further, we used chromatin conformation capture as a high-resolution approach to determine interchromosomal interactions and established that transcriptional activation is linked to a small yet significant repositioning of var2csa relative to heterochromatic telomeric clusters. Lastly, we demonstrated that occupancy of 5-methylcytosine was present in all var genes but independent of transcriptional repression and switching. All together, these findings provide insights at high resolution into the potential role of 5-methylcytosine in P. falciparum and increase our understanding of the mechanisms regulating antigenic variation at the epigenetics and chromatin structure level.

cell biology↗

bioRxiv2022

Evolution towards small colony variants of pandemic multidrug resistant ST131 Escherichia coli isolates from a 10-year bone infection

Chronic wounds are difficult to treat because underlying medical conditions can impair the mechanical and physiological first-line innate immune defenses, leading to persistent microbial infections. We report here the isolation, molecular and phenotypic characterization of seven E. coli strains that were isolated concomitantly with Enterococcus faecalis after an open foot fracture caused by the 2004 tsunami resulting in a 10-year chronic bone and joint infection. Initially present antimicrobial resistant E. coli ST405 and ST940 isolates were followed by host adapted isolates of ubiquitous ST131 clone presumably acquired from the environment already upon initial foot fracture. The E. coli ST131 clade C1 strains showed genomic alterations associated with virulence and persistence including large chromosomal inversions and, subsequently, a large deletion to cause small colony variants and higher susceptibility to formaldehyde and other stress provoking In this context deletion of hemB catalyzing an early step in the pathway for heme biosynthesis was the major, but presumably not the only cause of small colony variant emergence. Surprisingly, ST131 isolates did not display pronounced biofilm formation in conventional biofilm assays suggesting unconventional modes of persistence. In summary, the genomes of ST131 clone members are highly plastic which enables their persistence in novel ecological niches. In individuals with underlying metabolic diseases such as diabetes wound infection can prepare for colonization with ST131 E. coli isolates. FundingThis work was partially funded by ALF, the Petrus and Augusta Hedlunds Foundation and the Karolinska Institutet.

microbiology↗

bioRxiv2020

Clarithromycin Exerts an Antibiofilm Effect against Salmonella typhimurium rdar Biofilm Formation, and Transforms the Physiology towards an Apparent Oxygen-depleted Energy and Carbon Metabolism

Upon biofilm formation, production of extracellular matrix components and alteration in physiology and metabolism allows bacteria to build up multicellular communities which can facilitate nutrient acquisition during unfavorable conditions and provide protection towards various forms of environmental stresses to individual cells. Thus, bacterial cells become tolerant against antimicrobials and the immune system within biofilms. In the current study, we evaluated the antibiofilm activity of the macrolides clarithromycin and azithromycin. Clarithromycin showed antibiofilm activity against rdar (red, dry and rough) biofilm formation of the gastrointestinal pathogen Salmonella typhimurium ATCC14028 Nalr at 1.56 M subinhibitory concentration in standing culture and dissolved cell aggregates at 15 M in a microaerophilic environment suggesting that the oxygen level affects the activity of the drug. Treatment with clarithromycin significantly decreased transcription and production of the rdar biofilm activator CsgD, with biofilm genes such as csgB and adrA to be consistently downregulated. While fliA and other flagellar regulon genes were upregulated, apparent motility was downregulated. RNA sequencing showed a holistic cell response upon clarithromycin exposure, whereby not only genes involved in the biofilm-related regulatory pathways, but also genes that likely contribute to intrinsic antimicrobial resistance, and the heat shock stress response were differentially regulated. Most significantly, clarithromycin exposure shifts the cells towards an apparent oxygen- and energy-depleted status, whereby the metabolism that channels into oxidative phosphorylation is downregulated, and energy gain by degradation of propane 1,2-diol, ethanolamine and L-arginine catabolism is upregulated. This initial analysis will allow the subsequent identification of novel intrinsic antimicrobial resistance determinants.

microbiology↗