Analysis of essential gene dynamics under antibiotic stress in Streptococcus sanguinis

Abstract

The paradoxical response of Streptococcus sanguinis to drugs prescribed for dental and clinical practices has complicated treatment guidelines and raised the need for further investigation. We conducted a high throughput study on concomitant transcriptome and proteome dynamics in a time course to assess S. sanguinis behaviour under a sub-inhibitory concentration of ampicillin. Temporal changes at the transcriptome and proteome level were monitored to cover essential genes and proteins over a physiological map of intricate pathways. Our findings revealed that translation was the functional category in S. sanguinis that was most enriched in essential proteins. Moreover, essential proteins in this category demonstrated the greatest conservation across 2774 bacterial proteomes, in comparison to other essential functional categories like cell wall biosynthesis and energy production. In comparison to non-essential proteins, essential proteins were less likely to contain ‘degradation-prone’ amino acids at their N-terminal position, suggesting a longer half-life. Despite the ampicillin-induced stress, the transcriptional up-regulation of amino acid-tRNA synthetases and proteomic elevation of amino acid biosynthesis enzymes favoured the enriched components of essential proteins revealing ‘proteomic signatures’ that can be used to bridge the genotype–phenotype gap of S. sanguinis under ampicillin stress. Furthermore, we identified a significant correlation between the levels of mRNA and protein for essential genes and detected essential protein-enriched pathways differentially regulated through a persistent stress response pattern at late time points. We propose that the current findings will help characterize a bacterial model to study the dynamics of essential genes and proteins under clinically relevant stress conditions.

Elucidating the Influence of Chromosomal Architecture on Transcriptional Regulation in Prokaryotes – Observing Strong Local Effects of Nucleoid Structure on Gene Regulation

“…The observed patterns in expressional change cannot be accounted for by expression modulation through protein binding ( Figure 4 ), operon structure, or transcription induced supercoiling gradients, suggesting a more fundamental mechanism ( Figure 5 ). This notion is further supported by observations of periodicities in correlation of expressional change and distance between positions of the genome in RNA-seq data ( Figure 6C ) from both S. sanguinis SK36 (Data from BioProject PRJNA381491 available at GEO database; El-Rami et al, 2018 ), and L. monocytogenes (Data from BioProject PRJNA270808 available at GEO database; Tang et al, 2015 ). We thus speculate that the mechanism is related to the fundamental parts of the transcriptional machinery and nucleoid structure.…”

“…Left panel: Data from BioProject PRJNA270808 ( Tang et al, 2015 ), showing periodic patterns of ~23 kbp, within region 775–1,025 kbp of the Gram-positive Listeria monocytogenes . Right panel: Data from BioProject PRJNA381491 ( El-Rami et al, 2018 ), showing periodic patterns of ~25 kbp, within region 2000–2,250 kbp of the Gram-positive Streptococcus sanguinis SK36 .…”

“…To investigate the presence of periodic patterns in other species, RNA-seq as raw fastq data from the NCBI GEO database was retrieved and analyzed as described in 6.2 top section, see Figure 1A . Data used from Streptococcus sanguinis SK36 (Data from BioProject PRJNA381491 available at GEO database; El-Rami et al, 2018 ), and Listeria monocytogenes (Data from BioProject PRJNA270808 available at GEO database; Tang et al, 2015 ).…”

Mechanistic models of microbial community metabolism

“… 59 Gene essentiality analysis allows us to identify how essential genes change after a selective pressure is applied to a community, resulting in the loss or mutation of previously essential genes over time. 60 Cornerstone species in a community can be identified by finding the bacteria that provide the highest proportion of essential genes. 61 …”

Interaction between the Oral Microbiome and Dental Composite Biomaterials: Where We Are and Where We Should Go

“…However, an agent triggering reduced metabolic activity could yield misleading results. For the oral commensal species Streptococcus sanguinis , sublethal concentrations of ampicillin, an antibiotic that targets the cell wall, causes a transition to slower growth and reduced metabolism, but the cells remain viable (El-Rami et al 2018). Furthermore, persister cells and viable but nonculturable cells would likely be missed in metabolic assays but might still be capable of expressing certain virulence properties (Ramamurthy et al 2014).…”