Mechanisms of Virulence Reprogramming in Bacterial Pathogens

Zhou, Jianuan; Ma, Hongmei; Zhang, Lian-Hui

doi:10.1146/annurev-micro-032521-025954

Cited by 4 publications

(1 citation statement)

References 148 publications

(196 reference statements)

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“…In fact, the data from DEG can provide valuable references for bottom-up genome construction. Therefore, DEG has been recommended as a reference resource for studying the minimal gene set required for bacterial survival [157][158][159][160][161][162][163][164][165][166][167][168][169].…”

Section: Introduction Of the Deg Databasementioning

confidence: 99%

Recent advances in the characterization of essential genes and development of a database of essential genes

Liang,

Luo,

Lin

et al. 2024

iMeta

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Over the past few decades, there has been a significant interest in the study of essential genes, which are crucial for the survival of an organism under specific environmental conditions and thus have practical applications in the fields of synthetic biology and medicine. An increasing amount of experimental data on essential genes has been obtained with the continuous development of technological methods. Meanwhile, various computational prediction methods, related databases and web servers have emerged accordingly. To facilitate the study of essential genes, we have established a database of essential genes (DEG), which has become popular with continuous updates to facilitate essential gene feature analysis and prediction, drug and vaccine development, as well as artificial genome design and construction. In this article, we summarized the studies of essential genes, overviewed the relevant databases, and discussed their practical applications. Furthermore, we provided an overview of the main applications of DEG and conducted comprehensive analyses based on its latest version. However, it should be noted that the essential gene is a dynamic concept instead of a binary one, which presents both opportunities and challenges for their future development.

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Section: Introduction Of the Deg Databasementioning

confidence: 99%

Recent advances in the characterization of essential genes and development of a database of essential genes

Liang,

Luo,

Lin

et al. 2024

iMeta

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Highly Multiplexed Spatial Transcriptomics in Bacteria

Sarfatis,

Wang,

Twumasi-Ankrah

et al. 2024

Preprint

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Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hindered by the massive density of bacterial mRNA. To overcome this challenge, we combine 1000-fold volumetric expansion with multiplexed error robust fluorescencein situhybridization (MERFISH) to create bacterial-MERFISH. This method enables high-throughput, spatially resolved profiling of thousands of operons within individual bacteria. Using bacterial-MERFISH, we dissect the response ofE. colito carbon starvation, systematically map subcellular RNA organization, and chart the adaptation of a gut commensalB. thetaiotaomicronto micron-scale niches in the mammalian colon. We envision bacterial-MERFISH will be broadly applicable to the study of bacterial single-cell heterogeneity in diverse, spatially structured, and native environments.

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Polygenic TB control and the sequence of innate/adaptive immune responses to infection: MHC‐II alleles determine the size of the S100A8/9‐producing neutrophil population

Logunova,

Kapina,

Dyatlov

et al. 2024

Immunology

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Among several quantitative trait loci involved in tuberculosis (TB) control in mice, one was mapped within the chromosome 17 segment occupied by the H2 complex and another within the chromosome 3 segment comprising the S100A8/9 genes, which encode neutrophil inflammatory factor S100A8/9. Previously, we developed a panel of H2‐congenic mouse strains differing by small segments of the major histocompatibility complex Class II (MHC‐II) region from TB‐susceptible H2j mice transferred onto the genetic background of the TB‐resistant C57BL/6 (H2b) strain. Susceptible B6.I‐9.3 mice differ from B6 progenitors by the alleles of their only classical MHC‐II H2‐Aβ gene. The goals of the present study were to: (i) comprehensively characterise the differences in TB‐related phenotypes between mice of the two strains and (ii) decipher interactions between the H2‐Aβ and S100A8/9 genes. Here, we describe the dynamics of TB‐related phenotypes differentiating B6.I‐9.3 and B6 mice (colony forming units counts, histopathology, lung immune cell infiltration and cytokine profiles). We show that disproportionally diminished CD4+ T‐cell population, an enlarged S100A8/9‐positive neutrophil population and higher S100A8/9 serum levels in B6.I‐9.3 mice collectively form the ‘susceptible’ phenotype before infection. An increase in IL‐17 and a decrease in intrferon‐gamma production by CD4+ T‐cells in these mice provide a mechanistic explanation of this phenotype. Using F2 segregation analysis, we show that the number of S100A8/9‐producing neutrophils in lungs and spleens and the proportion of Th17 CD4+ T‐cells in lungs are significantly lower in the presence of the MHC‐II dominant ‘resistant’ b allele compared to the recessive ‘susceptible’ j/j genotype. This provides direct genetic evidence that MHC‐II‐regulated CD4+ T‐cell landscapes determine neutrophil abundance before infection, an important pathogenic factor in TB immunity.

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Mechanisms of Virulence Reprogramming in Bacterial Pathogens

Cited by 4 publications

References 148 publications

Recent advances in the characterization of essential genes and development of a database of essential genes

Recent advances in the characterization of essential genes and development of a database of essential genes

Highly Multiplexed Spatial Transcriptomics in Bacteria

Polygenic TB control and the sequence of innate/adaptive immune responses to infection: MHC‐II alleles determine the size of the S100A8/9‐producing neutrophil population

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