Genomic Islands in the Bacterial Chromosome – Paradigms of Evolution in Quantum Leaps

Background: Synechococcus sp. WH8102 is one of the most abundant photosynthetic organisms in many ocean regions. Objective: The aim of this study is to identify genomic islands (GIs) in Synechococcus sp. WH8102 with integrated methods. Methods: We have applied genomic barcode to identify the GIs in Synechococcus sp. WH8102, which could make genomic regions of different origins visually apparent. The gene expression data of the predicted GIs was analyzed through microarray data which was collected for functional analysis of the relevant genes. Results: Seven GIs were identified in Synechococcus sp. WH8102. Most of them are involved in cell surface modification, photosynthesis and drug resistance. In addition, our analysis also revealed the functions of these GIs, which could be used for in-depth study on the evolution of this strain. Conclusion: Genomic barcodes provide us with a comprehensive and intuitive view of the target genome. We can use it to understand the intrinsic characteristics of the whole genome and identify GIs or other similar elements.

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Tracking Bacterial Chromosome Dynamics with Microfluidics-Based Live Cell Imaging

Methods in Molecular Biology - SMC Complexes ◽

10.1007/978-1-4939-9520-2_17 ◽

2019 ◽

pp. 223-238 ◽

Cited By ~ 2

Author(s):

Suchitha Raghunathan ◽

Anjana Badrinarayanan

Keyword(s):

Live Cell Imaging ◽

Cell Imaging ◽

Live Cell ◽

Bacterial Chromosome ◽

Chromosome Dynamics

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Phylogenomic analysis of Clostridioides difficile ribotype 106 strains reveals novel genetic islands and emergent phenotypes

Scientific Reports ◽

10.1038/s41598-020-79123-2 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Bryan Angelo P. Roxas ◽

Jennifer Lising Roxas ◽

Rachel Claus-Walker ◽

Anusha Harishankar ◽

Asad Mansoor ◽

...

Keyword(s):

Biofilm Formation ◽

Diarrheal Disease ◽

The United States ◽

Genomic Islands ◽

Rapid Expansion ◽

Phylogenomic Analysis ◽

Community Settings ◽

Hamster Model ◽

Clostridioides Difficile ◽

Healthcare Associated

AbstractClostridioides difficile infection (CDI) is a major healthcare-associated diarrheal disease. Consistent with trends across the United States, C. difficile RT106 was the second-most prevalent molecular type in our surveillance in Arizona from 2015 to 2018. A representative RT106 strain displayed robust virulence and 100% lethality in the hamster model of acute CDI. We identified a unique 46 KB genomic island (GI1) in all RT106 strains sequenced to date, including those in public databases. GI1 was not found in its entirety in any other C. difficile clade, or indeed, in any other microbial genome; however, smaller segments were detected in Enterococcus faecium strains. Molecular clock analyses suggested that GI1 was horizontally acquired and sequentially assembled over time. GI1 encodes homologs of VanZ and a SrtB-anchored collagen-binding adhesin, and correspondingly, all tested RT106 strains had increased teicoplanin resistance, and a majority displayed collagen-dependent biofilm formation. Two additional genomic islands (GI2 and GI3) were also present in a subset of RT106 strains. All three islands are predicted to encode mobile genetic elements as well as virulence factors. Emergent phenotypes associated with these genetic islands may have contributed to the relatively rapid expansion of RT106 in US healthcare and community settings.

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panRGP: a pangenome-based method to predict genomic islands and explore their diversity

Bioinformatics ◽

10.1093/bioinformatics/btaa792 ◽

2020 ◽

Vol 36 (Supplement_2) ◽

pp. i651-i658 ◽

Cited By ~ 1

Author(s):

Adelme Bazin ◽

Guillaume Gautreau ◽

Claudine Médigue ◽

David Vallenet ◽

Alexandra Calteau

Keyword(s):

Escherichia Coli ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Species Level ◽

Genomic Islands ◽

Genome Plasticity ◽

Reference Dataset ◽

Prokaryotic Genomes ◽

Ideal Approach ◽

Genomic Regions

Abstract Motivation Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions of genome plasticity (RGPs) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to genomic islands (GIs). The study of those regions at the species level has become increasingly difficult with the data deluge of genomes. To date, no methods are available to identify GIs using hundreds of genomes to explore their diversity. Results We present here the panRGP method that predicts RGPs using pangenome graphs made of all available genomes for a given species. It allows the study of thousands of genomes in order to access the diversity of RGPs and to predict spots of insertions. It gave the best predictions when benchmarked along other GI detection tools against a reference dataset. In addition, we illustrated its use on metagenome assembled genomes by redefining the borders of the leuX tRNA hotspot, a well-studied spot of insertion in Escherichia coli. panRPG is a scalable and reliable tool to predict GIs and spots making it an ideal approach for large comparative studies. Availability and implementation The methods presented in the current work are available through the following software: https://github.com/labgem/PPanGGOLiN. Detailed results and scripts to compute the benchmark metrics are available at https://github.com/axbazin/panrgp_supdata.

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Ability of a bacterial chromosome segment to invert is dictated by included material rather than flanking sequence.

Genetics ◽

10.1093/genetics/129.4.1021 ◽

1991 ◽

Vol 129 (4) ◽

pp. 1021-1032 ◽

Cited By ~ 4

Author(s):

M J Mahan ◽

J R Roth

Keyword(s):

Homologous Recombination ◽

Parent Strain ◽

Genetic Material ◽

Chromosomal Inversion ◽

Chromosome Segment ◽

Bacterial Chromosome ◽

Flanking Sequence ◽

Flanking Sequences ◽

Almost All

Abstract Homologous recombination between sequences present in inverse order within the same chromosome can result in inversion formation. We have previously shown that inverse order sequences at some sites (permissive) recombine to generate the expected inversion; no inversions are found when the same inverse order sequences flank other (nonpermissive) regions of the chromosome. In hopes of defining how permissive and nonpermissive intervals are determined, we have constructed a strain that carries a large chromosomal inversion. Using this inversion mutant as the parent strain, we have determined the "permissivity" of a series of chromosomal sites for secondary inversions. For the set of intervals tested, permissivity seems to be dictated by the nature of the genetic material present within the chromosomal interval being tested rather than the flanking sequences or orientation of this material in the chromosome. Almost all permissive intervals include the origin or terminus of replication. We suggest that the rules for recovery of inversions reflect mechanistic restrictions on the occurrence of inversions rather than lethal consequences of the completed rearrangement.

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Pseudomonas aeruginosa PA80 is a cystic fibrosis isolate deficient in RhlRI quorum sensing

Scientific Reports ◽

10.1038/s41598-021-85100-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Syed A. K. Shifat Ahmed ◽

Michelle Rudden ◽

Sabrina M. Elias ◽

Thomas J. Smyth ◽

Roger Marchant ◽

...

Keyword(s):

Cystic Fibrosis ◽

Pseudomonas Aeruginosa ◽

Quorum Sensing ◽

Virulence Factors ◽

Genomic Islands ◽

Clinical Strain ◽

Whole Genome ◽

Synonymous Mutations ◽

Wide Range

AbstractPseudomonas aeruginosa uses quorum sensing (QS) to modulate the expression of several virulence factors that enable it to establish severe infections. The QS system in P. aeruginosa is complex, intricate and is dominated by two main N-acyl-homoserine lactone circuits, LasRI and RhlRI. These two QS systems work in a hierarchical fashion with LasRI at the top, directly regulating RhlRI. Together these QS circuits regulate several virulence associated genes, metabolites, and enzymes in P. aeruginosa. Paradoxically, LasR mutants are frequently isolated from chronic P. aeruginosa infections, typically among cystic fibrosis (CF) patients. This suggests P. aeruginosa can undergo significant evolutionary pathoadaptation to persist in long term chronic infections. In contrast, mutations in the RhlRI system are less common. Here, we have isolated a clinical strain of P. aeruginosa from a CF patient that has deleted the transcriptional regulator RhlR entirely. Whole genome sequencing shows the rhlR locus is deleted in PA80 alongside a few non-synonymous mutations in virulence factors including protease lasA and rhamnolipid rhlA, rhlB, rhlC. Importantly we did not observe any mutations in the LasRI QS system. PA80 does not appear to have an accumulation of mutations typically associated with several hallmark pathoadaptive genes (i.e., mexT, mucA, algR, rpoN, exsS, ampR). Whole genome comparisons show that P. aeruginosa strain PA80 is closely related to the hypervirulent Liverpool epidemic strain (LES) LESB58. PA80 also contains several genomic islands (GI’s) encoding virulence and/or resistance determinants homologous to LESB58. To further understand the effect of these mutations in PA80 QS regulatory and virulence associated genes, we compared transcriptional expression of genes and phenotypic effects with isogenic mutants in the genetic reference strain PAO1. In PAO1, we show that deletion of rhlR has a much more significant impact on the expression of a wide range of virulence associated factors rather than deletion of lasR. In PA80, no QS regulatory genes were expressed, which we attribute to the inactivation of the RhlRI QS system by deletion of rhlR and mutation of rhlI. This study demonstrates that inactivation of the LasRI system does not impact RhlRI regulated virulence factors. PA80 has bypassed the common pathoadaptive mutations observed in LasR by targeting the RhlRI system. This suggests that RhlRI is a significant target for the long-term persistence of P. aeruginosa in chronic CF patients. This raises important questions in targeting QS systems for therapeutic interventions.

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