Fig 1 - uploaded by Peter L. Moses
Content may be subject to copyright.
Prevalence and number of invertons per genome are enriched in host-associated species. (A and B) The percentage of genomes identified with invertons (A) and the number of invertons per genome (B) from aquatic, terrestrial, and host-associated isolates. (C and D) In the phylum Bacteroidetes, the percentage of genomes identified with invertons (C) and the number of invertons per genome (D) from aquatic, terrestrial, host sites other than gut, and host gut-associated isolates. **P ≤ 0.01, ***P ≤ 0.001.
Source publication
Switching ON resistance
Clonal bacterial colonies will often grow dissimilar patches, similar to a tortoiseshell pattern. These differing phenotypes arise by reversible mechanisms called phase variation. Jiang et al. developed an algorithm to survey bacterial genomes for invertible promoters that cause phase variation. Inverted repeats signal the p...
Contexts in source publication
Context 1
... predominantly found in one orientation within an individual with little or no fluctuation (mean > 95% and min > 75% for either the F or R ori- entation) (Fig. 4A); the orientations of 59 were relatively stable (max-min %R ≤ 50%) within an individual (Fig. 4B), whereas the orientations of 42 were unstable (max-min %R > 50%) within an individual (Fig. 4C and table ...
Context 2
... the orientations of 90% of invertons in the same individual were relatively stable over time, the orientations between individuals varied extensively ( Fig. 4D and fig. S10). The mean %R orientation of 214 out of 423 of the invertons varied by more than 50% between individuals. In 122 examples, averaging across time, the inver- ton was predominantly (>95%) in the F orienta- tion in at least one individual and predominantly (>95%) in the R orientation in another. Addi- tionally, 119 out of 238 invertons ...
Context 3
... we identified strains from the donor that engrafted into the patient's microbiome. To identify engraftment, we found cases where the same strain was present in the donor and in at least one patient after FMT, but absent in the same patient(s) before FMT (Fig. 4, E, G, and I, and fig. S11). We found three high-abundance species with invertons from the donor that en- grafted in patients: B. fragilis, B. vulgatus, and B. ...
Context 4
... we compared the orientations of in- vertons from the donor and patient after en- graftment and found that the orientations of 42.8% of invertons (48/112) diverged from the donor orientation (Wilcoxon rank sum test, FDR P < 0.05) (Fig. 4, F, H, and J, and fig. S12). In B. fragilis, two invertons (IBP183 and IBP198) engrafted in the opposite orientation of the donor strain and remained predominantly (87.2% and 87.1%) in the R orientation, but drifted toward F near the end of the sampling (Fig. 4F). For B. ovatus, a strain existed in Patient 014 before FMT but was replaced by the donor B. ovatus ...
Context 5
... (90.1% and 100%) in the R orientation, whereas the newly engrafted strain was oriented entirely in the F orientation and remained in the F orienta- tion over the course of sampling (Fig. 4H). In B. vulgatus, an inverton was initially present completely in the F orientation but over the course of 145 days completely reversed to the R orientation (Fig. 4J, IBP121). In addition to the invertons that reversed their orientations, we also identified examples of invertons that main- tained their orientations (Fig. 4F, IBP189; Fig. 4H, IBP166; Fig. 4J, ...
Context 6
... the course of sampling (Fig. 4H). In B. vulgatus, an inverton was initially present completely in the F orientation but over the course of 145 days completely reversed to the R orientation (Fig. 4J, IBP121). In addition to the invertons that reversed their orientations, we also identified examples of invertons that main- tained their orientations (Fig. 4F, IBP189; Fig. 4H, IBP166; Fig. 4J, ...
Context 7
... (Fig. 4H). In B. vulgatus, an inverton was initially present completely in the F orientation but over the course of 145 days completely reversed to the R orientation (Fig. 4J, IBP121). In addition to the invertons that reversed their orientations, we also identified examples of invertons that main- tained their orientations (Fig. 4F, IBP189; Fig. 4H, IBP166; Fig. 4J, ...
Context 8
... B. vulgatus, an inverton was initially present completely in the F orientation but over the course of 145 days completely reversed to the R orientation (Fig. 4J, IBP121). In addition to the invertons that reversed their orientations, we also identified examples of invertons that main- tained their orientations (Fig. 4F, IBP189; Fig. 4H, IBP166; Fig. 4J, ...
Similar publications
Fecal microbiota transplantation (FMT) is currently used in medicine to treat recurrent clostridial colitis and other intestinal diseases. However, neither the therapeutic mechanism of FMT nor the mechanism that allows the donor bacteria to colonize the intestine of the recipient has yet been clearly described. From a biological point of view, FMT...
Citations
... We note that a locus here could be a nucleotide, gene, or gene set --any contiguous or non-contiguous stretch of DNA in which multiple mutations interact with strong antagonism (e.g. two mutations in the same locus would be just as beneficial as only one of these). We next use equation (7) to obtain a formula for d N /d S that has only three free parameters when a single value for is chosen: µ [43]). Invertible promoters are restricted out of the genome and re-ligated in the opposite direction to turn gene expression on or off. ...
When examining bacterial genomes for evidence of past selection, the results obtained depend heavily on the mutational distance between chosen genomes. Even within a bacterial species, genomes separated by larger mutational distances exhibit stronger evidence of purifying selection as assessed by dN/dS, the normalized ratio of nonsynonymous to synonymous mutations. This dependence on mutational distance, and thus time, has been proposed to arise from the inefficiency of purifying selection at removing weakly deleterious mutations. Here, we revisit this assumption in light of abundant genomes from gut microbiomes and show that a model of weak purifying selection that fits the data leads to problematic mutation accumulation. We propose an alternative model to explain the timescale dependence of dN/dS, in which constantly changing environmental pressures select for revertants of previously adaptive mutations. Reversions that sweep within-host populations are nearly guaranteed in microbiomes due to large population sizes, short generation times, and variable environments. Using analytical and simulation approaches, we fit the adaptive reversion model to dN/dS decay curves and obtain estimates of local adaptation that are realistic in the context of bacterial genomes. These results argue for interpreting low values of dN/dS with caution, as they may emerge even when adaptive sweeps are frequent. This work reframes an old observation in bacterial evolution, illustrates the potential of mutation reversions to shape genomic landscapes over time, and highlights the need for additional research on bacterial genomic evolution on short time scales.
... Phase variation involves the reversible and heritable variation in the levels of expression of specific genes (typically switching between ON and OFF). This mechanism is ubiquitious in bacteria and can generate extensive phenotypic heterogeneity in host-associated bacteria such as pathogens and symbionts (2)(3)(4)(5)(6)(7)(8). Phase variation works through diverse genetic mechanisms, such as reversible DNA recombination, to create subpopulations with distinct patterns of gene expression (9). ...
Population heterogeneity can promote bacterial fitness in response to unpredictable environmental conditions. A major mechanism of phenotypic variability in the human gut symbiont Bacteroides spp. involves the inversion of promoters that drive the expression of capsular polysaccharides, which determine the architecture of the cell surface. High-throughput single-cell sequencing reveals substantial population heterogeneity generated through combinatorial promoter inversion regulated by a broadly conserved serine recombinase. Exploiting control over population diversification, we show that populations with different initial compositions converge to a similar composition over time. Combining our data with stochastic computational modeling, we demonstrate that the differential rates of promoter inversion are a major mechanism shaping population dynamics. More broadly, our approach could be used to interrogate single-cell combinatorial phase variable states of diverse microbes including bacterial pathogens.
... They are also among the most commonly recovered bacteria from extra-intestinal anaerobic infections and are increasingly resistant to many antibiotics, including cephalosporins and carbapenems 22,23 . Their broad phenotypic purview is enabled in part by phase variation, an array of polysaccharide utilization loci, and their use of invertible promoters 24,25 . ...
Three types of DNA methyl modifications have been detected in bacterial genomes, and mechanistic studies have demonstrated roles for DNA methylation in physiological functions ranging from phage defense to transcriptional control of virulence and host-pathogen interactions. Despite the ubiquity of methyltransferases and the immense variety of possible methylation patterns, epigenomic diversity remains unexplored for most bacterial species. Members of the Bacteroides fragilis group (BFG) reside in the human gastrointestinal tract as key players in symbiotic communities but also can establish anaerobic infections that are increasingly multi-drug resistant. In this work, we utilize long-read sequencing technologies to perform pangenomic (n = 383) and panepigenomic (n = 268) analysis of clinical BFG isolates cultured from infections seen at the NIH Clinical Center over four decades. Our analysis reveals that single BFG species harbor hundreds of DNA methylation motifs, with most individual motif combinations occurring uniquely in single isolates, implying immense unsampled methylation diversity within BFG epigenomes. Mining of BFG genomes identified more than 6000 methyltransferase genes, approximately 1000 of which were associated with intact prophages. Network analysis revealed substantial gene flow among disparate phage genomes, implying a role for genetic exchange between BFG phages as one of the ultimate sources driving BFG epigenome diversity.
... начинает экспрессироваться. В частности, были обнаружены инверсии, «включающие» гиперэкспрессию генов резистентности (эффлюкссистем, рРНКметилаз и др.) [19]. Большие делеции -делеции размером более 100 нуклеотидов -могут приводить к необратимым по ломкам одного или нескольких генов [20]. ...
The worldwide successful expansion of ESKAPE pathogens is largely due to their ability to rapidly acquire high antimicrobial resistance levels. The bacterial resistome includes (1) plasmid-encoded genes acquired as a result of horizontal gene transfer, and (2) chromosomal genes associated with the antimicrobial resistance development. This review represents the priority list of the ESKAPE group chromosomal genes, mutations in which are associated with antimicrobial resistance. The diversity of chromosomal genes carrying antimicrobial resistance (AMR) associated mutations confers the rapid pathogen adaptation to antimicrobials by generation of multilevel pathways to neutralize antibiotics. Analysis of the AMR mechanisms associated only with plasmid resistance genes is insufficient. A comprehensive description of AMR mechanisms should include also an analysis of chromosomal genes, mutations in which lead to increased levels of antimicrobial resistance.
... ICEs, IMEs, AICEs and CIMEs) are important hotspots for the accretion of defense systems, helping to protect the host from superinfection by other MGEs. Considering the known evolutionary relationship MGEs have with defense systems (2,4,(18)(19)(20), AMR (5,(20)(21)(22) and virulence genes (23), I also explore if these three functions are positively or negatively correlated across ciMGEs from multiple phyla. I found that (i) IMEs and ICEs are widespread across different phyla; (ii) ICEs are the most common ciMGEs for the accumulation of defense systems, AMR and virulence genes; (iii) these three functions are negatively correlated across ICEs and IMEs and (iv) ICEs and IMEs from multiple phyla share high genetic similarity and challenge interphylum barriers. ...
Mobile genetic elements (MGEs) are key promoters of microbial evolution. These elements can be located extrachromosomally or integrated into the chromosome. Well-known examples of chromosomally integrated MGEs (ciMGEs) are integrative and conjugative/mobilizable elements (ICEs and IMEs), and most studies to date have focused on the biological mechanisms that shape their lifestyle. It is crucial to profile the diversity and understand their distribution across the microbial community, as the number of genome sequences increases exponentially. Herein, I scanned a collection of >20 000 bacterial and archaeal non-redundant genomes and found over 13 000 ciMGEs across multiple phyla, representing a massive increase in the number of ciMGEs available in public databases (<1000). Although ICEs are the most important ciMGEs for the accretion of defense systems, virulence, and antimicrobial resistance (AMR) genes, IMEs outnumbered ICEs. Moreover, defense systems, AMR, and virulence genes were negatively correlated in both ICEs and IMEs. Multiple ciMGEs form heterogeneous communities and challenge inter-phylum barriers. Finally, I observed that the functional landscape of ICEs was populated by uncharacterized proteins. Altogether, this study provides a comprehensive catalog of nucleotide sequences and associated metadata for ciMGEs from 34 phyla across the bacterial and archaeal domains.
... One such mechanism is phase variation, which generates frequent and reversible modifications in protein expression within individual cells of a clonal population. 1 The molecular mechanisms governing phase variations range from epigenetic modifications via DNA methylation, to genetic alterations involving slipped strand mispairing or site-specific recombination within hypermutable loci. [2][3][4][5][6] In this regard, simple sequence repeats (SSRs) in specific loci can serve as mediators of hypermutations through slipped strand mispairing that can occur in these regions during DNA replication. [7][8][9][10] Accordingly, several studies have demonstrated enhanced adaptation to unstable environmental conditions through insertion or deletion (indels) of nucleotides generated by SSRs. ...
Microbial adaptation to changing environmental conditions is frequently mediated by hypermutable sequences. Here we demonstrate that such a hypermutable hotspot within a gene encoding a flagellar unit of Paenibacillus glucanolyticus generated spontaneous non-swarming mutants with increased stress resistance. These mutants, which survived conditions that eliminated wild-type cultures, could be carried by their swarming siblings when the colony spread, consequently increasing their numbers at the spreading edge. Of interest, the hypermutable nature of the aforementioned sequence enabled the non-swarming mutants to serve as “seeds” for a new generation of wild-type cells through reversion of the mutation.Using a mathematical model, we examined the survival dynamics of P. glucanolyticus colonies under fluctuating environments. Our experimental and theoretical results suggest that the non-swarming, stress-resistant mutants can save the colony from extinction. Notably, we identified this hypermutable sequence in flagellar genes of additional Paenibacillus species, suggesting that this phenomenon could be wide-spread and ecologically important.
... The production of type 1 fimbriae is subject to phase variation, with fimbriate and afimbriate cells coexisting in the same population [9,12]. This behaviour has been interpreted as a bet-hedging strategy that balances the risks of producing these highly immunogenic fimbriae (detection by the host immune system; the physiological cost of making, exporting and assembling the structures) with the benefits (biofilm-based community living; colonization of a host or another environmental niche) [13][14][15][16]. The invertible fimS genetic element is the basis of phase-variable fim operon expression. ...
The structural genes expressing type 1 fimbriae in Escherichia coli alternate between expressed (phase ON) and non-expressed (phase OFF) states due to inversion of the 314 bp fimS genetic switch. The FimB tyrosine integrase inverts fimS by site-specific recombination, alternately connecting and disconnecting the fim operon, encoding the fimbrial subunit protein and its associated secretion and adhesin factors, to and from its transcriptional promoter within fimS. Site-specific recombination by the FimB recombinase becomes biased towards phase ON as DNA supercoiling is relaxed, a condition that occurs when bacteria approach the stationary phase of the growth cycle. This effect can be mimicked in exponential phase cultures by inhibiting the negative DNA supercoiling activity of DNA gyrase. We report that this bias towards phase ON depends on the presence of the Fis nucleoid-associated protein. We mapped the Fis binding to a site within the invertible fimS switch by DNase I footprinting. Disruption of this binding site by base substitution mutagenesis abolishes both Fis binding and the ability of the mutated switch to sustain its phase ON bias when DNA is relaxed, even in bacteria that produce the Fis protein. In addition, the Fis binding site overlaps one of the sites used by the Lrp protein, a known directionality determinant of fimS inversion that also contributes to phase ON bias. The Fis-Lrp relationship at fimS is reminiscent of that between Fis and Xis when promoting DNA relaxation-dependent excision of bacteriophage λ from the E. coli chromosome. However, unlike the co-binding mechanism used by Fis and Xis at λ attR, the Fis-Lrp relationship at fimS involves competitive binding. We discuss these findings in the context of the link between fimS inversion biasing and the physiological state of the bacterium.
... As different phenotypes are often better equipped to overcome different challenges, such intra-population heterogeneity might allow the bacterial population a bet-hedging strategy to better survive sudden environmental challenges. Indeed, phase variation was observed in various bacterial processes (1)(2)(3)(4) and was shown to be important for survival in major environmental challenges faced by bacteria, including bacteriophages (5,6), antibiotic drugs (7,8) and virulence (9)(10)(11). ...
... The genomic signature of inverted repeats flanking programmed inversions, as well as the rapidly growing amount of publicly available DNA sequence data, provide an opportunity for computational identification of programmed inversions. Indeed, multiple methods to identify programmed inversions were developed and successfully deployed (7,8,12,17,18,(23)(24)(25)(26)(27). Yet, only a few of these methods were applied widely across the bacterial domain, specifically searching for programmed inversions that target promoters (7,8), or searching for gene-altering programmed inversions targeting a specific gene family, the Type I RM specificity subunit HsdS (17,18). ...
... Indeed, multiple methods to identify programmed inversions were developed and successfully deployed (7,8,12,17,18,(23)(24)(25)(26)(27). Yet, only a few of these methods were applied widely across the bacterial domain, specifically searching for programmed inversions that target promoters (7,8), or searching for gene-altering programmed inversions targeting a specific gene family, the Type I RM specificity subunit HsdS (17,18). A more comprehensive gene-independent search for programmed inversions was developed based on abnormally aligned shortreads and manual curation, and was used to identify programmed inversions, regardless of target, in over 200 genomes (27). ...
Programmed chromosomal inversions allow bacteria to generate intra-population genotypic and functional heterogeneity, a bet-hedging strategy important in changing environments. Some programmed inversions modify coding sequences, producing different alleles in several gene families, most notably in specificity-determining genes such as Type I restriction-modification systems, where systematic searches revealed cross phylum abundance. Yet, a broad, gene-independent, systematic search for gene-altering programmed inversions has been absent, and little is known about their genomic sequence attributes and prevalence across gene families. Here, identifying intra-species variation in genomes of over 35 000 species, we develop a predictive model of gene-altering inversions, revealing key attributes of their genomic sequence attributes, including gene-pseudogene size asymmetry and orientation bias. The model predicted over 11,000 gene-altering loci covering known targeted gene families, as well as novel targeted families including Type II restriction-modification systems, a protein of unknown function, and a fusion-protein containing conjugative-pilus and phage tail domains. Publicly available long-read sequencing datasets validated representatives of these newly predicted inversion-targeted gene families, confirming intra-population genetic heterogeneity. Together, these results reveal gene-altering programmed inversions as a key strategy adopted across the bacterial domain, and highlight programmed inversions that modify Type II restriction-modification systems as a possible new mechanism for maintaining intra-population heterogeneity.
... Identical genomic regions can give rise to different phenotypes depending on their orientation and association with other genomic regions (Evans et al., 2013;Jiang et al., 2019). To capture such paired interactions, we developed the 'paired regions' feature in PRAWNS: each feature corresponds to two conserved regions, r 1 and r 2 , and their relative orientations such that r 1 and r 2 are separated by at most a small distance D (user-defined, default: 50) nucleotides in ! ...
Motivation:
Scientists seeking to understand the genomic basis of bacterial phenotypes, such as antibiotic resistance, today have access to an unprecedented number of complete and nearly-complete genomes. Making sense of these data requires computational tools able to perform multiple-genome comparisons efficiently, yet currently available tools cannot scale beyond several tens of genomes.
Results:
We describe PRAWNS, an efficient and scalable tool for multiple-genome analysis. PRAWNS defines a concise set of genomic features (metablocks), as well as pairwise relationships between them, which can be used as a basis for large-scale genotype-phenotype association studies. We demonstrate the effectiveness of PRAWNS by identifying genomic regions associated with antibiotic resistance in Acinetobacter baumannii.
Availability:
PRAWNS is implemented in C ++ and Python3, licensed under the GPLv3 license, and freely downloadable from GitHub (https://github.com/KiranJavkar/PRAWNS.git).
Supplementary information:
Supplementary data are available at Bioinformatics online.
... Though it is costly, bacteria can ameliorate the fitness costs of maintaining ARGs through different strategies 9 , such as no-cost, low-cost or gain-of-fitness mutations 10,11 , compensatory mutations at a second site [12][13][14] , or genetic coselection of resistance genes in genetic linkage 15,16 . Phase-variable antibiotic resistance, which was only recently reported 17 , is a newly identified mechanism for antibiotic resistant bacteria to mitigate the fitness cost of encoding ARGs. ...
... Phase variation refers to a reversible change that generates phenotypic variation that helps bacteria adapt to rapidly changing environments 18,19 . Phase variation often manifests through reversible inversion of DNA regions containing promoters such that in one orientation, a downstream gene is expressed, while in the alternate orientation, the downstream gene is not expressed 17 . Such DNA inversions are generally mediated by invertases, which recognize inverted repeats flanking the invertible region and catalyze the reversible inversion [20][21][22] . ...
... Recent advances in computational methods have contributed to the effective identification of the intergenic invertible DNA regions in microbial genomes 17,28 . ARGs were found to be regulated by invertible promoters in certain human gut bacteria 17 . ...
Antibiotic-resistance genes (ARGs) regulated by invertible promoters can mitigate the fitness cost of maintaining ARGs in the absence of antibiotics and could potentially prolong the persistence of ARGs in bacterial populations. However, the origin, prevalence, and distribution of these ARGs regulated by invertible promoters remains poorly understood. Here, we sought to assess the threat posed by ARGs regulated by invertible promoters by systematically searching for ARGs regulated by invertible promoters in the human gut microbiome and examining their origin, prevalence, and distribution. Through metagenomic assembly of 2227 human gut metagenomes and genomic analysis of the Unified Human Gastrointestinal Genome (UHGG) collection, we identified ARGs regulated by invertible promoters and categorized them into three classes based on the invertase-regulating phase variation. In the human gut microbiome, ARGs regulated by invertible promoters are exclusively found in Bacteroidales species. Through genomic analysis, we observed that ARGs regulated by invertible promoters have convergently originated from ARG insertions into glycan-synthesis loci that were regulated by invertible promoters at least three times. Moreover, all three classes of invertible promoters regulating ARGs are located within integrative conjugative elements (ICEs). Therefore, horizontal transfer via ICEs could explain the wide taxonomic distribution of ARGs regulated by invertible promoters. Overall, these findings reveal that glycan-synthesis loci regulated by invertible promoters in Bacteroidales species are an important hotspot for the emergence of clinically-relevant ARGs regulated by invertible promoters.
