1
|
Fu J, Nisbett LM, Guo Y, Boon EM. NosP Detection of Heme Modulates Burkholderia thailandensis Biofilm Formation. Biochemistry 2023; 62:2426-2441. [PMID: 37498555 PMCID: PMC10478957 DOI: 10.1021/acs.biochem.3c00187] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Aggregated bacteria embedded within self-secreted extracellular polymeric substances, or biofilms, are resistant to antibiotics and cause chronic infections. As such, they are a significant public health threat. Heme is an abundant iron source for pathogenic bacteria during infection; many bacteria have systems to detect heme assimilated from host cells, which is correlated with the transition between acute and chronic infection states. Here, we investigate the heme-sensing function of a newly discovered multifactorial sensory hemoprotein called NosP and its role in biofilm regulation in the soil-dwelling bacterium Burkholderia thailandensis, the close surrogate of Bio-Safety-Level-3 pathogen Burkholderia pseudomallei. The NosP family protein has previously been shown to exhibit both nitric oxide (NO)- and heme-sensing functions and to regulate biofilms through NosP-associated histidine kinases and two-component systems. Our in vitro studies suggest that BtNosP exhibits heme-binding kinetics and thermodynamics consistent with a labile heme-responsive protein and that the holo-form of BtNosP acts as an inhibitor of its associated histidine kinase BtNahK. Furthermore, our in vivo studies suggest that increasing the concentration of extracellular heme decreases B. thailandensis biofilm formation, and deletion of nosP and nahK abolishes this phenotype, consistent with a model that BtNosP detects heme and exerts an inhibitory effect on BtNahK to decrease the biofilm.
Collapse
Affiliation(s)
- Jiayuan Fu
- Department of Chemistry and Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Lisa-Marie Nisbett
- Department of Chemistry and Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Yulong Guo
- Department of Chemistry and Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Elizabeth M Boon
- Department of Chemistry and Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794-3400, United States
| |
Collapse
|
2
|
Weltzer ML, Wall D. Social Diversification Driven by Mobile Genetic Elements. Genes (Basel) 2023; 14:648. [PMID: 36980919 PMCID: PMC10047993 DOI: 10.3390/genes14030648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/17/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Social diversification in microbes is an evolutionary process where lineages bifurcate into distinct populations that cooperate with themselves but not with other groups. In bacteria, this is frequently driven by horizontal transfer of mobile genetic elements (MGEs). Here, the resulting acquisition of new genes changes the recipient's social traits and consequently how they interact with kin. These changes include discriminating behaviors mediated by newly acquired effectors. Since the producing cell is protected by cognate immunity factors, these selfish elements benefit from selective discrimination against recent ancestors, thus facilitating their proliferation and benefiting the host. Whether social diversification benefits the population at large is less obvious. The widespread use of next-generation sequencing has recently provided new insights into population dynamics in natural habitats and the roles MGEs play. MGEs belong to accessory genomes, which often constitute the majority of the pangenome of a taxon, and contain most of the kin-discriminating loci that fuel rapid social diversification. We further discuss mechanisms of diversification and its consequences to populations and conclude with a case study involving myxobacteria.
Collapse
Affiliation(s)
- Michael L Weltzer
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| | - Daniel Wall
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
| |
Collapse
|
3
|
Lowrey LC, Kent LA, Rios BM, Ocasio AB, Cotter PA. An IS-mediated, RecA-dependent, bet-hedging strategy in Burkholderia thailandensis. eLife 2023; 12:84327. [PMID: 36715687 PMCID: PMC9946442 DOI: 10.7554/elife.84327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Adaptation to fluctuating environmental conditions is difficult to achieve. Phase variation mechanisms can overcome this difficulty by altering genomic architecture in a subset of individuals, creating a phenotypically heterogeneous population with subpopulations optimized to persist when conditions change, or are encountered, suddenly. We have identified a phase variation system in Burkholderia thailandensis that generates a genotypically and phenotypically heterogeneous population. Genetic analyses revealed that RecA-mediated homologous recombination between a pair of insertion sequence (IS) 2-like elements duplicates a 208.6 kb region of DNA that contains 157 coding sequences. RecA-mediated homologous recombination also resolves merodiploids, and hence copy number of the region is varied and dynamic within populations. We showed that the presence of two or more copies of the region is advantageous for growth in a biofilm, and a single copy is advantageous during planktonic growth. While IS elements are well known to contribute to evolution through gene inactivation, polar effects on downstream genes, and altering genomic architecture, we believe that this system represents a rare example of IS element-mediated evolution in which the IS elements provide homologous sequences for amplification of a chromosomal region that provides a selective advantage under specific growth conditions, thereby expanding the lifestyle repertoire of the species.
Collapse
Affiliation(s)
- Lillian C Lowrey
- Department of Microbiology and Immunology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Leslie A Kent
- Department of Microbiology and Immunology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Bridgett M Rios
- Department of Microbiology and Immunology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Angelica B Ocasio
- Department of Microbiology and Immunology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Peggy A Cotter
- Department of Microbiology and Immunology, University of North Carolina at Chapel HillChapel HillUnited States
| |
Collapse
|
4
|
Sulser S, Vucicevic A, Bellini V, Moritz R, Delavat F, Sentchilo V, Carraro N, van der Meer JR. A bistable prokaryotic differentiation system underlying development of conjugative transfer competence. PLoS Genet 2022; 18:e1010286. [PMID: 35763548 PMCID: PMC9286271 DOI: 10.1371/journal.pgen.1010286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 07/15/2022] [Accepted: 06/08/2022] [Indexed: 12/21/2022] Open
Abstract
The mechanisms and impact of horizontal gene transfer processes to distribute gene functions with potential adaptive benefit among prokaryotes have been well documented. In contrast, little is known about the life-style of mobile elements mediating horizontal gene transfer, whereas this is the ultimate determinant for their transfer fitness. Here, we investigate the life-style of an integrative and conjugative element (ICE) within the genus Pseudomonas that is a model for a widespread family transmitting genes for xenobiotic compound metabolism and antibiotic resistances. Previous work showed bimodal ICE activation, but by using single cell time-lapse microscopy coupled to combinations of chromosomally integrated single copy ICE promoter-driven fluorescence reporters, RNA sequencing and mutant analysis, we now describe the complete regulon leading to the arisal of differentiated dedicated transfer competent cells. The regulon encompasses at least three regulatory nodes and five (possibly six) further conserved gene clusters on the ICE that all become expressed under stationary phase conditions. Time-lapse microscopy indicated expression of two regulatory nodes (i.e., bisR and alpA-bisDC) to precede that of the other clusters. Notably, expression of all clusters except of bisR was confined to the same cell subpopulation, and was dependent on the same key ICE regulatory factors. The ICE thus only transfers from a small fraction of cells in a population, with an estimated proportion of between 1.7–4%, which express various components of a dedicated transfer competence program imposed by the ICE, and form the centerpiece of ICE conjugation. The components mediating transfer competence are widely conserved, underscoring their selected fitness for efficient transfer of this class of mobile elements. Horizontal gene transfer processes among prokaryotes have raised wide interest, which is attested by broad public health concern of rapid spread of antibiotic resistances. However, we typically take for granted that horizontal transfer is the result of some underlying spontaneous low frequency event, but this is not necessarily the case. As we show here, mobile genetic elements from the class of integrative and conjugative elements (ICEs) impose a coordinated program on the host cell in order to transfer, leading to an exclusive differentiated set of transfer competent cells. We base our conclusions on single cell microscopy studies to compare the rare activation of ICE promoters in individual cells in bacterial populations, and on mutant and RNA-seq analysis to show their dependency on ICE factors. This is an important finding because it implies that conjugation itself is subject to natural selection, which would lead to selection of fitter elements that transfer better or become more widespread.
Collapse
Affiliation(s)
- Sandra Sulser
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Andrea Vucicevic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Veronica Bellini
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Roxane Moritz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - François Delavat
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Carraro
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- * E-mail:
| |
Collapse
|
5
|
Cuthbert BJ, Hayes CS, Goulding CW. Functional and Structural Diversity of Bacterial Contact-Dependent Growth Inhibition Effectors. Front Mol Biosci 2022; 9:866854. [PMID: 35558562 PMCID: PMC9086364 DOI: 10.3389/fmolb.2022.866854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/07/2022] [Indexed: 12/25/2022] Open
Abstract
Bacteria live in complex communities and environments, competing for space and nutrients. Within their niche habitats, bacteria have developed various inter-bacterial mechanisms to compete and communicate. One such mechanism is contact-dependent growth inhibition (CDI). CDI is found in many Gram-negative bacteria, including several pathogens. These CDI+ bacteria encode a CdiB/CdiA two-partner secretion system that delivers inhibitory toxins into neighboring cells upon contact. Toxin translocation results in the growth inhibition of closely related strains and provides a competitive advantage to the CDI+ bacteria. CdiB, an outer-membrane protein, secretes CdiA onto the surface of the CDI+ bacteria. When CdiA interacts with specific target-cell receptors, CdiA delivers its C-terminal toxin region (CdiA-CT) into the target-cell. CdiA-CT toxin proteins display a diverse range of toxic functions, such as DNase, RNase, or pore-forming toxin activity. CDI+ bacteria also encode an immunity protein, CdiI, that specifically binds and neutralizes its cognate CdiA-CT, protecting the CDI+ bacteria from auto-inhibition. In Gram-negative bacteria, toxin/immunity (CdiA-CT/CdiI) pairs have highly variable sequences and functions, with over 130 predicted divergent toxin/immunity complex families. In this review, we will discuss biochemical and structural advances made in the characterization of CDI. This review will focus on the diverse array of CDI toxin/immunity complex structures together with their distinct toxin functions. Additionally, we will discuss the most recent studies on target-cell recognition and toxin entry, along with the discovery of a new member of the CDI loci. Finally, we will offer insights into how these diverse toxin/immunity complexes could be harnessed to fight human diseases.
Collapse
Affiliation(s)
- Bonnie J. Cuthbert
- Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Christopher S. Hayes
- Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Celia W. Goulding
- Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, United States
| |
Collapse
|
6
|
A comparative genomics approach identifies contact-dependent growth inhibition as a virulence determinant. Proc Natl Acad Sci U S A 2020; 117:6811-6821. [PMID: 32156726 DOI: 10.1073/pnas.1919198117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Emerging evidence suggests the Pseudomonas aeruginosa accessory genome is enriched with uncharacterized virulence genes. Identification and characterization of such genes may reveal novel pathogenic mechanisms used by particularly virulent isolates. Here, we utilized a mouse bacteremia model to quantify the virulence of 100 individual P. aeruginosa bloodstream isolates and performed whole-genome sequencing to identify accessory genomic elements correlated with increased bacterial virulence. From this work, we identified a specific contact-dependent growth inhibition (CDI) system enriched among highly virulent P. aeruginosa isolates. CDI systems contain a large exoprotein (CdiA) with a C-terminal toxin (CT) domain that can vary between different isolates within a species. Prior work has revealed that delivery of a CdiA-CT domain upon direct cell-to-cell contact can inhibit replication of a susceptible target bacterium. Aside from mediating interbacterial competition, we observed our virulence-associated CdiA-CT domain to promote toxicity against mammalian cells in culture and lethality during mouse bacteremia. Structural and functional studies revealed this CdiA-CT domain to have in vitro tRNase activity, and mutations that abrogated this tRNAse activity in vitro also attenuated virulence. Furthermore, CdiA contributed to virulence in mice even in the absence of contact-dependent signaling. Overall, our findings indicate that this P. aeruginosa CDI system functions as both an interbacterial inhibition system and a bacterial virulence factor against a mammalian host. These findings provide an impetus for continued studies into the complex role of CDI systems in P. aeruginosa pathogenesis.
Collapse
|
7
|
Diversity of Contact-Dependent Growth Inhibition Systems of Pseudomonas aeruginosa. J Bacteriol 2019; 201:JB.00776-18. [PMID: 31036723 DOI: 10.1128/jb.00776-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Contact-dependent growth inhibition (CDI) systems are used in bacterial competition to hinder the growth of neighboring microbes. These systems utilize a two-partner secretion mechanism to display the CdiA exoprotein at the bacterial cell surface. CdiA forms a long filamentous stalk that facilitates binding to a target cell and delivery of a C-terminal toxin (CT) domain. This CT domain is processed and delivered into the cytoplasm of a target cell upon contact. CDI systems also encode a cognate immunity protein (CdiI) that protects siblings and resistant targeted cells from intoxication by high-affinity binding to the CT. CdiA CT domains vary among strains within a species, and many alleles encode enzymatic functions that target nucleic acids. This variation is thought to help drive diversity and adaptation within a species. CdiA diversity is well studied in Escherichia coli and several other bacteria, but little is known about the extent of this diversity in Pseudomonas aeruginosa. The purpose of this review is to highlight the variability that exists in CDI systems of P. aeruginosa. We show that this diversity is apparent even among strains isolated from a single geographical region, suggesting that CDI systems play an important role in the ecology of P. aeruginosa.
Collapse
|