Bioinformatic Pipeline Predicts Unprecedented Diversity of Bacterial Siderophore Pathways from Genome Sequences

Core Concepts

Our bioinformatic pipeline can accurately predict the chemical structures of 188 different siderophore molecules and identify 94 distinct receptor groups for their uptake across 1,664 Pseudomonas strains, revealing an enormous yet overlooked diversity of iron-scavenging machineries in pseudomonads.

Abstract

The authors developed a knowledge-guided bioinformatic pipeline to precisely predict the synthesis, molecular structure, and uptake machinery of pyoverdines, a family of iron-scavenging siderophores produced by Pseudomonas bacteria. Key highlights: The pipeline improved gene annotation to recover complete pyoverdine synthetase gene clusters, even from fragmented draft genomes. A phylogeny-focused method was used to accurately predict the substrate specificity of 97.8% of the 18,292 enzymatic A domains involved in pyoverdine synthesis. The predicted pyoverdine structures were experimentally validated, revealing 151 new variants in addition to the 37 previously known structures. A region-based receptor identification method was developed to annotate 4,547 FpvA receptors, which segregated into 94 distinct groups, far exceeding the 3 groups previously reported. The uncovered diversity of pyoverdines and receptors suggests that iron competition plays a crucial role in shaping the evolution of siderophore systems across Pseudomonas species. The knowledge-guided, phylogeny-focused approach can be extended to study other secondary metabolites and microbial genera.

Stats

"The lengths of pyoverdine synthetic genes ranged between 7690 and 21333 amino acids, and the number of A domains per synthetase ranged between 6 and 17, with a total of 35,281 A domains being present across all strains." "Our prediction yielded 188 different pyoverdine molecules, out of which only 37 structures had been previously reported." "We found that 92% of the nearest FpvA genes were indeed located within 20 kb of their pyoverdine Pep genes." "Single-linkage clustering with an identity threshold of 70% revealed a total of 94 groups of FpvA receptors, out of which 43 groups contained more than 10 members."

Quotes

"Our analysis further shows that many strains have more than one FpvA receptor." "The extensive distribution may implie that pyoverdine serves as another 'shared language' in the bacterial community and plays a more important role than previously thought." "The uncovered diversity of pyoverdines and receptors suggests that iron competition plays a crucial role in shaping the evolution of siderophore systems across Pseudomonas species."

Key Insights Distilled From

From sequence to molecules: Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways

by Gu,S., Shao,... at www.biorxiv.org 11-01-2023

https://www.biorxiv.org/content/10.1101/2023.10.30.564663v3

Deeper Inquiries

How can the insights from this study be leveraged to understand the ecological and evolutionary dynamics of siderophore-mediated interactions within and across microbial communities?

The insights from this study provide a comprehensive understanding of the diversity and complexity of siderophore systems, particularly focusing on pyoverdines and their corresponding receptors in Pseudomonas bacteria. By accurately predicting the structure of pyoverdines and identifying a wide range of FpvA receptors, this study offers a valuable resource for studying the ecological and evolutionary dynamics of siderophore-mediated interactions within and across microbial communities. Ecological Dynamics: The diverse range of pyoverdine structures and FpvA receptors uncovered in this study can shed light on the ecological roles of siderophores in microbial communities. Understanding how different pyoverdine variants interact with specific FpvA receptors can provide insights into the competitive and cooperative dynamics of iron acquisition strategies among microbes. This knowledge can help elucidate how siderophores contribute to niche differentiation, community assembly, and microbial interactions in various environments. Evolutionary Dynamics: The phylogenetic analysis of FpvA receptors across different Pseudomonas strains reveals a high level of diversity and evolutionary divergence. By studying the evolutionary relationships and patterns of FpvA variants, researchers can gain insights into the evolutionary processes shaping siderophore systems. This information can help elucidate the mechanisms driving the diversification of siderophore pathways, including gene duplication, horizontal gene transfer, and adaptive evolution. Community Interactions: The discovery of novel pyoverdine structures and FpvA receptors suggests that siderophore-mediated interactions are more complex and diverse than previously thought. By studying the distribution and abundance of different pyoverdine variants and receptors in microbial communities, researchers can explore how these systems influence community structure, stability, and function. Understanding the co-evolution of siderophores and their receptors can provide valuable insights into the dynamics of interspecies interactions and the maintenance of microbial diversity. Biotechnological Applications: The knowledge gained from this study can also have implications for biotechnological applications, such as the development of novel antimicrobial strategies or biocontrol agents targeting iron acquisition pathways. By leveraging the diversity of siderophore systems, researchers can explore new avenues for manipulating microbial communities, enhancing nutrient uptake efficiency, and developing innovative approaches for combating pathogenic microbes. In summary, the insights from this study offer a foundation for exploring the ecological and evolutionary dynamics of siderophore-mediated interactions within and across microbial communities. By integrating genomic data, bioinformatic analyses, and experimental validation, researchers can unravel the intricate relationships between siderophores, receptors, and microbial communities, advancing our understanding of iron acquisition strategies in the microbial world.

How can the potential limitations of the knowledge-guided, phylogeny-focused approach be addressed when applied to secondary metabolites or microbial genera that are more phylogenetically diverse than Pseudomonas?

The knowledge-guided, phylogeny-focused approach utilized in this study for predicting secondary metabolite structures and identifying microbial receptors has demonstrated high accuracy and reliability within the context of Pseudomonas bacteria. However, when applying this approach to secondary metabolites or microbial genera that are more phylogenetically diverse than Pseudomonas, several potential limitations may arise. These limitations include: Limited Reference Data: One of the key challenges when dealing with more phylogenetically diverse microbial genera is the availability of reference data. The accuracy of the predictions heavily relies on the quality and diversity of the reference dataset. In more diverse microbial communities, the lack of comprehensive reference data for secondary metabolites and receptors can hinder the effectiveness of the knowledge-guided approach. Substrate Specificity: The substrate specificity of enzymes and receptors can vary significantly across different microbial genera. The phylogenetic signals that guide substrate predictions may not be as clear or consistent when dealing with a broader range of organisms. This can lead to challenges in accurately predicting the function and structure of secondary metabolites. Functional Diversity: The functional diversity of secondary metabolites and receptors in diverse microbial genera may introduce additional complexity to the prediction process. The interactions between different metabolites, enzymes, and receptors can be more intricate and context-dependent, making it challenging to generalize predictions based on phylogenetic relationships alone. To address these potential limitations when applying the knowledge-guided, phylogeny-focused approach to more diverse microbial genera, several strategies can be implemented: Expanded Reference Databases: Efforts should be made to expand and diversify the reference datasets by incorporating data from a wide range of microbial genera. This can involve collaborative efforts to collect and curate experimental data on secondary metabolites and receptors from diverse organisms. Adaptation of Algorithms: The algorithms and models used for substrate prediction and structure identification may need to be adapted and optimized for the specific characteristics of the target organisms. Machine learning approaches that can accommodate diverse datasets and complex interactions may be more suitable for predicting secondary metabolites in phylogenetically diverse genera. Experimental Validation: Experimental validation of predictions is crucial, especially in more diverse microbial communities where the functional diversity of secondary metabolites may be less predictable. Integrating experimental data with computational predictions can enhance the accuracy and reliability of the results. Integration of Multi-Omics Data: Incorporating multi-omics data, such as genomics, transcriptomics, and metabolomics, can provide a more comprehensive understanding of the secondary metabolite pathways and their ecological roles in diverse microbial communities. Integrative analyses can help elucidate the complex interactions and dynamics of secondary metabolites across different taxa. By addressing these potential limitations and implementing tailored strategies for handling the challenges of phylogenetic diversity, the knowledge-guided, phylogeny-focused approach can be effectively applied to a broader range of microbial genera and secondary metabolites, enabling a deeper exploration of the functional and evolutionary dynamics of microbial interactions.

Could the diversity of siderophore systems discovered in this study have implications for the development of novel antimicrobial strategies targeting iron acquisition pathways?

The diversity of siderophore systems uncovered in this study, particularly the extensive range of pyoverdine structures and FpvA receptors in Pseudomonas bacteria, has significant implications for the development of novel antimicrobial strategies targeting iron acquisition pathways. Siderophores play a crucial role in microbial iron acquisition, and their diversity and specificity offer unique opportunities for the design of antimicrobial agents that disrupt iron metabolism in pathogenic microbes. Here are some ways in which the diversity of siderophore systems discovered in this study could impact the development of novel antimicrobial strategies: Targeted Antimicrobial Agents: The diverse range of pyoverdine structures and FpvA receptors identified in this study provide a wealth of targets for the development of antimicrobial agents that specifically interfere with iron uptake in pathogenic bacteria. By targeting the iron acquisition pathways unique to different bacterial species, novel antimicrobial strategies can be designed to selectively inhibit the growth and virulence of specific pathogens. Disruption of Iron Homeostasis: Siderophores are essential for microbial iron acquisition and play a critical role in bacterial survival and pathogenicity. By disrupting the production or function of siderophores, antimicrobial agents can effectively limit the availability of iron to pathogenic bacteria, thereby compromising their ability to proliferate and cause infections. The diversity of siderophore systems offers a wide range of targets for disrupting iron homeostasis in pathogenic microbes. Combination Therapies: The discovery of novel pyoverdine structures and FpvA receptors suggests that combination therapies targeting multiple siderophore systems could enhance the efficacy of antimicrobial treatments. By targeting different iron acquisition pathways simultaneously, combination therapies can overcome resistance mechanisms and improve treatment outcomes for bacterial infections. Biocontrol Strategies: The insights gained from studying the diversity of siderophore systems can also inform the development of biocontrol strategies for managing microbial communities in various environments. By manipulating siderophore production and receptor specificity, it may be possible to modulate the interactions between beneficial and pathogenic microbes, leading to the development of eco-friendly biocontrol agents. Drug Development: The structural diversity of pyoverdines and FpvA receptors identified in this study can serve as a basis for the design of novel antimicrobial drugs that target specific iron acquisition pathways. By leveraging the unique features of siderophore systems, researchers can develop innovative drug candidates with enhanced efficacy and reduced side effects. In conclusion, the diversity of siderophore systems uncovered in this study offers valuable insights and opportunities for the development of novel antimicrobial strategies targeting iron acquisition pathways in pathogenic bacteria. By exploiting the complexity and specificity of siderophore systems, researchers can design targeted antimicrobial agents that disrupt iron metabolism and combat bacterial infections more effectively.