Biology subjects

Al-Bassam, M. M.

Publications and source records attributed to Al-Bassam, M. M..

5 recordsLinked to original sources

bioRxiv2023

Guild and Niche Determination Enable Targeted Alteration of the Microbiome

Microbiome science has greatly contributed to our understanding of microbial life and its essential roles for the environment and human health1-5. However, the nature of microbial interactions and how microbial communities respond to perturbations remains poorly understood, resulting in an often descriptive and correlation-based approach to microbiome research6-8. Achieving causal and predictive microbiome science would require direct functional measurements in complex communities to better understand the metabolic role of each member and its interactions with others. In this study we present a new approach that integrates transcription and translation measurements to predict competition and substrate preferences within microbial communities, consequently enabling the selective manipulation of the microbiome. By performing metatranscriptomic (metaRNA-Seq) and metatranslatomic (metaRibo-Seq) analysis in complex samples, we classified microbes into functional groups (i.e. guilds) and demonstrated that members of the same guild are competitors. Furthermore, we predicted preferred substrates based on importer proteins, which specifically benefited selected microbes in the community (i.e. their niche) and simultaneously impaired their competitors. We demonstrated the scalability of microbial guild and niche determination to natural samples and its ability to successfully manipulate microorganisms in complex microbiomes. Thus, the approach enhances the design of pre- and probiotic interventions to selectively alter members within microbial communities, advances our understanding of microbial interactions, and paves the way for establishing causality in microbiome science.

microbiology↗

bioRxiv2020

Competition-based screening secures the evolutionary stability of a defensive microbiome

Cuticular microbiomes of Acromyrmex leaf-cutting ants are exceptional because they are freely colonizable, and yet the prevalence of Pseudonocardia, a native vertically transmitted symbiont that controls Escovopsis fungus-garden disease, is never compromised. Game theory suggests that competition-based screening can allow the selective recruitment of antibiotic-producing bacteria from the environment, by fomenting and biasing competition for abundant host resources. Mutual symbiont aggression benefits the host and also maintains native symbiont viability. Here we use RNA-stable isotope probing (RNA-SIP) to confirm predictions that Acromyrmex cuticles can maintain a range of microbial symbionts. We then used dual-RNA-sequencing and bioassays to show that vertically transmitted Pseudonocardia strains produce antibacterials that differentially reduce the growth rates of other microbes, ultimately eliminating non-antibiotic-producing strains that might parasitize the symbiosis while still allowing antibiotic-producing Streptomyces strains to survive. Open cuticular microbiomes can thus maintain a specific co-evolved mutualism by restricting access for other bacterial strains.

evolutionary biology↗

bioRxiv2020

Nucleoid openness profiling links bacterial genome structure to phenotype

Gene expression requires specific structural alternations in the nucleoid structure to enable the access of the transcription machinery into the genomic DNA. In prokaryotes, DNA binding proteins, including nucleoid-associated proteins (NAPs) and transcription factors (TFs), drive the change in structure and gene expression. Currently, studies of global NAP and TF binding are often hindered by the lack of appropriate epigenomic tools. Here, we present POP-seq, a method that provides in vivo genome-wide openness profiles of the bacterial nucleoid. We demonstrate that POP-seq can be used to map the global in vivo protein-DNA binding events. Our results highlight a negative correlation between genome openness, compaction and transcription, suggesting that regions that are not accessible to Tn5 transposase are either too compacted or occupied by RNA polymerase. Importantly, we also show that the least open regions are enriched in housekeeping genes, while the most open regions are significantly enriched in genes important for fast adaptation to changing environment. Finally, we demonstrated that the genome openness profile is growth condition specific. Together, those results suggest a model where one can distinguish two types of epigenetic control: one stable, long-term silencing of highly compacted regions, and a second, highly responsive regulation through the dynamic competition between NAPs and RNA polymerase binding. Overall, POP-seq captures structural changes in the prokaryotic chromatin and provides condition-specific maps of global protein-DNA binding events, thus linking overall transcriptional and epigenetic regulation directly to phenotype.

microbiology↗

bioRxiv2020

Specialized and shared functions of diguanylate cyclases and phosphodiesterases in Streptomyces development.

Levels of the second messenger bis-3-5-cyclic di-guanosinemonophosphate (c-di-GMP) determine when Streptomyces initiate sporulation to survive under adverse conditions. c-di-GMP signals are integrated into the genetic differentiation network by the regulator BldD and the sigma factor {sigma}WhiG. However, functions of the development-specific c-di-GMP diguanylate cyclases (DGCs) CdgB and CdgC, and the phosphodiesterases (PDEs) RmdA and RmdB, are poorly understood. Here, we provide biochemical evidence that the GGDEF-EAL domain protein RmdB from S. venezuelae is a monofunctional PDE that hydrolyzes c-di-GMP to 5pGpG. Despite having an equivalent GGDEF-EAL domain arrangement, RmdA cleaves c-di-GMP to GMP and exhibits residual DGC activity. We show that an intact EAL motif is crucial for the in vivo function of both enzymes since strains expressing protein variants with an AAA motif instead of EAL are delayed in development, similar to null mutants. Global transcriptome analysis of {Delta}cdgB, {Delta}cdgC, {Delta}rmdA and {Delta}rmdB strains revealed that the c-di-GMP specified by these enzymes has a global regulatory role, with about 20 % of all S. venezuelae genes being differentially expressed in the cdgC mutant. Our data suggest that the major c-di-GMP-controlled targets determining the timing and mode of sporulation are genes involved cell division and the production of the hydrophobic sheath that covers Streptomyces aerial hyphae and spores. Altogether, this study provides a global view of the c-di-GMP-dependent genes that contribute to the hyphae-to-spores transition and sheds light on the shared and specific functions of the key enzymes involved in c-di-GMP metabolism in S. venezuelae. ImportanceStreptomyces are important producers of clinical antibiotics. The ability to synthesize these natural products is connected to their developmental biology, which includes a transition from filamentous cells to spores. The widespread bacterial second messenger c-di-GMP controls this complex switch and is a promising tool to improve antibiotic production. Here, we analyzed the enzymes that make and break c-di-GMP in S. venezuelae by studying the genome-wide transcriptional effects of the DGCs CdgB and CdgC and the PDEs RmdA and RmdB. We found that the c-di-GMP specified by these enzymes has a global regulatory role. However, despite shared enzymatic activities, the four c-di-GMP enzymes have specialized inputs into differentiation. Altogether, we demonstrate that altering c-di-GMP levels through the action of selected enzymes yields characteristically distinct transcriptional profiles; this can be an important consideration when modulating c-di-GMP for the purposes of natural product synthesis in Streptomyces.

microbiology↗

bioRxiv2019

c-di-AMP hydrolysis by a novel type of phosphodiesterase promotes differentiation of multicellular bacteria

Antibiotic-producing Streptomyces use the diadenylate cyclase DisA to synthesize the nucleotide second messenger c-di-AMP but the mechanism for terminating c-di-AMP signaling and the proteins that bind the molecule to effect signal transduction are unknown. Here, we identify the AtaC protein as a new type of c-di-AMP-specific phosphodiesterase that is also conserved in pathogens such as Streptococcus pneumoniae and Mycobacterium tuberculosis. AtaC is monomeric in solution and binds Mn2+ to specifically hydrolyze c-di-AMP to AMP via the intermediate 5-pApA. As an effector of c-di-AMP signaling, we characterize the RCK-domain protein CpeA as the first c-di-AMP-binding protein to be identified in Streptomyces. CpeA interacts with the predicted cation / proton antiporter, CpeB, linking c-di-AMP signaling to ion homeostasis in actinobacteria. Hydrolysis of c-di-AMP is critical for normal growth and differentiation in Streptomyces, connecting osmotic stress to development. Thus, we present the discovery of two novel components of c-di-AMP signaling in bacteria and show that precise control of this second messenger is essential for osmoregulation and coordinated development in Streptomyces.

microbiology↗