Biology subjects

Smug, B.

Publications and source records attributed to Smug, B..

3 recordsLinked to original sources

bioRxiv2025

Capsular specificity in temperate phages of Klebsiella pneumoniae is driven by diverse receptor-binding enzymes

In bacteriophages infecting Klebsiella pneumoniae, capsule specificity is a major determinant of host range due to the presence of capsule-specific depolymerases. Yet for temperate phages, the genetic and functional basis of this specificity remains less well understood. Depolymerases appear unexpectedly rare in prophage genomes, raising unresolved questions about which prophage genes mediate capsule tropism, whether this apparent scarcity reflects biological or ecological differences versus annotation limits, and whether prophage-encoded receptor-binding proteins (RBPs) are functionally active. To address these questions, we analysed 3,900 Klebsiella genomes from diverse ecological niches to identify prophage-encoded proteins mediating capsule tropism. We conducted a genome-wide association study (GWAS) correlating prophage protein clusters (from 8,105 prophages) with confidently assigned bacterial K-loci. GWAS identified high-confidence predictors for 16 out of 35 most diverse K-loci, of which 14 were receptor-binding proteins (RBPs) belonging to classical depolymerases (n = 6), SGNH hydrolases which deacetylate polysaccharides (n = 6), and structurally novel RBPs (n = 2). Overall, we predicted K-locus specificity for 26 putative depolymerases, of which 12 were deemed as strong predictions against 10 K-loci. In parallel, we attempted recombinant production of 50 putative depolymerases selected from 469 candidate proteins identified in prophages from a representative subset of 99 bacterial isolates, together with an additional 10 depolymerases selected based on GWAS predictions. All recombinant proteins were tested against a Klebsiella reference panel of 119 K-types. Of the 50 manually chosen putative depolymerases, 34 failed to yield detectable recombinant expression, a pattern unlikely to be explained by degraded or defective prophages. Of the 14 active enzymes, 5 targeted a K-locus different from that of their bacterial host, and enzyme specificity could not always be reliably inferred from sequence similarity or structural homology. Comparison of GWAS predictions with experimental validation results revealed that 10 of the 12 strongest GWAS predictors were confirmed experimentally, while 2 produced soluble protein but showed no detectable activity against the tested K-types. Together, these results highlight the intrinsic difficulty of predicting activity and capsule specificity of prophage-encoded RBPs from genomic information alone. Finally, analysis of 4,598 high-completeness prophages revealed that SGNH-domain hydrolases are among the most prevalent enzymatic domains in prophage RBPs. Two SGNH-domain RBPs identified by GWAS were experimentally confirmed as active esterases, supporting capsule deacetylation as a widespread alternative to polysaccharide depolymerisation in temperate phages. Our findings reveal that Klebsiella prophages encode structurally diverse RBPs, suggesting temperate phages may rely not only on depolymerisation but also on capsule modification--such as deacetylation--for infection. This also implies that capsule diversity in K. pneumoniae may be substantially underestimated, with implications for phage specificity, competition and vaccine design.

microbiology↗

bioRxiv2022

Protein modularity in phages is extensive and associated with functions linked to core replication machinery and host tropism determinants

Biological modularity enhances evolutionary adaptability by allowing rearrangement of functional components. One striking example are bacterial viruses (phages). They exhibit extensive genomic modularity by being built of independent functional modules that evolve separately and combine in various ways, making them astoundingly diverse. While multiple studies have investigated genomic modularity in phages, less attention has been given to protein modularity--proteins having distinct building blocks or domains that can evolve and recombine, enhancing functional and genetic diversity. To better understand the impact of protein modularity on viral evolution, we quantified it by detecting instances of domain mosaicism, defined as a homologous fragment sharing between two otherwise unrelated proteins. We used highly sensitive homology detection to quantify domain mosaicism between pairs of 133,574 representative phage proteins and to understand its relationship with functional diversity in phage genomes. We found that diverse functional classes often shared homologous domains. This phenomenon was often linked to protein modularity, particularly in receptor-binding proteins, endolysins and DNA polymerases. We also identified multiple instances of recent diversification via exchange and gain/loss of domains in receptor-binding proteins, neck passage structures, endolysins and some members of the core replication machinery. Diversification via protein fragment exchange often transcended distant taxonomic and ecological borders. We argue that the ongoing diversification via shuffling of protein domains associated with those functions is reflective of co-evolutionary arms race and the resulting diversifying selection to overcome multiple mechanisms of bacterial resistance against phages.

evolutionary biology↗

bioRxiv2021

Phenotypic heterogeneity is adaptive for microbial populations under starvation

To persist in variable environments populations of microorganisms have to survive periods of starvation and be able to restart cell division in nutrient-rich conditions. Typically, starvation signals initiate a transition to a quiescent state in a fraction of individual cells, while the rest of the cells remain non-quiescent. It is widely believed that, while quiescent cells (Q) help the population to survive long starvation, the non-quiescent cells (NQ) are a side effect of imperfect transition. We analysed regrowth of starved monocultures of Q and NQ cells compared to mixed, heterogeneous cultures in simple and complex starvation environments. Our experiments, as well as mathematical modelling, demonstrate that Q monocultures benefit from better survival during long starvation, and from a shorter lag phase after resupply of rich medium. However, when the starvation period is very short, the NQ monocultures outperform Q and mixed cultures, due to their short lag phase. In addition, only NQ monocultures benefit from complex starvation environments, where nutrient recycling is possible. Our study suggests that phenotypic heterogeneity in starved populations could be a form of bet hedging, which is adaptive when environmental determinants, such as the length of the starvation period, the length of the regrowth phase, and the complexity of the starvation environment vary over time. ImportanceNon-genetic cell heterogeneity is present in glucose starved yeast populations in the form of quiescent (Q) and nonquiescent (NQ) phenotypes. There is evidence that Q cells help the population to survive long starvation. However, the role of the NQ cell type is not known, and it has been speculated that the NQ phenotype is just a side effect of imperfect transition to the Q phenotype. Here we show that, in contrast, there are ecological scenarios in which NQ cells perform better than monocultures of Q cells or naturally occuring mixed populations containing both Q and NQ. NQ cells benefit when the starvation period is very short and environmental conditions allow nutrient recycling during starvation. Our experimental and mathematical modeling results suggest a novel hypothesis: the presence of both Q and NQ phenotypes within starved yeast populations may reflect a form of bet hedging, where different phenotypes provide fitness advantages depending on environmental conditions.

evolutionary biology↗