Biology subjects

Kasalo, N.

Publications and source records attributed to Kasalo, N..

6 recordsLinked to original sources

bioRxiv2025

Evolutionary expression patterns in developing biofilms of uropathogenic Escherichia coli reveal embryo-like features

Developing biofilms of the gram-positive, soil-dwelling bacterium Bacillus subtilis exhibit expression patterns and evolutionary imprints similar to those observed in eukaryotic embryos. However, the universality of these evolutionary and developmental regularities has not yet been explored in other biofilm-forming bacteria, including pathogens. To broaden the perspective on ontogeny-phylogeny correlations in bacteria, we recovered phylotranscriptomic and phyloproteomic trajectories throughout the entire biofilm development of uropathogenic Escherichia coli UTI89. Here, we show that biofilm growth in E. coli UTI89 positively correlates with the evolutionary age of expressed genes, with developing biofilms progressively expressing younger and more divergent genes. These findings suggest that biofilm formation in gram-negative bacteria is not macroevolutionarily naive and that evolutionary imprints are a pervasive feature of bacterial biofilm development. While these regularities apply to the developmental expression patterns of bulk biofilms, the question remains whether evolutionary stratification occurs within the spatial regions of individual biofilms. To address this, we analyzed expression profiles across concentric regions of E. coli UTI89 biofilms at three developmental stages. This analysis revealed that gene expression, functional patterns, and evolutionary imprints are influenced by both developmental timing and distance from the biofilm center. Together, these findings demonstrate that the growth of uropathogenic E. coli biofilms is governed by both temporal and spatial macroevolutionary logic, drawing intriguing parallels to organismal development in multicellular eukaryotic lineages.

evolutionary biology↗

bioRxiv2025

Convergence in amino acid outsourcing between animals and predatory bacteria

All animals have outsourced about half of the 20 proteinogenic amino acids (AAs). We recently demonstrated that the loss of biosynthetic pathways for these outsourced AAs is driven by energy-saving selection. Paradoxically, these metabolic simplifications enabled animals to use costly AAs more frequently in their proteomes, allowing them to explore sequence space more freely. Based on these findings, we proposed that environmental AA availability and cellular respiration mode are the two primary factors determining the evolution of AA auxotrophies in animals. Remarkably, our recent analysis showed that bacterial AA auxotrophies are also governed by energy-related selection, thereby roughly converging with animals. However, bacterial AA auxotrophies are highly heterogeneous and scattered across the bacterial phylogeny, making direct ecological and physiological comparisons with the animal AA outsourcing model challenging. To better test the universality of our model, we focused on Bdellovibrionota and Myxococcota--two closely related bacterial phyla that, through aerobic respiration and a predatory lifestyle, best parallel animals. Here, we show that Bdellovibrionota, driven by energy-related selection, outsourced a highly similar set of AAs to those in animals. This sharply contrasts with Myxococcota, which exhibit far fewer AA auxotrophies and rarely show signatures of energy-driven selection. These differences are also reflected in Bdellovibrionota proteomes, which are substantially more expensive than those of Myxococcota. Finally, we found evidence that the expression of costly proteins plays a crucial role in the predatory phase of the Bdellovibrio life cycle. Together, our findings suggest that Bdellovibrionota, through their obligate predatory lifestyle, exhibit the closest analogy to the AA auxotrophy phenotype observed in animals. In contrast, facultative predation, as seen in Myxococcota, appears to substantially limit the evolution of AA auxotrophies. These cross-domain convergences strongly support the general validity of our AA outsourcing model.

evolutionary biology↗

bioRxiv2025

Bacterial amino acid auxotrophies enable energetically costlier proteomes

The outsourcing of amino acid (AA) production to the environment is relatively common across the tree of life. We recently showed that the massive loss of AA synthesis capabilities in animals is governed by selective pressure linked to the energy costs of AA production. Paradoxically, these AA auxotrophies facilitated the evolution of costlier proteomes in animals by enabling the increased use of energetically expensive AAs. Experiments in bacteria have shown that AA auxotrophies can provide a fitness advantage in competition with prototrophic strains. However, it remains unclear whether energy-related selection also drives the evolution of bacterial AA auxotrophies and whether this affects the usage of expensive AAs in bacterial proteomes. To investigate these questions, we computationally determined AA auxotrophy odds across 980 bacterial genomes representing diverse taxa and calculated the energy costs of all their proteins. Here, we show that auxotrophic AAs are generally more expensive to synthesize than prototrophic AAs in bacteria. Moreover, we found that the cost of auxotrophic AAs significantly correlates with the cost of their respective proteomes. Interestingly, out of all considered taxa, Mollicutes and Borreliaceae--chronic pathogens highly successful in immune evasion--have the most AA auxotrophies and code for the most expensive proteomes. These findings indicate that AA auxotrophies in bacteria, similar to those in animals, are shaped by selective pressures related to energy management. Our study reveals that bacterial AA auxotrophies act as costly outsourced functions, enabling bacteria to explore protein sequence space more freely. It remains to be investigated whether this relaxed use of expensive AAs also enabled auxotrophic bacteria to evolve proteins with improved or novel functionality.

evolutionary biology↗

bioRxiv2024

Contrasting macroevolutionary patterns in the human N-glycosylation pathway

Building on coding mutations and splicing variants, post-translational modifications add a final layer to protein diversity that operates at developmental and physiological timescales. Although protein glycosylation is one of the most common post-translational modifications, its evolutionary origin remains largely unexplored. Here, we performed a phylostratigraphic tracking of glycosylation machinery genes and their targets -- glycosylated proteins -- in a broad phylogenetic context. Our results show that the vast majority of human glycosylation machinery genes trace back to two evolutionary periods: the origin of all cellular organisms and the origin of all eukaryotes. This indicates that protein glycosylation is an ancient process likely common to all life, further elaborated in early eukaryotes. In contrast, human glycoproteins exhibited prominent enrichment signals in more recent evolutionary periods, suggesting an important role in the transition from metazoans to vertebrates. Focusing specifically on the N-glycosylation pathway, we noted that the majority of N-glycosylation genes acting on the cytoplasmic side of the endoplasmic reticulum (ER) trace back to the origin of cellular organisms. This sharply contrasts with the rest of the N-glycosylation pathway, which is oriented toward the ER lumen, where genes of eukaryotic origin predominate. In the Golgi, we also identified an analogous binary evolutionary origin of glycosylation machinery genes. We discuss these findings in the context of the evolutionary emergence of the eukaryotic endomembrane system and propose that the ER evolved through the invagination of a prokaryotic cell membrane containing an N-glycosylation pathway.

evolutionary biology↗

bioRxiv2024

Massive outsourcing of energetically costly amino acids at the origin of animals

Animals are generally capable of synthesizing eleven amino acids, while the remaining nine, often referred to as essential, must be acquired through diet. This characteristic profoundly impacts animals by defining their ecological lifestyles and evolutionary trajectory. Recent phylogenomic studies reveal that this phenotype results from gene losses that occurred at the root of the animal tree. However, it remains unclear which selective forces, if any, directed this far-reaching metabolic simplification event. Here, we show that essential amino acids are energetically far more expensive to synthesize than non-essential ones, particularly under high respiratory conditions--a hallmark of animal lifestyle. By applying permutation tests, we found that these difference in energy costs, counteracted by pleiotropy, created a selective pressure which led to the outsourcing of essential amino acids. Remarkably, we also found that extant animals use expensive amino acids more frequently compared to their closest unicellular relatives. This shows that animals significantly removed constraints on the usage of essential amino acids under high respiratory conditions by externalizing their production. Together, this implies that stabilizing selection underpinned by energy management drove this metabolic outsourcing in nutrient rich environments, thereby allowing animal genes to evolve more freely through protein sequence space. In this context, we propose that the origin of animals is tightly linked to energy-related adaptations rather than to unpredictable stochastic events, as recently suggested.

evolutionary biology↗

bioRxiv2024

Somatic embryogenesis of grapevine (Vitis vinifera) expresses a transcriptomic hourglass

At the molecular level, multicellular eukaryotic lineages and bacterial biofilms show predictable evolutionary footprints in their development. For instance, the zygotic embryogenesis of Arabidopsis, which is initiated by gamete fusion, shows hourglass-shaped ontogeny-phylogeny correlations at the transcriptome level. However, many plants are capable of yielding a fully viable next generation by somatic embryogenesis -- a comparable developmental process that usually starts by the embryogenic induction of a diploid somatic cell. This leads to the question: is the hourglass-shaped ontogeny-phylogeny correlation preserved in somatic embryogenesis? To explore the correspondence between ontogeny and phylogeny in this alternative developmental route in plants, we developed a new and highly efficient model of somatic embryogenesis in grapevine (Vitis vinifera) and sequenced its developmental transcriptomes. By combining the evolutionary properties of grapevine genes with their expression values, which were recovered from early induction until the formation of juvenile plants, we found a strongly supported hourglass-shaped developmental trajectory. However, in contrast to zygotic embryogenesis in Arabidopsis where the torpedo stage was evolutionary the most inert, we found that in the somatic embryogenesis of grapevine the heart stage expressed evolutionary the oldest and the most conserved transcriptome. This is a surprising finding because it suggests a better evolutionary system-level analogy between animal development and plant somatic embryogenesis than zygotic embryogenesis. We conclude that macroevolutionary logic is deeply hardwired in plant ontogeny and that somatic embryogenesis is likely a primordial embryogenic program in plants.

evolutionary biology↗