Biology subjects

Tsuru, S.

Publications and source records attributed to Tsuru, S..

10 recordsLinked to original sources

bioRxiv2026

Lineage-Independent Modular Evolution of Carbon-Source Utilization

Metabolic phenotypes vary within microbial species, yet how such variation is organized remains unclear. Diversification in carbon-source utilization, in particular, often appears idiosyncratic, showing weak correspondence to phylogeny or simple gene content. Here, we combine quantitative growth phenotyping of natural Escherichia coli isolates across 32 carbon sources with diversification observed during de novo laboratory evolution, together with a reaction-level description of metabolic similarity. Despite deep phylogenetic divergence, growth-rate profiles varied independently of lineage. Instead, growth rates across carbon sources covaried in recurrent modular patterns aligned with similarities in required metabolic reactions. Closely analogous modular relationships re-emerged during de novo evolution, indicating parallel diversification across evolutionary contexts. Growth-rate variation in natural and experimentally evolved datasets collapsed onto a shared low-dimensional variance structure. Together, our results indicate that quantitative metabolic phenotypes vary along a limited set of recurring, module-linked axes, providing an organizational perspective on intraspecific metabolic diversity despite weak phylogenetic signal.

evolutionary biology↗

bioRxiv2025

Carbon source diversity shapes bacterial interspecies interactions

Bacterial communities exhibit various classes of interspecies interactions, ranging from cooperative to competitive. As these interaction classes play a crucial role in determining characteristics of bacterial communities, including species composition and community stability, understanding of the mechanisms that shape them is warranted. While several studies have suggested that cooperative interactions are rare, a study focused on single-carbon-source environments reported them to be relatively common. This discrepancy highlights the potential role of carbon source diversity in shaping interaction classes, although the quantitative relationship remains unclear. To elucidate this relationship, we examined 896 interspecies interactions among 28 synthetic bacterial pairs, isolated from various environments, under 32 conditions with varying levels of carbon source diversity. As a result, we frequently observed cooperative interactions in single-carbon-source environments, with the interactions shifting to competitive as the carbon source diversity increased. Further analyses suggested that this shift was driven by intensified resource competition in more complex media. Our findings provide new insights into how environmental factors, particularly carbon source diversity, shape bacterial interactions in synthetic communities, offering potential strategies for manipulating bacterial communities in ecological and biotechnological contexts.

microbiology↗

bioRxiv2025

Repeatability of protein structural evolution following convergent gene fusions

Convergent evolution of proteins provides insights into repeatability of genetic adaptation. While local convergence of proteins at residue or domain level has been characterized, global structural convergence by inter-domain/molecular interactions remains largely unknown. Here we present structural convergent evolution on fusion enzymes of aldehyde dehydrogenases (ALDHs) and alcohol dehydrogenases (ADHs). We discovered BdhE (bifunctional dehydrogenase E), an enzyme clade that emerged independently from the previously known AdhE family through distinct gene fusion events. AdhE and BdhE showed shared enzymatic activities and non-overlapping phylogenetic distribution, suggesting common functions in different species. Cryo-electron microscopy revealed BdhEs form donut-like homotetramers, contrasting AdhEs helical homopolymers. Intriguingly, despite distinct quaternary structures and >70% unshared amino acids, both enzymes form resembled dimeric structure units by ALDH-ADH interactions via convergently elongated loop structures. These findings suggest convergent gene fusions recurrently led to substrate channeling evolution to enhance two-step reaction efficiency. Our study unveils structural convergence at inter-domain/molecular level, expanding our knowledges on patterns behind molecular evolution exploring protein structural universe.

evolutionary biology↗

bioRxiv2024

Congruence between noise and plasticity in protein expression

Gene expression responds to various perturbations, such as mutations, environmental changes, and stochastic perturbations. The variability in gene expression levels differs among genes, influencing the availability of adaptive variants or mutants and thereby affecting nongenetic and genetic adaptations. Different types of variability are interdependent, suggesting global canalization/decanalization against different perturbations and a common underlying mechanism. Despite this, the relationship between plasticity (variability in response to environmental changes) and noise (variability among cells under the same conditions) in gene expression remains debatable. Previous studies reported a positive correlation between plasticity and noise, but these variabilities are often measured at different levels: plasticity at the mRNA level and noise at the protein level. This methodological discrepancy complicates the understanding of their relationship. We investigated this by measuring protein expression levels of essential and nonessential genes in Escherichia coli. Using flow cytometry, we quantified noise and plasticity from the same dataset. Essential genes exhibited lower noise and plasticity than nonessential genes. Nonessential genes showed a positive correlation between noise and plasticity, while essential genes did not. This study provides empirical evidence of essentiality-dependent coupling between noise and plasticity in protein expression, highlighting the organization of different types of variabilities.

systems biology↗

bioRxiv2024

Laboratory evolution of the bacterial genome structure through insertion sequence activation

The genome structure critically impacts bacterial physiology, ecology, and evolution. However, its evolution, driven by transposons called insertion sequences (IS), has been challenging to track in laboratories due to its slow pace. Here, we accelerated this process by introducing multiple copies of a high-activity IS into Escherichia coli. Mimicking bursts of IS copies in host-restricted endosymbionts and pathogens, we evolved the bacteria under relaxed neutral conditions. Within ten weeks, we observed a median of 24.5 IS insertions per genome, comparable to a decade of wild-type evolution. Long-read sequencing revealed extensive IS-mediated genome rearrangements, resulting in novel IS variants and genome size changes exceeding {+/-}5 %. By achieving such drastic genome evolution under relaxed selection, our study establishes a baseline for assessing the fitness effects of IS insertions, genome size changes, and rearrangements. This work paves the way for experimentally studying bacterial genome structure evolution, complementing analyses of genome structures in nature.

microbiology↗

bioRxiv2024

Promoter constrains evolution of expression levels of essential genes inEscherichia coli

Variability in expression levels in response to random genomic mutations varies among genes, influencing both the facilitation and constraint of phenotypic evolution in organisms. Despite its importance, both the underlying mechanisms and evolutionary origins of this variability remain largely unknown due to the mixed contributions of cis- and trans-acting elements. To address this issue, we focused on the mutational variability of cis-acting elements, that is, promoter regions, in Escherichia coli. Random mutations were introduced into the natural and synthetic promoters to generate mutant promoter libraries. By comparing the variance in promoter activity of these mutant libraries, we found no significant difference in mutational variability in promoter activity between promoter groups, suggesting the absence of a signature of natural selection for mutational robustness. In contrast, the promoters controlling essential genes exhibited a remarkable bias in mutational variability, with mutants displaying higher activities than the wild types being relatively rare compared to those with lower activities. Our evolutionary simulation on a rugged fitness landscape provided a rationale for this vulnerability. These findings suggest that past selection created non-uniform mutational variability in promoters biased toward lower activities of random mutants now constrain future evolution of downstream essential genes toward higher expression levels.

evolutionary biology↗

bioRxiv2024

Genetic properties underlying transcriptional variability in Escherichia coli

AbstractThe rate and direction of phenotypic evolution depend on the availability of phenotypic variants induced genetically or environmentally. It is widely accepted that organisms do not display uniform phenotypic variation, with certain variants arising more frequently than others in response to genetic or environmental perturbations. Previous studies have suggested that gene regulatory networks channel both environmental and genetic influences. However, how the gene regulatory networks influence phenotypic variation remains unclear. To address this, we characterize transcriptional variations in Escherichia coli under environmental and genetic perturbations. Based on the current understanding of transcriptional regulatory networks, we identify genetic properties that explain gene-to-gene differences in transcriptional variation. Our findings highlight the role of gene regulatory networks in shaping the shared phenotypic variability across different perturbations.

evolutionary biology↗

bioRxiv2022

Purifying selection enduringly acts on the sequence evolution of highly expressed proteins in Escherichia coli

The evolutionary speed of a protein sequence is constrained by its expression level, with highly expressed proteins evolving relatively slowly. This negative correlation between expression levels and evolutionary rates (known as the E-R anticorrelation) has already been widely observed in past macroevolution between species from bacteria to animals. However, it remains unclear whether this seemingly general law also governs recent evolution, including past and de novo, within a species. However, the advent of genomic sequencing and high-throughput phenotyping, particularly for bacteria, has revealed fundamental gaps between the two evolutionary processes and has provided empirical data opposing the possible underlying mechanisms which are widely believed. These conflicts raise questions about the generalization of the E-R anticorrelation and the relevance of plausible mechanisms. To explore the ubiquitous impact of expression level on molecular evolution, and to test the relevance of the possible underlying mechanisms, we analyzed the genome sequences of 99 strains of Escherichia coli for microevolution in nature. We also analyzed genomic mutations accumulated under laboratory conditions as a model of de novo microevolution. Here, we show that the E-R anticorrelation is significant in both past and de novo microevolution in E. coli. Our data also confirmed ongoing purifying selection acting on highly expressed genes. Ongoing selection included codon-level purifying selection, supporting the relevance of the underlying mechanisms. However, their contributions to the constraints in recent evolution might be smaller than previously expected from past macroevolution.

evolutionary biology↗

bioRxiv2021

Operon formation by insertion sequence IS3 in Escherichia coli

Operons are a hallmark of the genomic and regulatory architecture of prokaryotes. However, the mechanism by which two genes placed far apart gradually come close and form operons remains to be elucidated. Here, we propose a new model of the origin of operons: Mobile genetic elements called insertion sequences can facilitate the formation of operons by consecutive insertion-deletion-excision reactions. This mechanism barely leaves traces of insertion sequences and is difficult to detect in evolution in nature. We performed, to the best of our knowledge, the first experimental demonstration of operon formation, as a proof of concept. The insertion sequence IS3 and the insertion sequence excision enhancer are genes found in a broad range of bacterial species. We introduced these genes into insertion sequence-less Escherichia coli and found that, supporting our hypothesis, the activity of the two genes altered the expression of genes surrounding IS3, closed a 2.7 kilobase pair gap between a pair of genes, and formed new operons. This study shows how insertion sequences can facilitate the rapid formation of operons through locally increasing the structural mutation rates and highlights how coevolution with mobile elements may shape the organization of prokaryotic genomes and gene regulation.

genomics↗

bioRxiv2020

Transcriptome signature in E. coli under a prolonged starvation environment

Background"Non-growing" is a dominant life form of microorganisms in nature, where available nutrients and resources are extremely limited. However, the knowledge of the manner in which microorganisms resist nutrient deficiency is still rudimentary compared to those of the growing cells. In laboratory culture, Escherichia coli can survive for several years under starvation, denoted as long-term stationary phase (LSP), where a small fraction of the cells survive by recycling resources released from the starved nonviable cells and constitute a model system for understanding survival mechanisms under long-term starvation. Although the physiology by which viable cells in LSP adapt to long-term starvation is of great interest, their genome-wide response has not yet been fully understood. ResultsTo understand the physiological state of viable cells in the LSP environment, we analyzed the transcriptional profiles of cells exposed to the supernatant of LSP culture. We found that high expression of transporter genes and low expression of biosynthesis genes are the primary responses of the cells in the LSP supernatant compared to growing cells, which display similar responses to cells entering the stationary phase from the exponential growth phase. We also revealed some specific transcriptional responses in the LSP supernatant, such as higher expression of stress-response genes and lower expression of translation-related genes, compared to other non-growing conditions. This suggests that cells in LSP are highly efficient in terms of cellular survival and maintenance functions under starvation conditions. We also found population-density-dependent gene expression profiles in LSP, which are also informative to understand the survival mechanism of bacterial population. ConclusionOur current comprehensive analysis of the transcriptome of E. coli cells provides an overview of the genome-wide response to the long-term starvation environment. We detected both common and distinctive responses in the primary transcriptional changes between the short- and long-term stationary phase cultures, which could provide clues to understand the possible molecular mechanisms underlying survivability in the starved environment.

microbiology↗