Biology subjects

Ledezma-Tejeida, D.

Publications and source records attributed to Ledezma-Tejeida, D..

4 recordsLinked to original sources

bioRxiv2026

Potential benefit of loss-of-function on bacterial fitness

Escherichia coli is a well-studied organism with extensive genomic and proteomic data. This study examines how gene loss reallocates cellular resources and impacts fitness. Genes were classified based on fitness measurements as essential, important, mean-effect, or fitness-enhancing. Using proteomic data, we analyzed the relationship between protein production cost and fitness, finding that genes with a high proteomic mass fraction are more likely to affect fitness, while fitness-enhancing deletions rarely improve fitness by reducing proteomic burden. We calculated the cumulative of proteome fractions encoded by genes classified as mean-effect and compared it with the results from the ME-model simulations. The mean-effect category constitutes 31-75% of the proteome, with the highest proportion LB, while enrichment analysis of core mean-effect genes highlighted transmembrane transport as the main functional category. Furthermore, we identified a subset of genes whose deletion increased fitness compared to the mean; they generally have low expression, and many have unknown functions. AI-assisted structural analyses identified domains and conserved features compatible with DNA-binding proteins, suggesting that some may represent putative transcriptional regulators requiring further validation. RpoS, stress sigma factor controlling up to 15% of the proteome is one of the transcriptional regulators in the fitness-enhancing category. Our findings suggest that the cost of being a generalist is linked to transcriptional regulation, while molecular transport represents a high burden for nutrient readiness. ImportanceThis study provides new insights into how gene loss benefits bacteria by identifying gene categories and their associated protein fractions whose disruption does not impose large fitness penalties. Additionally, it uncovers specific fitness-enhancing genes and generates hypotheses based on structural analyses for previously uncharacterized ones. Our findings suggest that several of these genes may encode putative transcriptional regulators, highlighting a potential role for regulatory complexity in cellular efficiency. By revealing how certain gene deletions enhance fitness and which gene categories are nonessential, this work advances our understanding of bacterial adaptation and genome streamlining. These insights have broad implications for evolutionary biology, metabolic engineering, and biotechnology, offering strategies to optimize microbial function by selectively reducing genetic and regulatory burden.

systems biology↗

bioRxiv2024

Putrescine acts as a signaling metabolite in the transition from nodulation to nitrogen fixation in Rhizobium phaseoli

Growth of the common bean plant Phaseolus vulgaris is tightly linked to its symbiotic relationship with diverse rhizobial species, particularly Rhizobium phaseoli, an alphaproteobacteria that forms root nodules and provides high levels of nitrogen to the plant. Molecular cross-talk is known to happen via plant-derived metabolites, but only flavonoids have been identified as signals. Flavonoids are transported inside the bacteria, where they signal the NodD regulator to elicit nodulation. Although seven other regulators are known to be involved, our knowledge of the regulatory mechanisms underlying the nodulation, and nitrogen fixation processes is limited, and the signals recognized by regulators are mostly unknown. Here, we identified 75 transcription factors in R. phaseoli genome through sequence conservation from Escherichia coli, and assembled a transcriptional regulatory network comprising 24 regulators, and 652 target genes. We identified the interactions relevant to nodulation via gene expression, and signaled out putrescine as a signaling metabolite. We propose a model where putrescine acts as a switch on the transition from nodulation to nitrogen fixation via the dual transcription factor PuuR, and its regulation of the nodI and nifU2 genes. ImportanceThis study provides new insights into the molecular cross-talk between Phaseolus vulgaris and Rhizobium phaseoli, which is crucial for the development of alternative cropping strategies, including biopesticides and biofertilizers. In addition, we present the first transcriptional regulatory network systematically assembled for Rhizobium phaseoli, which opens new avenues of research in the relationship between the transcriptional regulation and metabolism of these organisms.

microbiology↗

bioRxiv2021

Hierarchical control of microbial community assembly

Metabolic processes that fuel the growth of heterotrophic microbial communities are initiated by specialized biopolymer degraders that decompose complex forms of organic matter. It is unclear, however, to what extent degraders control the downstream assembly of the community that follows polymer breakdown. Investigating a model marine microbial community that degrades chitin, we show that chitinases secreted by different degraders produce oligomers of specific chain lengths that not only select for specialized consumers but also influence the metabolites secreted by these consumers into a shared resource pool. Each species participating in the breakdown cascade exhibits unique hierarchical preferences for substrates, which underlies the sequential colonization of metabolically distinct groups as resource availability changes over time. By identifying the metabolic underpinnings of microbial community assembly, we reveal a hierarchical crossfeeding structure that allows biopolymer degraders to shape the dynamics of community assembly. One sentence summarySpecialized biopolymer degraders direct the trajectory of microbial community assembly through interconnected modes of nutrient crossfeeding.

microbiology↗

bioRxiv2018

Limits to a classic paradigm: Most transcription factors regulate genes in multiple biological processes

Transcription factors (TFs) are important drivers of cellular decision-making. When bacteria encounter a change in the environment, transcription factors alter the expression of a defined set of genes in order to adequately respond. It is commonly assumed that genes regulated by the same TF should be involved in the same biological process. Examples of this are methods that rely on coregulation to infer function of not yet annotated genes. We have previously shown that only 21% of TFs regulate functionally homogeneous genes based on the proximity of their catalyzed reactions in the metabolic network. Here, we provide more evidence to support the claim that a one TF/one process relationship is not a general property. We show that the observed functional heterogeneity of regulons is not a result of the quality of the annotation of regulatory interactions, or the absence of protein-metabolite interactions, and is also present when function is defined by Gene Ontology terms. Furthermore, the observed functional heterogeneity is different from the one expected by chance, supporting the notion that it is a biological property. To further explore the relationship between transcriptional regulation and metabolism, we analyze 5 other types of regulatory groups and identify complex regulons (i.e. genes regulated by the same combination of TFs) as the most functionally homogeneous, which is supported by coexpression data. Whether higher levels of related functions exist beyond metabolism and current functional annotations, remains an open question.

bioinformatics↗