Biology subjects

de Jong, H.

Publications and source records attributed to de Jong, H..

15 recordsLinked to original sources

bioRxiv2026

Fluorescent proteins misreport ribosome abundance under translation inhibition

Fluorescent proteins are widely used as quantitative reporters of protein abundance in living cells. Here we show that this relationship can break down under translation inhibition: the cellular ribosomal abundance can increase while fluorescence intensity remains unchanged or even decreases. Using fluorescent reporters of ribosome abundance in Escherichia coli and Bacillus subtilis, we find that cellular fluorescence intensity quantitatively tracks ribosome abundance, inferred by RNA-to-protein ratio, under nutrient-limited growth but that is no longer true during chloramphenicol treatment. In E. coli, the discrepancy occurs with transcriptional and translational reporters and with both ribosomal protein and ribosomal RNA promoters. To distinguish changes in fluorescence output per reporter from changes in reporter abundance, we constructed a fluorescent protein-LacZ dual reporter in which fluorescence and an independent enzymatic estimate of reporter abundance are obtained from the same protein. Under translation inhibition, LacZ-derived reporter abundance increases whereas fluorescence intensity remains approximately constant, showing that fluorescence output per unit reporter abundance decreases. In a companion study, Bakshi and colleagues demonstrate that the effect extends to other fluorescent proteins and other translation inhibitors, indicating that it is not specific to a particular fluorescent protein or translation inhibitor. Our results show that fluorescent-protein calibration can be condition-dependent and cannot be assumed to transfer across physiological perturbations.

biophysics↗

bioRxiv2026

Pareto Suboptimal Resource Allocation and Microbial Growth

Microbial growth has often been analyzed under the assumption that microorganisms have evolved to optimize phenotypic characteristics of interest, such as growth rate and growth yield. This assumption has been useful, for example, for the genome-scale modeling of metabolism and the study of the allocation of cellular resources to physiological processes. In many experimental situations of interest, however, microorganisms are found to be suboptimal with respect to phenotypic characteristics that are thought to be favorable in that situation. Whereas a strong theoretical framework exists to mathematically relate cellular resource allocation strategies to Pareto optimality of microbial growth and other biological processes, much less is known about the consequences of Pareto suboptimality. We extend the framework to the latter case and show that a given Pareto suboptimal phenotype can be explained by a range of underlying resource allocation strategies, each corresponding to a different growth physiology and biomass composition. We test the predictions with the help of a coarse-grained model of microbial growth and published experimental data, which relate Pareto suboptimal rate-yield phenotypes of Escherichia coli and the microalga Tisochrysis lutea to the macromolecular composition of the cells (storage metabolite and total protein contents). Changing the focus from Pareto optimality to suboptimality provides interesting leads to exploring the diversity of growth strategies that can support a given phenotype. This change of perspective is of practical interest, because some of the growth physiologies within this range may be important for biotechnological applications

systems biology↗

bioRxiv2026

Multi-Species, Genome-Wide Metabolic Network Reconstructions Reveal the Basis for Metabolic Versatility in Mycobacteria

The genus Mycobacterium comprises over 200 species, many of which now have complete genome sequences. Some are major pathogens causing diseases like tuberculosis and leprosy, while others are harmless environmental organisms with useful abilities such as degrading pollutants. Environmental mycobacteria are often seen as metabolic generalists, able to utilise a wider range of carbon sources than host-associated species, which are typically more specialised due to their restricted habitats. This metabolic versatility has been proposed to stem from differences in nutrient uptake capabilities rather than catabolic pathways. In order to test this explanation, we developed and validated genome-scale metabolic models for five Mycobacterium species with varying lifestyles and growth rates, creating a computational approach enabled by CarveMe that allows rapid construction of models from genome information. By combining these models with microbiology experiments the study showed that the capacity of the bacteria to transport nutrients into the cell is indeed key to metabolic versatility. We notably found through load-partition experiments that, if a transporter is present but cannot take up its substrate at a rate sufficient for growth, the supply of multiple substrates can mitigate this rate-limiting step. This suggests that mycobacterial species have evolved high-affinity, low-rate systems for nutrient uptake in their ecological niches. More generally, our results demonstrate that a combination of automated annotation methods and straightforward bacterial physiology experiments allow the reconstruction of metabolic models of good predictive quality for hitherto little studied mycobacterial species.

microbiology↗

bioRxiv2025

Three novel genomes broaden the wild side of the Capsicum pangenome

This study presents three genome assemblies within the Capsicum genus, enabling comprehensive comparative analyses for the Annuum and Baccatum complexes within the genus. We produced highly continuous assemblies of the nuclear genomes and complete chloroplast assemblies. Subsequent genome annotation identified 34,580 genes in non-pungent C. annuum cv. ECW, and 32,704 and 33,994 genes in pungent C. chacoense and C. galapagoense, respectively. These assemblies, including the first complete genomes for C. chacoense and C. galapagoense, provide additional genomic resolution within the Capsicum genus. The novel genomes were analyzed within a pangenomic framework, integrating 16 Capsicum genomes across the Annuum, Baccatum, and Pubescens complexes. Homology grouping was used to identify core, accessory and unique genes and showed a wide spectrum of genetic diversity, particularly in homology groups exclusive to C. chacoense and C. galapagoense. Out of 79,267 homology groups identified, 13% were core groups, present in all accessions, corresponding to approximately 30% of core genes per genome. Comparative analyses revealed distinct species and genus specific genomic characteristics. Additionally, we used the graph pangenome to illustrate locus-level exploration by examining the Pun1 locus associated with capsaicinoid biosynthesis, identifying multiple Pun1-like genes including their genomic position and homology information. The integration of these new resources into a dynamic Capsicum pangenome framework provides a versatile platform for extracting genetic information relevant to both fundamental research and breeding applications.

genomics↗

bioRxiv2025

Predicting coarse-grained representations of biogeochemical cycles from metabarcoding data

MotivationTaxonomic analysis of environmental microbial communities is now routinely performed thanks to advances in DNA sequencing. Determining the role of these communities in global biogeochemical cycles requires the identification of their metabolic functions, such as hydrogen oxidation, sulfur reduction, and carbon fixation. These functions can be directly inferred from metagenomics data, but in many environmental applications metabarcoding is still the method of choice. The reconstruction of metabolic functions from metabarcoding data and their integration into coarse-grained representations of geobiochemical cycles remains a difficult bioinformatics problem today. ResultsWe developed a pipeline, called Tabigecy, which exploits taxonomic affiliations to predict metabolic functions constituting biogeochemical cycles. In a first step, Tabigecy uses the tool EsMeCaTa to predict consensus proteomes from input affiliations. To optimise this process, we generated a precomputed database containing information about 2,404 taxa from UniProt. The consensus proteomes are searched using bigecyhmm, a newly developed Python package relying on Hidden Markov Models to identify key enzymes involved in metabolic function of biogeochemical cycles. The metabolic functions are then projected on coarse-grained representation of the cycles. We applied Tabigecy to two salt cavern datasets and validated its predictions with microbial activity and hydrochemistry measurements performed on the samples. The results highlight the utility of the approach to investigate the impact of microbial communities on geobiochemical processes.

bioinformatics↗

bioRxiv2024

Glycoengineering with neuraminic acid analogs to label lipooligosaccharides and detect native sialyltransferase activity in Gram-negative bacteria

Lipooligosaccharides (LOS) are the most abundant cell surface glycoconjugates on the outer membrane of Gram-negative bacteria. They play important roles in host-microbe interactions. Certain Gram-negative pathogenic bacteria cap their LOS with the sialic acid, N-acetylneuraminic acid (Neu5Ac), to mimic host glycans that among others protects these bacteria from recognition by the hosts immune system. This process of molecular mimicry is not fully understood and remains under investigated. To explore the functional role of sialic acid-capped lipooligosaccharides (LOS) at the molecular level, it is important to have tools readily available for the detection and manipulation of both Neu5Ac on glycoconjugates and the involved sialyltransferases, preferably in live bacteria. We and others have shown that the native sialyltransferases of some Gram-negative bacteria can incorporate extracellular unnatural sialic acid nucleotides onto their LOS. We here report on the expanded use of native bacterial sialyltransferases to incorporate neuraminic acids analogs with a reporter group into the LOS of a variety of Gram-negative bacteria. We show that this approach offers a quick strategy to screen bacteria for the expression of functional sialyltransferases and the ability to use exogenous CMP-Neu5Ac to decorate their glycoconjugates. For selected bacteria we also show this strategy complements two other glycoengineering techniques, Metabolic Oligosaccharide Engineering (MOE) and Selective Exo-Enzymatic Labelling (SEEL), and that together they provide tools to modify, label, detect and visualize sialylation of bacterial LOS.

microbiology↗

bioRxiv2024

Single-cell data reveal heterogeneity of resource allocation across a bacterial population

Ribosomes are responsible for the synthesis of proteins, the major component of cellular biomass. Classical experiments have established a linear relationship between the fraction of resources invested in ribosomal proteins and the rate of balanced growth of a microbial population. We extended the study of ribosomal resource allocation from populations to single cells, using a combination of time-lapse fluorescence microscopy and statistical inference. We found a large variability of ribosome concentrations and growth rates in conditions of balanced growth of the model bacterium Escherichia coli. Moreover, the ribosome concentrations and growth rates of individual cells are uncorrelated, contrary to what would be expected from the population-level growth law. A similar large heterogeneity was found during the transition of the bacteria from a poor to a rich growth medium. Whereas some cells immediately adapt ribosomal resource allocation to the new environment, others do so only gradually. Our results thus reveal distinct strategies for investing resources in the molecular machines at the heart of cellular self-replication. This raises the interesting question whether the observed variability is an intrinsic consequence of the stochastic nature of the underlying biochemical processes or whether it improves the fitness of Escherichia coli in its natural environment.

microbiology↗

bioRxiv2022

Structure-activity relationship of 2,4-D correlates auxin activity with the induction of somatic embryogenesis in Arabidopsis thaliana

2,4-dichlorophenoxyacetic acid (2,4-D) is a synthetic analogue of the plant hormone auxin that is commonly used in many in vitro plant regeneration systems, such as somatic embryogenesis (SE). Its effectiveness in inducing SE, compared to the natural auxin indole-3-acetic acid (IAA), has been attributed to the stress triggered by this compound rather than its auxin activity. However, this hypothesis has never been thoroughly tested. Here we used a library of 40 2,4-D analogues to test the structure-activity relationship with respect to the capacity to induce SE and auxin activity in Arabidopsis thaliana. Four analogues induced SE as effectively as 2,4-D and 13 analogues induced SE but were less effective. Based on root growth inhibition and auxin response reporter expression, the 2,4-D analogues were classified into different groups, ranging from very active auxins to not active. A halogen at the 4-position of the aromatic ring was important for auxin activity, whereas a halogen at the 3-position resulted in reduced activity. Moreover, a small substitution at the carboxylate chain was tolerated, as was extending the carboxylate chain with two but not with one carbon. In the process, we also identified two 2,4-D analogues as efficient inducers of adventitious root formation and several possible anti-auxins. The auxin activity of the 2,4-D analogues was consistent with their simulated TIR1-Aux/IAA coreceptor binding characteristics. A strong correlation was observed between SE induction efficiency and auxin activity, indicating that the stress-related effects triggered by 2,4-D that are considered important for SE induction are down-stream of auxin signaling.

plant biology↗

bioRxiv2022

Pollen sequencing reveals barriers and aberrant patterns of recombination in interspecific tomato hybrids

Tomato is the most consumed vegetable in the world. Increasing its natural resistance and resilience is key for ensuring food security within a changing climate. Plant breeders improve those traits by generating crosses of cultivated tomatoes with their wild relatives. Specific allele introgression relying on meiotic recombination, is hampered by structural divergence between parental genomes. However, previous studies of interspecific tomato hybridization focused in single cross or lacked resolution due to prohibitive sequencing costs of large segregating populations. Here, we used pooled-pollen sequencing to reveal unprecedented details of recombination patterns in five interspecific tomato hybrids. We detected hybrid-specific recombination coldspots that underscore the influence of structural divergence in shaping recombination landscape. Crossover regions and coldspots show strong association with specific TE superfamilies exhibiting differentially accessible chromatin between somatic and meiotic cells. We also found gene complexes associated with metabolic processes, stress resistance and domestication syndrome traits, revealing undesired consequences of recombination suppression to phenotypes. Finally, we demonstrate that by using resequencing data of wild and domesticated tomato populations, we can screen for alternative parental genomes to overcome recombination barriers. Overall, our results will allow breeders better informed decisions on generating disease-resistant and climate-resilient tomato.

genomics↗

bioRxiv2022

Resource allocation accounts for the large variabilityof rate-yield phenotypes across bacterial strains

Different strains of a microorganism growing in the same environment display a wide variety of growth rates and growth yields. We developed a coarse-grained model to test the hypothesis that different resource allocation strategies, corresponding to different compositions of the proteome, can account for the observed rate-yield variability. The model predictions were verified by means of a database of hundreds of published rate-yield and uptake-secretion phenotypes of Escherichia coli strains grown in standard laboratory conditions. We found a very good quantitative agreement between the range of predicted and observed growth rates, growth yields, and glucose uptake and acetate secretion rates. These results support the hypothesis that resource allocation is a major explanatory factor of the observed variability of growth rates and growth yields across different bacterial strains. An interesting prediction of our model, supported by the experimental data, is that high growth rates are not necessarily accompanied by low growth yields. The resource allocation strategies enabling high-rate, high-yield growth of E. coli lead to a higher saturation of enzymes and ribosomes, and thus to a more efficient utilization of proteomic resources. Our model thus contributes to a fundamental understanding of the quantitative relationship between rate and yield in E. coli and other microorganisms. It may also be useful for the rapid screening of strains in metabolic engineering and synthetic biology.

systems biology↗

bioRxiv2022

Optimal protein production by a synthetic microbial consortium: Coexistence, distribution of labor, and syntrophy

The bacterium E. coli is widely used to produce recombinant proteins such as growth hormone and insulin. One inconvenience with E. coli cultures is the secretion of acetate through overflow metabolism. Acetate inhibits cell growth and represents a carbon diversion, which results in several negative effects on protein production. One way to over-come this problem is the use of a synthetic consortium of two different E. coli strains, one producing recombinant proteins and one reducing the acetate concentration. In this paper, we study a chemostat model of such a synthetic community where both strains are allowed to produce recombinant proteins. We give necessary and sufficient conditions for the existence of a coexistence equilibrium and show that it is unique. Based on this equilibrium, we define a multi-objective optimization problem for the maximization of two important bioprocess performance metrics, process yield and productivity. Solving numerically this problem, we find the best available trade-offs between the metrics. Under optimal operation of the mixed community, both strains must produce the protein of interest, and not only one (distribution instead of division of labor). Moreover, in this regime acetate secretion by one strain is necessary for the survival of the other (syntrophy). The results thus illustrate how complex multi-level dynamics shape the optimal production of recombinant proteins by synthetic microbial consortia.

synthetic biology↗

bioRxiv2021

Genome and transcriptome architecture of allopolyploid okra (Abelmoschus esculentus)

We present the first annotated genome assembly of the allopolyploid okra (Abelmoschus esculentus). Analysis of telomeric repeats and gene rich regions suggested we obtained whole chromosome and chromosomal arm scaffolds. Besides long distal blocks we also detected short interstitial TTTAGGG telomeric repeats, possibly representing hallmarks of chromosomal speciation upon polyploidization of okra. Ribosomal RNA genes are organized in 5S clusters separated from the 18S-5.8S-28S units, clearly indicating an S-type rRNA gene arrangement. The assembly is consistent with cytogenetic and cytometry observations, identifying 65 chromosomes and 1.45Gb of expected genome size in a haploid sibling. Approximately 57% of the genome consists of repetitive sequence. BUSCO scores and A50 plot statistics indicated a nearly complete genome. Kmer distribution analysis suggests that approximately 75% has a diploid nature, and at least 15% of the genome is heterozygous. We did not observe aberrant meiotic configurations, suggesting there is no recombination among the sub-genomes. BUSCO configurations as well as k-mer clustering analysis pointed to the presence of at least 2 sub-genomes. These observations are indicative for an allopolyploid nature of the okra genome. Structural annotation, using gene models derived from mapped IsoSeq transcriptome data, generated over 130,000 putative genes. Mapped transcriptome data from public okra accessions of Asian origin confirmed the predicted genes, showing limited genetic diversity of 1SNP/2.1kb. The discovered genes appeared to be located predominantly at the distal ends of scaffolds, gradually decreasing in abundance toward more centrally positioned scaffold domains. In contrast, LTR retrotransposons were more abundant in centrally located scaffold domains, while less frequently represented in the distal ends. This gene and LTR-retrotransposon distribution is consistent with the observed heterochromatin organization of pericentromeric heterochromatin and distal euchromatin. The derived amino acid queries of putative genes were subsequently used for phenol biosynthesis pathway annotation in okra. Comparison against manually curated reference KEGG pathways from related Malvaceae species revealed the genetic basis for putative enzyme coding genes that likely enable metabolic reactions involved in the biosynthesis of dietary and therapeutic compounds in okra.

genomics↗

bioRxiv2020

Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Tropical Asian collection using DArTseq based SNP markers

This study explored a germplasm consisting of 112 Luffa acutangula (ridge gourd) accessions mainly from Thailand, and some accessions from Vietnam, China, Philippines, Indonesia, USA, Bangladesh and Laos for an analysis of the population structure and underlying genetic diversity using 2,834 SNPs. STRUCTURE analysis ({Delta}K at K=6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. The phylogenetic tree showed the diversity of L. acutangula in Thailand, and accessions from other countries apart from Thailand were grouped together in the same branches. In STRUCTURE, subpopulation 2 contained only accessions from Thailand while other subpopulations contained a combination of accessions from Thailand and from other countries. When plotted, the STRUCTURE bars to the area of collection, it revealed the geneflow from the surrounding places nearby as indicated by the admixed genetic in the STRUCTURE bars. AMOVA based on STRUCTURE clustering showed the variation between populations (12.83%) and confirmed the absence of population structure in subpopulations (-10.59%). There was a distinguishing characteristic fruit shape and length in each subpopulation. The ample genetic diversity found in the L. acutangula germplasm can be utilized in ridge gourd breeding programs to help meet the demands and needs of both consumers and farmers.

genomics↗

bioRxiv2020

Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs

Synthetic microbial consortia have been increasingly utilized in biotechnology and experimental evidence shows that suitably engineered consortia can outperform individual species in the synthesis of valuable products. Despite significant achievements, though, a quantitative understanding of the conditions that make this possible, and of the trade-offs due to the concurrent growth of multiple species, is still limited. In this work, we contribute to filling this gap by the investigation of a known prototypical synthetic consortium. A first E. coli strain, producing a heterologous protein, is sided by a second E. coli strain engineered to scavenge toxic byproducts, thus favoring the growth of the producer at the expense of diverting part of the resources to the growth of the cleaner. The simplicity of the consortium is ideal to perform an in depth-analysis and draw conclusions of more general interest. We develop a coarse-grained mathematical model that quantitatively accounts for literature data from different key growth phenotypes. Based on this, assuming growth in chemostat, we first investigate the conditions enabling stable coexistence of both strains and the effect of the metabolic load due to heterologous protein production. In these conditions, we establish when and to what extent the consortium outperforms the producer alone in terms of productivity. Finally, we show in chemostat as well as in a fed-batch scenario that gain in productivity comes at the price of a reduced yield, reflecting at the level of the consortium resource allocation trade-offs that are well-known for individual species.

systems biology↗

bioRxiv2018

A complete chromosome substitution mapping panel reveals genome-wide epistasis in Arabidopsis

Chromosome substitution lines (CSLs) are tentatively supreme resources to investigate non-allelic genetic interactions. However, the difficulty of generating such lines in most species largely yielded imperfect CSL panels, prohibiting a systematic dissection of epistasis. Here, we present the development and use of a unique and complete panel of CSLs in Arabidopsis thaliana, allowing the full factorial analysis of epistatic interactions. A first comparison of reciprocal single chromosome substitutions revealed a dependency of QTL detection on different genetic backgrounds. The subsequent analysis of the complete panel of CSLs enabled the mapping of the genetic interactors and identified multiple two- and three-way interactions for different traits. Some of the detected epistatic effects were as large as any observed main effect, illustrating the impact of epistasis on quantitative trait variation. We, therefore, have demonstrated the high power of detection and mapping of genome-wide epistasis, confirming the assumed supremacy of comprehensive CSL sets.\n\nOne sentence summaryDevelopment of a complete panel of chromosome substitution lines enables high power mapping of epistatic interactions in Arabidopsis thaliana.

genetics↗