Biology subjects

Rech, E.

Publications and source records attributed to Rech, E..

6 recordsLinked to original sources

bioRxiv2026

Machine-learning-driven prediction and design of intrinsic transcription terminators

Intrinsic transcription terminators are biological parts critical for controlling gene expression in natural genomes and are fundamental to the modularity and predictability of synthetic gene circuits. Despite their simplicity of structure and function, we have not yet been able to rationally engineer synthetic terminators with a pre-defined strength, nor to accurately predict their strength from sequence. Here, we leveraged a curated library of bacterial terminators to train a data-driven predictive model, and, building on this surrogate, developed open-source software tools for predicting terminator performance and designing new intrinsic terminator sequences. Model interpretability analysis indicates that U-tract features emphasize a distal region longer than previously anticipated and that the initial hairpin GC content influence extends beyond the reported range. Using the final trained model, we implemented two software tools. The Terminator Strength Predictor (TerSP) computes the full feature representation directly from an input sequence and outputs a quantitative strength prediction together with a binary strong/weak classification. We validated TerSP using experimentally characterized terminators from bacteria other than E. coli. The Terminator Factory (TerFac) implements a surrogate-based optimization framework for target-driven terminator design under user-defined strength and length constraints. Using TerFac, we enumerated length-specific sets of maximally strong terminators, designed optimized synthetic terminators, and optimized a wild-type terminator. The designed terminators were validated in vivo in E. coli and in vitro, using a newly developed assay based on fluorescent RNA aptamers. The TerFac-designed terminators showed the expected strength, and the strongest one outperformed the best reference terminator in the training dataset, both in vivo and in vitro. These results indicate that the model captured sequence-to-function rules that are informative both for forward prediction (TerSP) and for the design of terminators with defined strength (TerFac).

synthetic biology↗

bioRxiv2025

Bridging Gaps in Soil Ecology: Metagenomic Insights into Microbial Diversity and Functionality Across Brazil's Biomes.

Microorganisms participate in complex interactions involving different kingdoms, so rhizosphere biodiversity mapping is essential for understanding how microbes interact with each other in the soil and with roots. Although soil microbial communities are remarkably diverse and technological advances have provided a high capacity to acquire reliable sequence data, unique microbial taxa in soil, root and rhizosphere samples remain poorly described. For the first time, we organized a consortium to collect soil samples covering all Brazilian biomes, providing a comprehensive and unprecedented view of soil microbial diversity. This understanding is critical, especially within the context of climate change, which affects plant physiology, root exudation and, consequently, the composition and functionality of soil microbial communities. The interactions between soil, roots and rhizosphere are influenced by evolutionary and adaptive forces and shape the production of microbial natural products, which exhibit great therapeutic potential and Mapping and studying rhizosphere microbial biodiversity not only increases our knowledge of soil ecology but also offers valuable insights for developing sustainable practices. We employed both 16S/18S/ITS amplicon and metagenomic short-read shotgun sequencing methods to examine and catalogue the large-scale genomes of culture-independent rhizosphere microbes and their interactions with roots in six terrestrial Brazilian biomes, namely, the Amazon, Atlantic Forest, Cerrado, Caatinga, Pampa and Pantanal. Our results revealed the ubiquity of Proteobacteria, which reflects their adaptability to contrasting environments. Biomes with greater moisture availability, such as the Amazon and Pantanal, exhibited greater diversity and abundance of fast-growing bacteria, such as Proteobacteria, and nutrient cyclers, such as Thaumarchaeota. Arid and semiarid biomes, such as the Caatinga, were dominated by microorganisms tolerant to drought and nutrient-limited environments, such as Actinobacteria. Acidobacteria, which thrive in acidic, nutrient-poor soils, were very abundant in forest biomes. The Planctomycetes phylum also occurred more frequently in areas with a relatively high soil organic matter content, such as the Cerrado. Bacteroidetes was significantly more abundant in Pampa than in the other biomes. The results provide comprehensive insights into soil, root and rhizosphere biodiversity and not only enhance the knowledge of the fundamental biological processes sustaining plant life but also constitute a reliable sequencing databank to address present-day agricultural and environmental challenges.

microbiology↗

bioRxiv2025

GENETIC ENGINEERING THROUGH QUANTUM CIRCUITS: CONSTRUCTION OF CODES AND ANALYSIS OF GENETIC ELEMENTS BIOBLOQU

Quantum biology is an emergent field that investigates quantum-mechanical phenomena, such as superposition, tunneling, and entanglement, in the context of data manipulation from living systems. The exploration and engineering of nucleotide sequences rely on quantum mechanical principles, particularly the use of qubit states for the development of quantum codes. Biological sequencing data is produced at about 1 Gb/h, but analysis lags due to complexity and the limitations of classical computing. Despite these challenges, quantum computing offers a potential tool for analyzing and assembling biological data. Here, we developed quantum codes for genetic engineering. The developed quantum computational framework identifies sequences of interest within a genomic database. It locates the left and right boundaries of the scar region in the JCVI-Syn3B genome and detects 20 nucleotides flanking each boundary. After confirming the left and right ends of the scar, a secondary computational routine performs the targeted insertion of the BioBloQu structure, composed of genetic elements, into the previously characterized scar region. Our algorithms constitute a unique starting point for advanced genetic data manipulation. This tool could accelerate the exploration of large volumes of genetic data and enable the developmental design and assembly of synthetic genomes enhanced by quantum computing. Further improvements in algorithms and codes, along with the expanded availability of devices, will accelerate the search for data for applied genetic research.

bioinformatics↗

bioRxiv2025

Cell-Free production of soybean leghemoglobins and non-symbiotic hemoglobin

Hemoglobins are heme proteins and are present in some microorganisms, higher plants and mammals. In legume nodules there are two types: leghemoglobin (LegH) or symbiotic and non-symbiotic (nsHb). LegHs are present in high amounts at legumes roots and are responsible together with bacteroides for the nitrogen fixation process. Non-symbiotic hemoglobins Class 1 protein have very high affinity for O2 and are found in monocotyledons and legumes. LegH has aroused great interest in the vegetable meat industry due to its organoleptic and nutritional properties. Here, we demonstrated that soybean LegH A, C1, C2, C3 and nsHb are produced by E. coli-based cell-free protein synthesis (CFPS) and correctly synthesized in its amino acids sequence. In addition, it was also possible to reproduce some post-translational modifications confirmed by LC/MS analysis. All LegHs produced in this system showed peroxidase activity and heme binding correlated with its concentration in the assays. Furthermore, all proteins were readily digested by pepsin within 1 minute in analog digestion conditions. Therefore, LegHs and nsHb proteins were synthesized using cell-free systems (CFSs), maintaining their functionality and being digestible. These findings suggest that they could serve as viable alternative food additives for plant-based meat. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC="FIGDIR/small/643390v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@504374org.highwire.dtl.DTLVardef@17c8d73org.highwire.dtl.DTLVardef@2aad12org.highwire.dtl.DTLVardef@1c8a3e9_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2024

The Soil Microbiome of the Caatinga Drylands in Brazil

Drylands represent a significant part of the Earths surface and include essential and vulnerable ecosystems for the global ecological balance. The Caatinga, with its unique biodiversity adapted to the extreme conditions of this semi-arid region, offers a valuable opportunity to expand our knowledge about these ecosystems. Here, this work reveals the high microbial diversity in the soil and rhizosphere of the Caatinga, with the roots presenting more specialized communities. Bacteria such as Bacilli, Alphaproteobacteria and Firmicutes excelled in critical functions such as nutrient cycling. Interplant differences suggested the influence of root exudates. The metagenomic study of interactions between microorganisms in the rhizosphere of selected plants revealed microbial biodiversity and contributed to our understanding of nutrient cycling, plant growth and resistance to water stress. In addition, they demonstrate biotechnological potential to address global challenges such as desertification and food security.

microbiology↗

bioRxiv2024

Development of Int-Plex@ binary memory switch system: plant genome modulation driven by large serine-integrases.

The comprehension of virus-host interactions has allowed numerous advances in developing biotechnological methodologies for plant genome editions, constituting a promising path for plant genetic engineering. Among these advancements, phage- encoded large serine-integrases have emerged as noteworthy tools to modulate plant metabolic pathways by inserting, excising, or inverting DNA stretches in a reversible and specific way. The present work shows the foundation of the Int-Plex@ (INTegrase PLant EXpression) binary memory switch system, which consists of the application of four distinct orthogonal prophage large serine-integrases (Int) (BxB1, phiC31, Int13, and Int9) as an input trigger mechanism for the inversion or excision of genomic DNA. The memory genetic switch is divided into the excision module and the inversion module. The excision module is activated by BxB1 or phiC31 enzymes (input). In this case, the DNA sequence flanked by its attachment sites is excised from the genome (output). The inversion module is activated by Int9 or Int13 (input). The inverted mgf gene sequence is flipped to its functional coding sequence, and the switch output is mGFP. Moreover, prokaryotic-based cell-free in vitro transcription-translation reactions (TxTl) were used as a fast platform for testing Ints attB/P in tandem site activity. Furthermore different plasmid delivery strategies for plant cell Int heterologous expression were tested: leaf tissue agroinfiltration of Agrobacterium tumefaciens transformed with binary plasmids and a biolistic system. After each treatment, the edited genomic DNA sequences were amplified and verified by Sanger and Nanopore sequencing. Despite the challenges of using Ints, the potential benefits are significant and deserve deeper exploration and development. The Int-Plex@ binary genome memory switch system can be applied to produce genetic circuits combined with omics tools and sgRNAs to engineer and modulate plant metabolic pathways temporally and reversibly.

synthetic biology↗