Biology subjects

Silva-Rocha, R.

Publications and source records attributed to Silva-Rocha, R..

At least 19 recordsLinked to original sources

bioRxiv2023

Identification and functional analysis of novel stress-resistance genes from metagenomes of extreme environments

Currently, industrial bioproducts are less competitive than chemically produced goods due to the shortcomings of conventional microbial hosts. Metagenomic approaches from extreme environments can provide useful biological parts to improve bacterial robustness to process-specific parameters. Here, in order to build synthetic genetic circuits that increase bacterial resistance to diverse stress conditions, we mined novel stress tolerance genes from metagenomic databases using an in silico approach based on Hidden-Markov-Model profiles. For this purpose, we used metagenomic shotgun sequencing data from microbial communities of extreme environments to identify genes encoding chaperones and other proteins that confer resistance to stress conditions. We identified and characterized ten novel protein-encoding sequences related to the DNA-binding protein HU, the ATP-dependent protease ClpP, and the chaperone protein DnaJ. By expressing these genes in Escherichia coli under several stress conditions (including high temperature, acidity, oxidative and osmotic stress, and UV radiation), we identified five genes conferring resistance to at least two stress conditions when expressed in E. coli. Moreover, one of the identified HU coding-genes which was retrieved from an acidic soil metagenome increased E. coli tolerance to four different stress conditions, implying its suitability for the construction of a synthetic circuit directed to expand broad bacterial resistance.

bioengineering↗

bioRxiv2022

Metagenomic insights for antimicrobial resistance surveillance in soils with different land uses in Brazil

Anthropization in terrestrial environments commonly leads to land use transformation, changing soil properties and their microbial communities. This, combined with the exacerbated use of antibiotics in human and animal health promotes the expansion of the soil resistome. Considering the urgent need for surveillance of antimicrobial resistance (AMR), we aimed to evaluate how different land practices (urban, farming and forest) can affect the soil resistome and the dynamics of their bacterial communities. We collected eight soil samples from different locations in the countryside of Sao Paulo (Brazil), assessed the community profiles based on 16S rRNA sequencing and analyzed the soil metagenomes based on shotgun sequencing. Our results highlight differences in the communities structure and their dynamics which were correlated with land practices. Additionally, differences were observed in the abundance and diversity of antibiotic resistance genes (ARGs) and virulence factors (VFs) across studied soils, where a higher presence and homogeneity of vanRO, mtrA and rbpA genes were detected in livestock soils. We observed that Staphylococcus and Bacillus are positively correlated with each other and are markers for agricultural communities. Moreover, the abundance and diversity of ARGs and VFs observed in farming soils raises concerns regarding the potential spread of these genes in the environment. Together, our findings reinforce the importance and urgency of AMR surveillance in the environment, especially in soils undergoing deep land use transformations due to anthropic activity.

microbiology↗

bioRxiv2022

Mining novel cis-regulatory elements from the emergent host Rhodosporidium toruloides using transcriptomic data

The demand for robust microbial cell factories that can produce valuable biomaterials while being resistant to stresses imposed by current bioprocesses is rapidly growing. R. toruloides is an emerging host that presents desirable features for bioproduction, since it can grow in a wide range of substrates and tolerate a variety of toxic compounds. In order to explore R. toruloides suitability for application as a cell factory in biorefineries, we sought to understand the transcriptional responses of this yeast when growing under experimental settings that simulated those used in biofuels-related industries. Thus, we performed RNA sequencing of the oleaginous, carotenogenic yeast in different contexts. The first ones were stress-related: two conditions of high temperature (37 {degrees}C and 42 {degrees}C) and two ethanol concentrations (2% and 4%), while the other was using the inexpensive and abundant sugarcane juice as substrate. Using transcriptomic data, differential expression and functional analysis were implemented to select differentially expressed genes and enriched pathways from each set-up. A reproducible bioinformatics workflow was developed for mining new regulatory elements. We then predicted, for the first time in this yeast, binding motifs for several transcription factors, including HAC1, ARG80, RPN4, ADR1, and DAL81. Most of the putative transcription factors uncovered here were involved in stress responses and found in the yeast genome. Our method for motif discovery provides a new realm of possibilities in the study of gene regulatory networks, not only for the emerging host R. toruloides, but for other organisms of biotechnological importance.

bioinformatics↗

bioRxiv2021

ChiMera: An easy to use pipeline for Bacterial Genome Based Metabolic Network Reconstruction, Evaluation and Visualization

Several genome scale metabolic reconstruction tools have been developed in the last decades. They have helped to construct many metabolic models, which have contributed to a variety of fields, e.g., genetic engineering, drug discovery, prediction of phenotypes, and other model-driven discoveries. However, the use of these programs requires a higher level of bioinformatic skills, and most of them are not scalable for multiple genomes. Moreover, the functionalities required to build models are generally scattered through multiple tools, requiring knowledge of their utilization. Here, we present ChiMera, which combines the most efficient tools in model reconstruction, prediction, and visualization. ChiMera uses CarveMe top-down approach based on genomic evidence to prune a global model with a high level of curation, generating a draft genome able to produce growth predictions using flux balance analysis for gram-positive and gram-negative bacteria. ChiMera also contains two modules of visualization implemented, predefined and universal. The first generates maps for the most important pathways, e.g., core-metabolism, fatty acid oxidation and biosynthesis, nucleotides and amino acids biosynthesis, glycolysis, and others. The second module produces a genome-wide metabolic map, which can be used to harvest KEGG pathway information for each compound in the model. A module of gene essentiality and knockout is also present. Overall, ChiMera combines model creation, gap-filling, FBA and metabolic visualization to create a simulation ready genome-scale model, helping genetic engineering projects, prediction of phenotypes, and other model-driven discoveries in a friendly manner.

bioinformatics↗

bioRxiv2021

Nanopore sequencing provides rapid and reliable insight into microbial profiles of Intensive Care Units

Fast and accurate identification of pathogens is an essential task in healthcare settings. Next generation sequencing platforms such as Illumina have greatly expanded the capacity with which different organisms can be detected in hospital samples, and third-generation nanopore-driven sequencing devices such as Oxford Nanopores minION have recently emerged as ideal sequencing platforms for routine healthcare surveillance due to their long-read capacity and high portability. Despite its great potential, protocols and analysis pipelines for nanopore sequencing are still being extensively validated. In this work, we assess the ability of nanopore sequencing to provide reliable community profiles based on 16S rRNA sequencing in comparison to traditional Illumina platforms using samples collected from Intensive Care Units from a hospital in Brazil. While our results point that lower throughputs may be a shortcoming of the method in more complex samples, we show that the use of single-use Flongle flowcells in nanopore sequencing runs can provide insightful information on the community composition in healthcare settings.

microbiology↗

bioRxiv2021

Chromatin profiling reveals genome stability heterogeneity in clinical isolates of the human pathogen Aspergillus fumigatus

Invasive Pulmonary aspergillosis is a life-threatening infection in immunosuppressed patients caused by the filamentous fungus Aspergillus fumigatus. Chromatin structure regulation is important for genome stability maintenance and has the potential to lead to genome rearrangements driving differences in virulence and pathogenesis of different A. fumigatus isolates. Here, we compared the chromatin activities of the most investigated clinical isolates Af293 and CEA17 and uncovered striking differences in the number, locations and expression of transposable elements. We found evidence for higher genome instability in Af293 as compared to CEA17 and identified a spontaneous Af293 variant that exhibits gross chromosomal alterations including the loss of a 320 kb long segment in chromosome VIII and the amplification of a biosynthetic gene cluster. As a consequence of these re-arrangements, the variant shows increased secondary metabolites production, growth and virulence. Our work emphasizes genome stability heterogeneity as an evolutionary driver of A. fumigatus fitness and virulence.

molecular biology↗

bioRxiv2021

PredicTF: a tool to predict bacterial transcription factors in complex microbial communities.

Transcription Factors (TFs) are proteins that control the flow of genetic information by regulating cellular gene expression. Here we describe PredicTF, a first platform supporting the prediction and classification of novel bacterial TF in complex microbial communities. We evaluated PredicTF using a two-step approach. First, we tested PredictTFs ability to predict TFs for the genome of an environmental isolate. In the second evaluation step, PredicTF was used to predict TFs in a metagenome and 11 metatranscriptomes recovered from a community performing anaerobic ammonium oxidation (anammox) in a bioreactor. PredicTF is open source pipeline available at https://github.com/mdsufz/PredicTF.

bioinformatics↗

bioRxiv2020

Standardization of inducer-activated broad host range expression modules: Debugging and refactoring an alkane-responsive AlkS/PalkB device

Although inducible heterologous expression systems have been available since the birth of recombinant DNA technology, the diversity of devices and genetic architectures of the corresponding vectors have often resulted in a lack of reproducibility and interoperability. In an effort to increase predictability of expression of genes of interest in a variety of possible bacterial hosts we propose a composition standard for debugging and reassembling all regulatory parts that participate in the performance of such devices. As a case study we address the n-octane and dicyclopropyl ketone (DCPK)-inducible PalkB promoter of the alkane biodegradation pOCT plasmid of Pseudomonas putida. The standardized expression module consisted of an edited alkS regulatory gene that is divergently expressed and separated of PalkB by a synthetic DNA buffer sequence. The native DNA sequence of the structural alkS gene was modified to alleviate the catabolite repression exerted by some carbon and nitrogen sources through the Crc/Hfq complex of some hosts. The PalkB promoter along with the alkS variants were then formatted as SEVA (Standard European Vector Architecture) cargoes and their activity parameters in P. putida determined with GFP and luminiscent reporters. The thereby refactored system showed improvements in various features desirable in conditional expression modules: inducibility, capacity, noise reduction and on/off ratio. When applied to other promoter/regulator pairs, the compositional standard thereby implemented in the AlkS/PalkB module will enable more complex genetic programming in non-model bacteria.

synthetic biology↗

bioRxiv2020

Combining functional and structural genomics to track antibiotic resistance genes in mobile elements in clinical bacterial strains

The rise of multi-antibiotics resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in bacteria of several species isolated from an intensive care unit in Brazil. We used whole-genome analysis to identify antibiotic resistance genes (ARGs) and plasmids in 35 strains of Gram-negative and Gram-positive bacteria, including the first genomic description of Morganella morganii and Ralstonia mannitolilytica clinical isolates from South America. We identify a high abundance of beta-lactamase genes in highly resistant organisms, including seven extended-spectrum {beta}-lactamases shared between organisms from different species. Additionally, we identify several ARGs-carrying plasmids indicating the potential for fast transmission of resistance mechanism between bacterial strains, comprising a novel IncFII plasmid recently introduced in Brazil from Asia. Through comparative genomic analysis, we demonstrate that some pathogens identified here are very distantly related to other bacteria isolated worldwide, demonstrating the potential existence of endemic bacterial pathogens in Brazil. Also, we uncovered at least two couples of (near)-identical plasmids exhibiting multi-drug resistance, suggesting that plasmids were transmitted between bacteria of the same or different species in the hospital studied. Finally, since many highly resistant strains carry several different ARGs, we used functional genomics to investigate which of them were indeed functional. In this sense, for three bacterial strains (Escherichia coli, Klebsiella pneumoniae, and M. morganii), we identify six beta-lactamase genes out of 15 predicted in silico as the main responsible for the resistance mechanisms observed, corroborating the existence of redundant resistance mechanisms in these organisms. ImportanceBig data and large-scale sequencing projects have revolutionized the field, achieving a greater understanding of ARGs identification and spreading at global level. However, given that microbiota and associated ARGs may fluctuate across geographic zones, hospital-associated infections within clinical units still remain underexplored in Brazil - the largest country in South America; 210 million inhabitants - and neighboring countries. This work highlighted the identification of several ARGs shared between species co-occurring simultaneously into a Brazilian hospital, some of them associated with large plasmids, mostly endowed with transposable elements. Also, genomic features of clinically underrepresented pathogens such M. morganii and B. cepacia were revealed. Taken together, our results demonstrate how structural and functional genomics can help to identify emerging mechanisms of shared antibiotic resistance in bacteria from clinical environments. Systematic studies as the one presented here should help to prevent outbreaks of novel multidrug resistance bacteria in healthcare facilities.

microbiology↗

bioRxiv2020

Benchmarking available bacterial promoter prediction tools: potentialities and limitations

BackgroundThe promoter region is a key element required for the production of RNA in bacteria. While new high-throughput technology allows massive mapping of promoter elements, we still mainly relay on bioinformatic tools to predict such elements in bacterial genomes. Additionally, despite many different prediction tools have become popular to identify bacterial promoters, there is no systematic comparison of such tools. ResultsHere, we performed a systematic comparison between several widely used promoter prediction tools (BPROM, bTSSfinder, BacPP, CNNProm, IBBP, Virtual Footprint, IPro70-FMWin, 70ProPred, iPromoter-2L and MULTiPly) using well-defined sequence data sets and standardized metrics to determine how well those tools performed related to each other. For this, we used datasets of experimentally validated promoters from Escherichia coli and a control dataset composed by randomly generated sequences with similar nucleotide distributions. We compared the performance of the tools using metrics such as specificity, sensibility, accuracy and Matthews Correlation Coefficient (MCC). We show that the widely used BPROM presented the worse performance among compared tools, while four tools (CNNProm, IPro70-FMWin, 70ProPreda and iPromoter-2L) offered high predictive power. From these, iPro70-FMWin exhibited the best results for most of the metrics used. ConclusionsTherefore, we exploit here some potentials and limitations of available tools and hope future works can be built upon our effort to systematically characterize such quite useful class of bioinformatics tools.

bioinformatics↗

bioRxiv2020

Turning the screw: engineering extreme pH resistance in Escherichia coli through combinatorial synthetic operons

Adoption of microorganisms as platforms for sustainable biobased production requires host cells to be able to withstand harsh industrial conditions, which are usually far from the ones where these organisms are naturally adapted to thrive. However, novel survival mechanisms unearthed by the study of microbiomes from extreme habitats may be exploited to enhance microbial robustness under the strict conditions needed for different applications. In this work, synthetic biology approaches were used to engineer enhanced acidic tolerance in Escherichia coli under extreme conditions through the characterization of a library of twenty-seven unique operons composed of combinatorial assemblies of three novel genes from an extreme environment and three synthetic ribosome binding sites. The results here presented illustrate the efficacy of combining different metagenomic genes for tolerance in truly synthetic genetic operons, as expression of these gene clusters increased hundred-fold the survival percentage of cells exposed to an acidic shock in minimal media at pH 1.9 under aerobic conditions.

synthetic biology↗

bioRxiv2020

Functional characterization of clinical isolates of the opportunistic fungal pathogen Aspergillus nidulans

Aspergillus nidulans is an opportunistic fungal pathogen in patients with immunodeficiency and virulence of A. nidulans isolates has mainly been studied in the context of the chronic granulomatous disease (CGD), with characterization of clinical isolates obtained from non-CGD patients remaining elusive. This study therefore carried out a detailed biological characterization of two A. nidulans clinical isolates (CIs), obtained from a patient with breast carcinoma and pneumonia and from a patient with cystic fibrosis that underwent lung transplantation, and compared them to the reference, non-clinical A4 strain. Both CIs presented increased growth in comparison to the reference strain in the presence of physiologically-relevant carbon sources. Metabolomic analyses showed that the three strains are metabolically very different from each other in these carbon sources. Furthermore, the CIs were highly susceptible to cell wall perturbing agents but not to other physiologically-relevant stresses. Genome analyses identified several frame-shift variants in genes encoding cell wall integrity (CWI) signalling components. Significant differences in CWI signalling were confirmed by western blotting among the three strains. In vivo virulence studies using several different models revealed that strain MO80069 had significantly higher virulence in hosts with impaired neutrophil function when compared to the other strains. In summary, this study presents detailed biological characterization of two A. nidulans sensu stricto clinical isolates. Just like in A. fumigatus, strain heterogeneity exists in A. nidulans clinical strains that can define virulence traits. Further studies are required to fully characterize A. nidulans strain-specific virulence traits and pathogenicity. ImportanceImmunocompromised patients are susceptible to infections with opportunistic filamentous fungi from the genus Aspergillus. Although A. fumigatus is the main etiological agent of Aspergillus spp.-related infections, other species, such as A. nidulans are prevalent in a condition-specific manner. A. nidulans is a predominant infective agent in patients suffering from chronic granulomatous disease (CGD). A. nidulans isolates have mainly been studied in the context of CGD, although infection with A. nidulans also occurs in non-CGD patients. This study carried out a detailed biological characterization of two non-CGD A. nidulans clinical isolates and compared it to a reference strain. Phenotypic, metabolomic and genomic analyses highlight fundamental differences in carbon source utilization, stress responses and maintenance of cell wall integrity among the strains. One clinical strain had increased virulence in models with impaired neutrophil function. Just as in A. fumigatus, strain heterogeneity exists in A. nidulans clinical strains that can define virulence traits.

microbiology↗

bioRxiv2019

Microbial communities profiling in intensive care units expose limitations in current sanitary standards

Hospital-associated infections (HAIs) are the leading cause of morbidity and mortality in intensive care units (ICUs) and neonatal intensive care units (NICUs). Organisms causing these infections are often present on surfaces around the patient. Given that microbiotas may vary across different ICUs, the HAI-related microbial signatures within these units remain underexplored. In this study, we use deep-sequencing analyses to explore and compare the structure of bacterial communities at inanimate surfaces of the ICU and NICU wards of The Medical School Clinics Hospital (Brazil). The data revealed that NICU presents higher biodiversity than ICU and surfaces closest to the patient showed a peculiar microbiota, distinguishing one unit from the other. Several facultative anaerobes or obligate anaerobes HAI-related genera were classified as biomarkers for the NICU, whereas Pseudomonas was the main biomarker for ICU. Correlation analyses revealed a distinct pattern of microbe-microbe interactions for each unit, including bacteria able to form multi-genera biofilms. Furthermore, we evaluated the effect of concurrent cleaning over the ICU bacterial community. The results showed that, although some bacterial populations decreased after cleaning, various HAI-related genera were quite stable to sanitization, suggesting being well-adapted to the ICU environment. Overall, these results enabled identification of discrete ICU and NICU reservoirs of potentially pathogenic bacteria and provided evidence for the presence of a set of biomarkers that distinguish these units. Moreover, the study exposed the inconsistencies of the routine cleaning to minimize HAI-related genera contamination.\n\nIMPORTANCEDue to the high impact of HAIs, there is an urgent need for the development of robust policies on microbial surveillance to help guide procedures, improving infection control. To the best of our knowledge, this is the first comprehensive study, using a high-throughput approach, focused on comparing the microbiota peculiarities of the ICU and NICU in one of the largest public hospitals in Brazil. The work highlighted bacteria associated with nosocomial infections, identifying the most potent reservoirs of contamination, and evaluated the microbiota changes related to the cleaning procedure. Therefore, this study contributes to increase the knowledge about (N)ICUs microbiomes and may help to reduce health-care-associated infections, especially in developing countries.

microbiology↗

bioRxiv2019

CRZ1 regulator and calcium cooperatively modulate holocellulases gene expression in Trichoderma reesei QM6a

BackgroundTrichoderma reesei is the main filamentous fungus used in industry to produce cellulases. Over the last decades, there have been a strong increase in the understanding of the regulatory network controlling cellulase-coding gene expression in response to a number of inducers and environmental signals. In this sense, the role of calcium and the Calcineurin-responsive protein (CRZ1) has been investigated in industrially relevant strains of T. reesei RUT-C30, but this system has not been investigated in wild-type reference strain of this fungus.\n\nResultsHere, we investigated the role of CRZ1 and Ca2+ signaling in the fungus T. reesei QM6a. For this, we first searched for potential CRZ1 binding sites in promoter regions of key genes coding holocellulases, as well as transcriptional regulators and sugar and calcium transporters. Using a nearly constructed T. reesei {Delta}crzl strain, we demonstrated that most of the genes expected to be regulated by CRZ1 were affected in the mutant strain induced with sugarcane bagasse (SCB) and cellulose. In particular, our data demonstrate that Ca2+ acts synergistically with CRZ1 to modulate gene expression, but also exerts CRZ1-independent regulatory role in gene expression in T. reesei, suggesting the existence of additional Ca2+ sensing mechanisms in this fungus.\n\nConclusionsThis work presents new evidence on the regulatory role of CRZ1 and Ca2+ sensing in the regulation of cellulolytic enzymes in T. reesei, evidencing significant and previously unknown function of this Ca2+ sensing system in the control key transcriptional regulators (XYR1 and CRE1) and on the expression of genes related to sugar and Ca2+ transport. Taken together, the data obtained here provide new evidence on the regulatory network of T. reesei related to plant biomass deconstruction.

microbiology↗

bioRxiv2019

Modulating Fis and IHF binding specificity, crosstalk and regulatory logic through the engineering of complex promoters

Bacterial promoters are usually formed by multiple cis-regulatory elements recognized by a plethora of transcriptional factors (TFs). From those, global regulators are key elements since these TFs are responsible for the regulation of hundreds of genes in the bacterial genome. For instance, Fis and IHF are two global regulators which play a major role in gene expression control in Escherichia coli and usually multiple cis-regulatory elements for these proteins co-occur at target promoters. Here, we investigated the relationship between the architecture of the cis-regulatory elements for Fis and IHF in E. coli. For this, we constructed 42 synthetic promoter variants harboring consensus cis-elements for Fis and IHF at different distances from a core -35/-10 region and in different numbers and combinations. We first demonstrated that although Fis preferentially recognizes its consensus cis-element, it can also recognize, to some extent, the consensus binding site for IHF, and the same was true for IHF, which was also able of recognizing Fis binding sites. However, changing the arrangement of the cis-elements (i.e., the position or the number of sites) can completely abolish unspecific binding of both TFs. More remarkably, we demonstrate that combining cis-elements for both TFs could result in Fis and IHF repressed or activated promoters depending on the final architecture of the promoters in an unpredictable way. Taken together, the data presented here demonstrate how small changes in the architecture of bacterial promoters could result in drastic changes in the final regulatory logic of the system, with important implications for the understanding of natural complex promoters in bacteria and their engineering for novel applications.\n\nImportanceThe understanding of the regulatory complex in bacteria is a key issue in modern microbiology. Here, we constructed synthetic bacterial promoters in order to investigate how binding of transcriptional factors to multiple target sites at the promoters can influence gene expression. Our results demonstrate in a systematic way that the arrangement and number of these cis-regulatory elements are crucial for the final expression dynamics of the target promoters. In particular, we show that TF binding specificity or promiscuity can be modulated using different promoter architectures based on consensus cis-regulatory elements, and that transcriptional repression and activation can also be affected by promoter architecture. These results are relevant both for the understanding of natural systems and for the construction of synthetic circuits for biotechnological applications.

synthetic biology↗

bioRxiv2019

A toolset of constitutive promoters for metabolic engineering of Rhodosporidium toruloides

BackgroundRhodosporidium toruloides is a promising host for the production of bioproducts from lignocellulosic biomass. A key prerequisite for efficient pathway engineering is the availability of robust genetic tools and resources. However, there is a lack of characterized promoters to drive expression of heterologous genes for strain engineering in R. toruloides.\n\nResultsOur data describes a set of native R. toruloides promoters, characterized over time in four different media commonly used for cultivation of this yeast. The promoter sequences were selected using transcriptional analysis and several of them were found to drive expression bidirectionally. We measured promoter expression strength by flow cytometry using a dual fluorescent reporter system. From these analyses, we found a total of 20 constitutive promoters (12 monodirectional and 8 bidirectional) of potential value for genetic engineering of R. toruloides.\n\nConclusionsWe present a list of robust and constitutive, native promoters to facilitate genetic engineering of R. toruloides. This set of thoroughly characterized promoters significantly expands the range of engineering tools available for this yeast and can be applied in future metabolic engineering studies.

synthetic biology↗

bioRxiv2018

Expanding the toolbox of broad host-range transcriptional terminators for Proteobacteria through metagenomics

As the field of synthetic biology moves towards the utilization of novel bacterial chassis, there is a growing need for biological parts with enhanced performance in a wide number of hosts. Is not unusual that biological parts (such as promoters and terminators), initially characterized in the model bacteria Escherichia coli, do not perform well when implemented in alternative hosts, such as Pseudomonas, therefore limiting the construction of synthetic circuits in industrially relevant bacteria. In order to address this limitation, we present here the mining of transcriptional terminators through functional metagenomics to identify novel parts with broad host-range activity. Using a GFP-based terminator trap strategy and a broad host-range plasmid, we identified 20 clones with potential terminator activity in Pseudomonas putida. Further characterization allowed the identification of 4 unique sequences between 58 bp and 181 bp long that efficiently terminates transcription in P. putida, E. coli, Burkholderia phymatum and two Pseudomonas strains isolated from Antarctica. Therefore, this work presents a new set of biological parts useful for the engineering of synthetic circuits in Proteobacteria.

synthetic biology↗

bioRxiv2018

TFound: A Software to Map Cis-Regulatory Elements in Yeast

Transcription factors (TFs) are responsible for regulating the rate of transcription of genes in all organisms. These factors can be represented computationally by position weight matrices (PWM). TFound was developed to allow the detailed visualization of predicted binding sites of transcription factors in multiple sequences based on the PWMs, by using the graphic user interface (GUI). The tool was loaded with the genome of Saccharomyces cerevisiae and PWMs from the YeTFaSCo database (http://yetfasco.ccbr.utoronto.ca/), also allowing the insertion of new sequences and PWMs. Thus, the user is allowed to load custom PWMs and genomes to perform easily mining and visualization of binding site motifs of cis-regulatory elements of interest, permitting an efficient way to inspect DNA assembly projects for complex synthetic circuits. This work describes the functionality of the current version of the tool, which is coded in Python and is freely available at the repository https://github.com/adri4nogomes/TFound.

synthetic biology↗