Protein Citrullination by Peptidyl Arginine Deiminase/Arginine Deiminase Homologs in Members of the Human Microbiota and Its Recognition by Anti-Citrullinated Protein Antibodies.

The human microbiome exists throughout the body, and it is essential for maintaining various physiological processes, including immunity, and dysbiotic events, which are associated with autoimmunity. Peptidylarginine deiminase (PAD) enzymes can citrullinate self-proteins related to rheumatoid arthritis (RA) that induce the production of anti-citrullinated protein antibodies (ACPAs) and lead to inflammation and joint damage. The present investigation was carried out to demonstrate the expression of homologs of PADs or arginine deiminases (ADs) and citrullinated proteins in members of the human microbiota. To achieve the objective, we used 17 microbial strains and specific polyclonal antibodies (pAbs) of the synthetic peptide derived from residues 100-200 of human PAD2 (anti-PAD2 pAb), and the recombinant fragment of amino acids 326 and 611 of human PAD4 (anti-PAD4 pAb), a human anti-citrulline pAb, and affinity ACPAs of an RA patient. Western blot (WB), enzyme-linked immunosorbent assay (ELISA), elution, and a test with Griess reagent were used. This is a cross-sectional case-control study on patients diagnosed with RA and control subjects. Inferential statistics were applied using the non-parametric Kruskal-Wallis test and Mann-Whitney U test generated in the SPSS program. Some members of phyla Firmicutes and Proteobacteria harbor homologs of PADs/ADs and citrullinated antigens that are reactive to the ACPAs of RA patients. Microbial citrullinome and homolog enzymes of PADs/ADs are extensive in the human microbiome and are involved in the production of ACPAs. Our findings suggest a molecular link between microorganisms of a dysbiotic microbiota and RA pathogenesis.

Transcriptional condensates: a blessing or a curse for gene regulation?

Whether phase-separation is involved in the organization of the transcriptional machinery and if it aids or inhibits the transcriptional process is a matter of intense debate. In this Mini Review, we will cover the current knowledge regarding the role of transcriptional condensates on gene expression regulation. We will summarize the latest discoveries on the relationship between condensate formation, genome organization, and transcriptional activity, focusing on the strengths and weaknesses of the experimental approaches used to interrogate these aspects of transcription in living cells. Finally, we will discuss the challenges for future research.

Multiple horizontal gene transfer events have shaped plant glycosyl hydrolase diversity and function.

Plant glycosyl hydrolases (GHs) play a crucial role in selectively breaking down carbohydrates and glycoconjugates during various cellular processes, such as reserve mobilization, pathogen defense, and modification/disassembly of the cell wall. In this study, we examined the distribution of GH genes in the Archaeplastida supergroup, which encompasses red algae, glaucophytes, and green plants. We identified that the GH repertoire expanded from a few tens of genes in early archaeplastidians to over 400 genes in modern angiosperms, spanning 40 GH families in land plants. Our findings reveal that major evolutionary transitions were accompanied by significant changes in the GH repertoire. Specifically, we identified at least 23 GH families acquired by green plants through multiple horizontal gene transfer events, primarily from bacteria and fungi. We found a significant shift in the subcellular localization of GH activity during green plant evolution, with a marked increase in extracellular-targeted GH proteins associated with the diversification of plant cell wall polysaccharides and defense mechanisms against pathogens. In conclusion, our study sheds light on the macroevolutionary processes that have shaped the GH repertoire in plants, highlighting the acquisition of GH families through horizontal transfer and the role of GHs in plant adaptation and defense mechanisms.

Overcoming class imbalance in drug discovery problems: Graph neural networks and balancing approaches.

This research investigates the application of Graph Neural Networks (GNNs) to enhance the cost-effectiveness of drug development, addressing the limitations of cost and time. Class imbalances within classification datasets, such as the discrepancy between active and inactive compounds, give rise to difficulties that can be resolved through strategies like oversampling, undersampling, and manipulation of the loss function. A comparison is conducted between three distinct datasets using three different GNN architectures. This benchmarking research can steer future investigations and enhance the efficacy of GNNs in drug discovery and design. Three hundred models for each combination of architecture and dataset were trained using hyperparameter tuning techniques and evaluated using a range of metrics. Notably, the oversampling technique outperforms eight experiments, showcasing its potential. While balancing techniques boost imbalanced dataset models, their efficacy depends on dataset specifics and problem type. Although oversampling aids molecular graph datasets, more research is needed to optimize its usage and explore other class imbalance solutions.

The use of artificial intelligence tools in cancer detection compared to the traditional diagnostic imaging methods: An overview of the systematic reviews.

BACKGROUND AND PURPOSE: In comparison to conventional medical imaging diagnostic modalities, the aim of this overview article is to analyze the accuracy of the application of Artificial Intelligence (AI) techniques in the identification and diagnosis of malignant tumors in adult patients. DATA SOURCES: The acronym PIRDs was used and a comprehensive literature search was conducted on PubMed, Cochrane, Scopus, Web of Science, LILACS, Embase, Scielo, EBSCOhost, and grey literature through Proquest, Google Scholar, and JSTOR for systematic reviews of AI as a diagnostic model and/or detection tool for any cancer type in adult patients, compared to the traditional diagnostic radiographic imaging model. There were no limits on publishing status, publication time, or language. For study selection and risk of bias evaluation, pairs of reviewers worked separately. RESULTS: In total, 382 records were retrieved in the databases, 364 after removing duplicates, 32 satisfied the full-text reading criterion, and 09 papers were considered for qualitative synthesis. Although there was heterogeneity in terms of methodological aspects, patient differences, and techniques used, the studies found that several AI approaches are promising in terms of specificity, sensitivity, and diagnostic accuracy in the detection and diagnosis of malignant tumors. When compared to other machine learning algorithms, the Super Vector Machine method performed better in cancer detection and diagnosis. Computer-assisted detection (CAD) has shown promising in terms of aiding cancer detection, when compared to the traditional method of diagnosis. CONCLUSIONS: The detection and diagnosis of malignant tumors with the help of AI seems to be feasible and accurate with the use of different technologies, such as CAD systems, deep and machine learning algorithms and radiomic analysis when compared with the traditional model, although these technologies are not capable of to replace the professional radiologist in the analysis of medical images. Although there are limitations regarding the generalization for all types of cancer, these AI tools might aid professionals, serving as an auxiliary and teaching tool, especially for less trained professionals. Therefore, further longitudinal studies with a longer follow-up duration are required for a better understanding of the clinical application of these artificial intelligence systems. TRIAL REGISTRATION: Systematic review registration. Prospero registration number: CRD42022307403.

Engineering the catalytic activity of an Antarctic PET-degrading enzyme by loop exchange.

Several hydrolases have been described to degrade polyethylene terephthalate (PET) at moderate temperatures ranging from 25°C to 40°C. These mesophilic PET hydrolases (PETases) are less efficient in degrading this plastic polymer than their thermophilic homologs and have, therefore, been the subject of many protein engineering campaigns. However, enhancing their enzymatic activity through rational design or directed evolution poses a formidable challenge due to the need for exploring a large number of mutations. Additionally, evaluating the improvements in both activity and stability requires screening numerous variants, either individually or using high-throughput screening methods. Here, we utilize instead the design of chimeras as a protein engineering strategy to increase the activity and stability of Mors1, an Antarctic PETase active at 25°C. First, we obtained the crystal structure of Mors1 at 1.6 Å resolution, which we used as a scaffold for structure- and sequence-based chimeric design. Then, we designed a Mors1 chimera via loop exchange of a highly divergent active site loop from the thermophilic leaf-branch compost cutinase (LCC) into the equivalent region in Mors1. After restitution of an active site disulfide bond into this chimera, the enzyme exhibited a shift in optimal temperature for activity to 45°C and an increase in fivefold in PET hydrolysis when compared with wild-type Mors1 at 25°C. Our results serve as a proof of concept of the utility of chimeric design to further improve the activity and stability of PETases active at moderate temperatures.

Characterization of avian pathogenic Escherichia coli isolates based on biofilm formation, ESBL production, virulence-associated genes, and phylogenetic groups.

Escherichia coli is a part of both animal and human commensal microbiota. Avian pathogenic E. coli (APEC) is responsible for colibacillosis in poultry, an economically important disease. However, the close similarities among APEC isolates make it difficult to differentiate between pathogenic and commensal bacteria. The aim of this study was to determine phenotypic and molecular characteristics of APEC isolates and to compare them with their in vivo pathogenicity indices. A total of 198 APEC isolates were evaluated for their biofilm-producing ability and extended-spectrum ß-lactamase (ESBL) production phenotypes. In addition, 36 virulence-associated genes were detected, and the isolates were classified into seven phylogenetic groups using polymerase chain reaction. The sources of the isolates were not associated with biofilms, ESBL, genes, or phylogroups. Biofilm and ESBL production were not associated with pathogenicity. Group B2 had the highest pathogenicity index. Groups B2 and E were positively associated with high-pathogenicity isolates and negatively associated with low-pathogenicity isolates. In contrast, groups A and C were positively associated with apathogenic isolates, and group B1 was positively associated with low-pathogenicity isolates. Some virulence-associated genes showed positive or negative associations with specific phylogenetic groups. None of the individual techniques produced results that correlated with the in vivo pathogenicity index. However, the combination of two techniques, namely, detection of virulence-associated genes and the phylogenetic groups, could help the classification of the isolates as pathogenic or commensal.

Crosstalk between Gut Microbiota and Epigenetic Markers in Obesity Development: Relationship between Ruminococcus, BMI, and MACROD2/SEL1L2 Methylation.

Changes in gut microbiota composition and in epigenetic mechanisms have been proposed to play important roles in energy homeostasis, and the onset and development of obesity. However, the crosstalk between epigenetic markers and the gut microbiome in obesity remains unclear. The main objective of this study was to establish a link between the gut microbiota and DNA methylation patterns in subjects with obesity by identifying differentially methylated DNA regions (DMRs) that could be potentially regulated by the gut microbiota. DNA methylation and bacterial DNA sequencing analysis were performed on 342 subjects with a BMI between 18 and 40 kg/m2. DNA methylation analyses identified a total of 2648 DMRs associated with BMI, while ten bacterial genera were associated with BMI. Interestingly, only the abundance of Ruminococcus was associated with one BMI-related DMR, which is located between the MACROD2/SEL1L2 genes. The Ruminococcus abundance negatively correlated with BMI, while the hypermethylated DMR was associated with reduced MACROD2 protein levels in serum. Additionally, the mediation test showed that 19% of the effect of Ruminococcus abundance on BMI is mediated by the methylation of the MACROD2/SEL1L2 DMR. These findings support the hypothesis that a crosstalk between gut microbiota and epigenetic markers may be contributing to obesity development.

A Mouse Systems Genetics Approach Reveals Common and Uncommon Genetic Modifiers of Hepatic Lysosomal Enzyme Activities and Glycosphingolipids.

Identification of genetic modulators of lysosomal enzyme activities and glycosphingolipids (GSLs) may facilitate the development of therapeutics for diseases in which they participate, including Lysosomal Storage Disorders (LSDs). To this end, we used a systems genetics approach: we measured 11 hepatic lysosomal enzymes and many of their natural substrates (GSLs), followed by modifier gene mapping by GWAS and transcriptomics associations in a panel of inbred strains. Unexpectedly, most GSLs showed no association between their levels and the enzyme activity that catabolizes them. Genomic mapping identified 30 shared predicted modifier genes between the enzymes and GSLs, which are clustered in three pathways and are associated with other diseases. Surprisingly, they are regulated by ten common transcription factors, and their majority by miRNA-340p. In conclusion, we have identified novel regulators of GSL metabolism, which may serve as therapeutic targets for LSDs and may suggest the involvement of GSL metabolism in other pathologies.

Occurrence of ESBL-producing avian pathogenic Escherichia coli (APEC) isolates in spiced chicken meat in Goias, Brazil.

Some extraintestinal pathogenic Escherichia coli isolates (ExPEC), obtained from humans and chickens avian pathogenic E. coli (APEC), share similar virulence genes. Thus, products of avian origin can be a source of human infection. Moreover, these APEC isolates are resistant to antimicrobials and can spread in the environment through the chicken feces. Although the development of multidrug-resistant (MDR) microorganisms in poultry is on the rise, healthcare entities have raised concerns since MDRs can horizontally transfer resistance genes to other microorganisms and complicate the management of human infections by MDR APEC. The results of our study showed that of 80 investigated spiced chicken meat samples, 55% were contaminated with E. coli, of which 34% (15/44) contaminate with APEC. No diarrheagenic E. coli (DEC) pathotypes were found. Twenty-six isolates were MDR E. coli. Among the APEC isolates, 87% (13/15) produced extended-spectrum beta-lactamase (ESBL). The emergence of MDR/ESBL-producing APEC with zoonotic potential for humans is extremely worrying. Therefore, further studies are required to identify the prevalence of MDR/ESBL-producing APEC in the entire chicken production chain from creation, slaughter, processing, and butchery.

Aging reduces ABHD5 protein content in the adipose tissue of mice: The reversal effect of exercise.

Dysfunction of the adipose tissue metabolism is considered as a significant hallmark of aging. It has been proposed that α-ß hydrolase domain containing 5 (ABHD5) plays a critical role in the control of lipolysis. However, the role of ABHD5 in the control of lipolysis during aging or exercise is unknown. Here we combined the experimental mouse model with transcriptomic analyzes by using murine and human databases to explore the role of ABHD5 in the adipose tissue during aging and in response to exercise. Transcriptomic data revealed a downregulation of Abhd5 messenger RNA levels in the subcutaneous white adipose tissue (scWAT) over time in individuals from 20 to 69 years old. Aged mice displayed dramatic reduction of ABHD5 protein content and lipolytic-related proteins in the scWAT. Interestingly, 4 weeks of high-intensity interval training increased ABHD5 protein level and restored the lipolytic pathway in the scWAT of aged mice. Altogether, our findings demonstrated that aging affects ABHD5 content in the adipose tissue of mice and humans. Conversely, exercise increases ABHD5 activity, recovering the lipolytic activity in aged mice.

Novel fungal organophosphorus hydrolases in acidic media: an application to apples decontamination.

Organophosphorus pesticides bring significant improvements in agriculture, but their toxicity causes environmental and health negative impacts. The aim of this work was the development of robust biocatalysts to be applied in bioremediation. Four fungi were evaluated as hydrolase sources capable of degrading organophosphorus pesticides: Aspergillus niger, Fusarium sp., Penicillium chrysogenum, and Penicillium nalgiovense. The hydrolysis rates of methyl paraoxon obtained under acidic conditions were in the range of 10 to 21 mg L-1 d-1, which is remarkable since most similar biocatalysts are active under alkaline conditions. Penicillium chrysogenum activity was outstanding, and it was selected to prepare, characterize, and study the applications of its enzymatic extract. It was used to evaluate the bioremediation of apple surfaces at pH 2 in the presence of SDS, achieving complete methyl paraoxon degradation under proposed conditions. These results indicate that this biocatalyst could complement industrialized fruit washing processes for the elimination of organophosphorus pesticides.

The Giardial Arginine Deiminase Participates in Giardia-Host Immunomodulation in a Structure-Dependent Fashion via Toll-like Receptors.

Beyond the problem in public health that protist-generated diseases represent, understanding the variety of mechanisms used by these parasites to interact with the human immune system is of biological and medical relevance. Giardia lamblia is an early divergent eukaryotic microorganism showing remarkable pathogenic strategies for evading the immune system of vertebrates. Among various multifunctional proteins in Giardia, arginine deiminase is considered an enzyme that plays multiple regulatory roles during the life cycle of this parasite. One of its most important roles is the crosstalk between the parasite and host. Such a molecular "chat" is mediated in human cells by membrane receptors called Toll-like receptors (TLRs). Here, we studied the importance of the 3D structure of giardial arginine deiminase (GlADI) to immunomodulate the human immune response through TLRs. We demonstrated the direct effect of GlADI on human TLR signaling. We predicted its mode of interaction with TLRs two and four by using the AlphaFold-predicted structure of GlADI and molecular docking. Furthermore, we showed that the immunomodulatory capacity of this virulent factor of Giardia depends on the maintenance of its 3D structure. Finally, we also showed the influence of this enzyme to exert specific responses on infant-like dendritic cells.

RLPredictiOme, a Machine Learning-Derived Method for High-Throughput Prediction of Plant Receptor-like Proteins, Reveals Novel Classes of Transmembrane Receptors.

Cell surface receptors play essential roles in perceiving and processing external and internal signals at the cell surface of plants and animals. The receptor-like protein kinases (RLK) and receptor-like proteins (RLPs), two major classes of proteins with membrane receptor configuration, play a crucial role in plant development and disease defense. Although RLPs and RLKs share a similar single-pass transmembrane configuration, RLPs harbor short divergent C-terminal regions instead of the conserved kinase domain of RLKs. This RLP receptor structural design precludes sequence comparison algorithms from being used for high-throughput predictions of the RLP family in plant genomes, as has been extensively performed for RLK superfamily predictions. Here, we developed the RLPredictiOme, implemented with machine learning models in combination with Bayesian inference, capable of predicting RLP subfamilies in plant genomes. The ML models were simultaneously trained using six types of features, along with three stages to distinguish RLPs from non-RLPs (NRLPs), RLPs from RLKs, and classify new subfamilies of RLPs in plants. The ML models achieved high accuracy, precision, sensitivity, and specificity for predicting RLPs with relatively high probability ranging from 0.79 to 0.99. The prediction of the method was assessed with three datasets, two of which contained leucine-rich repeats (LRR)-RLPs from Arabidopsis and rice, and the last one consisted of the complete set of previously described Arabidopsis RLPs. In these validation tests, more than 90% of known RLPs were correctly predicted via RLPredictiOme. In addition to predicting previously characterized RLPs, RLPredictiOme uncovered new RLP subfamilies in the Arabidopsis genome. These include probable lipid transfer (PLT)-RLP, plastocyanin-like-RLP, ring finger-RLP, glycosyl-hydrolase-RLP, and glycerophosphoryldiester phosphodiesterase (GDPD, GDPDL)-RLP subfamilies, yet to be characterized. Compared to the only Arabidopsis GDPDL-RLK, molecular evolution studies confirmed that the ectodomain of GDPDL-RLPs might have undergone a purifying selection with a predominance of synonymous substitutions. Expression analyses revealed that predicted GDPGL-RLPs display a basal expression level and respond to developmental and biotic signals. The results of these biological assays indicate that these subfamily members have maintained functional domains during evolution and may play relevant roles in development and plant defense. Therefore, RLPredictiOme provides a framework for genome-wide surveys of the RLP superfamily as a foundation to rationalize functional studies of surface receptors and their relationships with different biological processes.

First characterization of PIWI-interacting RNA clusters in a cichlid fish with a B chromosome.

BACKGROUND: B chromosomes are extra elements found in several eukaryote species. Usually, they do not express a phenotype in the host. However, advances in bioinformatics over the last decades have allowed us to describe several genes and molecular functions related to B chromosomes. These advances enable investigations of the relationship between the B chromosome and the host to understand how this element has been preserved in genomes. However, considering that transposable elements (TEs) are highly abundant in this supernumerary chromosome, there is a lack of knowledge concerning the dynamics of TE control in B-carrying cells. Thus, the present study characterized PIWI-interacting RNA (piRNA) clusters and pathways responsible for silencing the mobilization of TEs in gonads of the cichlid fish Astatotilapia latifasciata carrying the B chromosome. RESULTS: Through small RNA-seq and genome assembly, we predicted and annotated piRNA clusters in the A. latifasciata genome for the first time. We observed that these clusters had biased expression related to sex and the presence of the B chromosome. Furthermore, three piRNA clusters, named curupira, were identified in the B chromosome. Two of them were expressed exclusively in gonads of samples with the B chromosome. The composition of these curupira sequences was derived from LTR, LINE, and DNA elements, representing old and recent transposition events in the A. latifasciata genome and the B chromosome. The presence of the B chromosome also affected the expression of piRNA pathway genes. The mitochondrial cardiolipin hydrolase-like (pld6) gene is present in the B chromosome, as previously reported, and an increase in its expression was detected in gonads with the B chromosome. CONCLUSIONS: Due to the high abundance of TEs in the B chromosome, it was possible to investigate the origin of piRNA from these jumping genes. We hypothesize that the B chromosome has evolved its own genomic guardians to prevent uncontrolled TE mobilization. Furthermore, we also detected an expression bias in the presence of the B chromosome over A. latifasciata piRNA clusters and pathway genes.

Metal Ions and Chemical Modification Reagents Inhibit the Enzymatic Activity of Lecithin-Dependent Hemolysin from Vibrio parahaemolyticus.

Lecithin-dependent thermolabile hemolysin (LDH) is a virulence factor excreted by Vibrio parahaemolyticus, a marine bacterium that causes important losses in shrimp farming. In this study, the function of LDH was investigated through its inhibition by metal ions (Mg2+, Ca2+, Mn2+, Co2+, Ni2+ and Cu2+) and chemical modification reagents: ß-mercaptoethanol (ßME), phenylmethylsulfonyl fluoride (PMSF) and diethyl pyrocarbonate (DEPC). LDH was expressed in the Escherichia coli strain BL-21, purified under denaturing conditions, and the enzymatic activity was evaluated. Cu2+, Ni2+, Co2+ and Ca2+ at 1 mmol/L inhibited the LDH esterase activity by 20−95%, while Mg2+ and Mn2+ slightly increased its activity. Additionally, PMSF and DEPC at 1 mmol/L inhibited the enzymatic activity by 40% and 80%, respectively. Dose-response analysis showed that DEPC was the best-evaluated inhibitor (IC50 = 0.082 mmol/L), followed by Cu2+ > Co2+ > Ni2+ and PMSF (IC50 = 0.146−1.5 mmol/L). Multiple sequence alignment of LDH of V. parahaemolyticus against other Vibrio species showed that LDH has well-conserved GDSL and SGNH motifs, characteristic of the hydrolase/esterase superfamily. Additionally, the homology model showed that the conserved catalytic triad His-Ser-Asp was in the LDH active site. Our results showed that the enzymatic activity of LDH from V. parahaemolyticus was modulated by metal ions and chemical modification, which could be related to the interaction with catalytic amino acid residues such as Ser153 and/or His 393.

Cold-adapted strains as plant growth-promoting bacteria on soybean seeds and biocontrol agents against Macrophomina phaseolina.

AIM: The aim was to characterize cold-adapted bacteria by testing their PGP features and antagonistic activity against Macrophomina phaseolina, both in vitro and coating soybean seeds (Glycine max [L.] Merr.). METHODS AND RESULTS: Burkholderia gladioli MB39, Serratia proteamaculans 136 and Serratia proteamaculans 137 were evaluated. In vitro tests showed that S. proteamaculans 136 and 137 produce siderophore and indole-acetic acid (IAA), solubilize phosphate and fix nitrogen. Additionally, B. gladioli MB39 and S. proteamaculans 137 showed hydrolase activity and potent antifungal effects. The biocontrol efficacy over soybean seeds was evaluated using in vitro and greenhouse methods by immersing seeds into each bacterial suspension. As a result, S. proteamaculans 136 has improved the performance in all the seed germination evaluated parameters. In addition, S. proteamaculans 137 and B. gladioli MB39 strongly inhibited M. phaseolina, reducing the infection index values to 10% and 0%, respectively. CONCLUSION: Serratia proteamaculans 136, 137 and Burkholderia gladioli MB39 showed plant growth promotion features and inhibition of Macrophomina phaseolina infection by producing different antifungal compounds. SIGNIFICANCE AND IMPACT OF THE STUDY: Our results reinforce the application of cold-adapted Serratia proteamaculans and Burkholderia gladioli bacterial strains as candidates for developing microbial formulation to promote plant growth and guarantee antifungal protection in soybean crops.

Genomic Characterization of Bacillus safensis Isolated from Mine Tailings in Peru and Evaluation of Its Cyanide-Degrading Enzyme CynD.

Understanding the biochemistry and metabolic pathways of cyanide degradation is necessary to improve the efficacy of cyanide bioremediation processes and industrial requirements. We have isolated and sequenced the genome of a cyanide-degrading Bacillus strain from water in contact with mine tailings from Lima, Peru. This strain was classified as Bacillus safensis based on 16S rRNA gene sequencing and core genome analyses and named B. safensis PER-URP-08. We searched for possible cyanide-degradation enzymes in the genome of this strain and identified a putative cyanide dihydratase (CynD) gene similar to a previously characterized CynD from Bacillus pumilus C1. Sequence analysis of CynD from B. safensis and B. pumilus allow us to identify C-terminal residues that differentiate both CynDs. We then cloned, expressed in Escherichia coli, and purified recombinant CynD from B. safensis PER-URP-08 (CynDPER-URP-08) and showed that in contrast to CynD from B. pumilus C1, this recombinant CynD remains active at up to pH 9. We also showed that oligomerization of CynDPER-URP-08 decreases as a function of increased pH. Finally, we demonstrated that transcripts of CynDPER-URP-08 in B. safensis PER-URP-08 are strongly induced in the presence of cyanide. Our results suggest that the use of B. safensis PER-URP-08 and CynDPER-URP-08 as potential tool for cyanide bioremediation warrants further investigation. IMPORTANCE Despite being of environmental concern around the world due to its toxicity, cyanide continues to be used in many important industrial processes. Thus, searching for cyanide bioremediation methods is a matter of societal concern and must be present on the political agenda of all governments. Here, we report the isolation, genome sequencing and characterization of cyanide degradation capacity of a bacterial strain isolated from an industrial mining site in Peru. We characterize a cyanide dehydratase (CynD) homolog from one of these bacteria, Bacillus safensis PER-URP-08.

Enzimas exógenas na dieta de leitões desmamados / Exogenous enzymes in the diet of weaned piglets

O desmame é caracterizado como o período mais crítico da produção de suínos devido à imaturidade digestiva e à baixa concentração de enzimas digestivas, como carboidrases, proteases e fitases, nas primeiras semanas do pós-desmame, o que ocasiona o baixo desempenho dos leitões. Neste caso, há a necessidade de suplementação exógena de enzimas que atuam na degradação de frações do alimento, aumentando o aproveitamento da dieta. A nutrição enzimática exógena tem sido considerada uma alternativa eficaz frente à baixa concentração de enzimas endógenas nas primeiras semanas após o desmame por contribuir para o aumento na digestibilidade das dietas sólidas e, deste modo, para um maior aproveitamento dos ingredientes. Na nutrição de suínos, as enzimas exógenas mais utilizadas são as carboidrases, as proteases e as fitases. Ademais, a utilização de blends enzimáticos também é considerada uma ótima alternativa, pois contribui para a inibição de fatores antinutricionais, os quais são responsáveis por indisponibilizar nutrientes necessários para o desenvolvimento e desempenho dos animais. Diante do exposto, o objetivo deste estudo foi apresentar as principais enzimas exógenas utilizadas na nutrição de leitões desmamados, bem como seus efeitos no desempenho animal.

Weaning is characterized as the most critical period in swine production due to digestive immaturity and low concentration of digestive enzymes, such as carbohydrases, proteases, and phytases, in the first weeks after weaning, which causes poor performance of piglets. In this case, there is the need for exogenous supplementation of enzymes that act on the degradation of food fractions, increasing diet utilization. Exogenous enzyme nutrition has been considered an effective alternative to the low concentration of endogenous enzymes in the first weeks after weaning, as it contributes to an increase in the digestibility of solid diets and, consequently, greater use of the ingredients. In swine nutrition, the most used exogenous enzymes are carbohydrases, proteases, and phytases. Furthermore, the use of enzymatic blends is also considered a great alternative, as they contribute to the inhibition of anti-nutritional factors, which are responsible for making nutrients necessary for the development and performance of animals unavailable. Therefore, this study aimed to present the main exogenous enzymes used in the nutrition of weaned piglets, as well as their effects on animal performance.

Antarctic Polyester Hydrolases Degrade Aliphatic and Aromatic Polyesters at Moderate Temperatures.

Polyethylene terephthalate (PET) is one of the most widely used synthetic plastics in the packaging industry, and consequently has become one of the main components of plastic waste found in the environment. However, several microorganisms have been described to encode enzymes that catalyze the depolymerization of PET. While most known PET hydrolases are thermophilic and require reaction temperatures between 60°C and 70°C for an efficient hydrolysis of PET, a partial hydrolysis of amorphous PET at lower temperatures by the polyester hydrolase IsPETase from the mesophilic bacterium Ideonella sakaiensis has also been reported. We show that polyester hydrolases from the Antarctic bacteria Moraxella sp. strain TA144 (Mors1) and Oleispira antarctica RB-8 (OaCut) were able to hydrolyze the aliphatic polyester polycaprolactone as well as the aromatic polyester PET at a reaction temperature of 25°C. Mors1 caused a weight loss of amorphous PET films and thus constitutes a PET-degrading psychrophilic enzyme. Comparative modeling of Mors1 showed that the amino acid composition of its active site resembled both thermophilic and mesophilic PET hydrolases. Lastly, bioinformatic analysis of Antarctic metagenomic samples demonstrated that members of the Moraxellaceae family carry candidate genes coding for further potential psychrophilic PET hydrolases. IMPORTANCE A myriad of consumer products contains polyethylene terephthalate (PET), a plastic that has accumulated as waste in the environment due to its long-term stability and poor waste management. One promising solution is the enzymatic biodegradation of PET, with most known enzymes only catalyzing this process at high temperatures. Here, we bioinformatically identified and biochemically characterized an enzyme from an Antarctic organism that degrades PET at 25°C with similar efficiency to the few PET-degrading enzymes active at moderate temperatures. Reasoning that Antarctica harbors other PET-degrading enzymes, we analyzed available data from Antarctic metagenomic samples and successfully identified other potential enzymes. Our findings contribute to increasing the repertoire of known PET-degrading enzymes that are currently being considered as biocatalysts for the biological recycling of plastic waste.