Co-Fermentation and Genomic Insights into Lactic Acid Bacteria for Enhanced Propionic Acid Production Using a Non-GMO Approach

Propionic acid (PA) is an important organic acid with applications in food preservation, feed additives, and bio-based chemical production. While industrial PA is mostly derived from petrochemical processes, sustainable microbial alternatives are gaining attention. In this study, we explored a co-fermentation strategy using lactic acid bacteria (LAB) with complementary metabolic capabilities to enhance PA biosynthesis via the 1,2-propanediol (PDO) pathway. Genome-based screening identified a metabolic division between strains capable of producing PDO (e.g., Carnobacterium maltaromaticum IBB3447) and those converting PDO to PA (e.g., Levilactobacillus brevis IBB3735). Notably, we discovered that C. maltaromaticum IBB3447 is capable of PDO 24 biosynthesis, a function previously undescribed in this species. Phenotypic assays confirmed glycerol metabolism and acid tolerance among strains. In co-culture fermentation trials, the highest PA concentration (6.87 mM) was achieved using simultaneous fermentation in a fructose–sorbitol–glucose (FRC-SOR-GLC) medium, accompanied by prior PDO accumulation (up to 13.13 mM). No single strain produced PA independently, confirming that metabolic cooperation is required. These findings reveal a novel LAB-based bioprocess for sustainable PA and PDO production, using cross-feeding interactions and the valorization of industrial waste streams. The study supports future optimization and scale-up for circular bioeconomy applications

Streptococcus anginosus orchestrates antibacterial potential of NETs facilitating survival of accompanying pathogens

Streptococcus anginosus is considered an emerging opportunistic pathogen causing life-threatening infections, including abscesses and empyema. Noticeably, clinical data revealed that S. anginosus also constitutes an important component of polymicrobial infections. Here, we showed for the first time that S. anginosus inactivates the antibacterial potential of neutrophil extracellular traps (NETs). The process is determined by a cell wall-anchored nuclease referred to as SanA, which high expression dominates in clinical strains isolated from severe infections. Nuclease activity protects S. anginosus against the antibacterial activity of NETs, supporting at the same time the survival of coexisting highly pathogenic species of Enterobacteriales. Obtained data suggest that SanA nuclease should be recognized as a critical S. anginosus virulence factor determining severe monospecies purulent infections but also shielding other pathogens promoting the development of polymicrobial infections

Multiple mechanisms of termination modulate the dynamics of RNAPI transcription

Transcription elongation is stochastic, driven by a Brownian ratchet, making it subject to changes in velocity. On the rDNA, multiple polymerases are linked by "torsional entrainment" generated by DNA rotation. We report that release of entrainment by co-transcriptional 3' end cleavage, is permissive for relative movement between polymerases, promoting pausing and backtracking. Subsequent termination (polymerase release) is facilitated by the 5' exonuclease Rat1 (Xrn2) and backtracked transcript cleavage by the RNA polymerase I (RNAPI) subunit Rpa12. These activities are reproduced in vitro. Short nascent transcripts close to the transcriptional start site, combined with nascent transcript folding energy, similarly facilitate RNAPI pausing. Nascent, backtracked transcripts at pause sites are terminated by forward and reverse "torpedoes": Rat1 and the exosome cofactor Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP), respectively. Topoisomerase 2 localizes adjacent to RNAPI pause sites, potentially allowing continued elongation by downstream polymerases. Mathematical modeling supported substantial premature termination. These basic insights into transcription in vivo will be relevant to many systems

The TRAPPC8/TRS85 subunit of the Arabidopsis TRAPPIII tethering complex regulates endoplasmic reticulum function and autophagy

Transport protein particle (TRAPP) tethering complexes are known for their function as Rab GTPase exchange factors. Two versions of the complex are considered functionally separate: TRAPPII, an activator of the Rab11 family (RabA in plants) GTPases that function in post-Golgi sorting, and TRAPPIII, activating Rab1 family (RabD in plants) members that regulate endoplasmic reticulum (ER)-to-Golgi trafficking and autophagy. In Arabidopsis (Arabidopsis ahaliana), the TRAPPIII complex has been identified and its subunit composition established, but little is known about its functions. Here, we found that binary subunit interactions of the plant TRAPPIII complex are analogous to those of metazoan TRAPPIII, with the 2 large subunits TRAPPC8 and TRAPPC11 linking the TRAPP core and the small C12 to C13 dimer. To gain insight into the functions of TRAPPIII in plants, we characterized 2 A. thaliana trappc8 mutants. These mutants display abnormalities in plant morphology, particularly in flower and seed development. They also exhibit autophagic defects, a constitutive ER stress response, and elevated levels of the ER lipid dolichol (Dol), which is an indispensable cofactor in protein glycosylation. These results indicate that plant TRAPPC8 is involved in multiple cellular trafficking events and suggest a link between ER stress responses and Dol levels

Exon 4 and intron 4 TP53 are both methylated in advanced‑stage ovarian carcinomas

Although intragenic CpG dinucleotides are conserved during evolution, they are also sensitive to methylation‑dependent mechanisms. Methylation status of the TP53 introns 1, 3 and 4 have been analysed in stage III ovarian carcinoma (OC). In the present study, the methylation of exon 4 (10 CpG pairs) was analysed in advanced‑stage OC to investigate TP53 methylation and compare exon and intron 4 methylation patterns. A total of 80 samples from patients with advanced‑stage OC and metastatic lesions were examined, along with 80 samples derived from healthy patients who had never been diagnosed with cancer. Methylation analysis of the human A2780 ovarian cancer cell line was also performed. Exon and intron 4 were methylated in OC, corresponding metastases and paired healthy tissue. The DNA from the human A2780 ovarian cancer cell line and the normal samples from healthy subjects was also methylated. The data indicate the existence of an intragenic mechanism of regulation of TP53 activity that involves demethylation/methylation processes. This mechanism provides the ability to alter the response from cell cycle arrest to apoptosis by manipulating only the expression of long or short p53 isoforms

Gene regulation in Bacteroides fragilis: adaptive control in a dynamic host environment

Bacteroides fragilis occupies a dynamic position within the human gut. Though it comprises a relatively minor fraction of the gut microbiota, it is disproportionately enriched at extraintestinal sites of infection. This ability to survive in contrasting host environments pivots on a regulatory framework that is both modular and highly plastic. Rather than deploying a suite of hierarchical global regulators, B. fragilis employs numerous operon-embedded transcriptional switches, including site-specific DNA inversions, phase-variable epigenetic systems, extracytoplasmic function sigma/ anti-sigma factor pairs, and hybrid two-component systems. These networks are further complemented by cis-regulatory elongation checkpoints and post-transcriptional control by small RNAs. This review explores the full spectrum of these regulatory mechanisms, highlighting how they facilitate niche adaptation, surface variation, immune evasion, and metabolic prioritization. It also explores intraspecies variation focusing on glycan metabolism, antibiotic resistance, and virulence. Additionally, it outlines recombination-driven regulation, alongside extracytoplasmic function sigma factor diversification, flexible promoter architecture, and elongation checkpoints, each contributing to the evolution of transcriptional control in B. fragilis. Finally, it outlines unanswered questions, including the largely unexplored sRNA regulon, the coordination of DNA inversions, elongation control, and phase-variable methylation, and proposes experimental strategies to investigate the integration of these regulatory systems during environmental transitions. Taken together, B. fragilis emerges as a model bacterium for studying decentralized gene regulation in complex microbial ecosystems, with implications for both microbial ecology and therapeutic targeting of the gut microbiota

SorCS2 Is Important for Astrocytic Function in Neurovascular Signaling

Introduction: The receptor SorCS2 is involved in the trafficking of membrane receptors and transporters. It has been implicated in brain disorders and has previously been reported to be indispensable for ionotropic glutamatergic neurotransmission in the hippocampus. Aim: We aimed to study the role of SorCS2 in the control of astrocyte-neuron communication, critical for neurovascular coupling. Methods: Brain slices from P8 and 2-month-old wild-type and SorCS2 knockout (Sorcs2−/−) mice were immunostained for SorCS2, GFAP, AQP4, IB4, and CD31. Neurovascular coupling was assessed in vivo using laser speckle contrast imaging and ex vivo in live brain slices loaded with calcium-sensitive dye. Bulk and cell surface fraction proteomics was analyzed on freshly isolated and cultured astrocytes, respectively, and validated with Western blot and qPCR. Results: SorCS2 was strongly expressed in astrocytes, primarily in their endfeet, of P8 mice; however, it was sparsely repre-sented in 2-month-old mice. Sorcs2−/− mice demonstrated reduced neurovascular coupling associated with a reduced astrocytic calcium response to neuronal excitation. No differences in vascularization or endothelium-dependent relaxation ex vivo between the 2-month-old groups were observed. Proteomics suggested changes in glutamatergic signaling and suppressed calcium sign-aling in Sorcs2−/− brains from both P8 and 2-month-old mice. The increased abundance of glutamate metabotropic receptor 3 in Sorcs2−/− astrocytes was validated by PCR and Western blot. In cultured Sorcs2−/− astrocytes, AQP4 abundance was increased in the bulk lysate but reduced in the cell surface fraction, suggesting impaired trafficking

A Comparison of the Response of the Human Intestinal Microbiota to Probiotic and Nutritional Interventions In Vitro and In Vivo—A Case Study

Background/Objectives: With increasing knowledge of the role of the microbiota in health and disease, the need for the reliable simulation of its behavior in response to various factors, such as diet and probiotic administration in in vitro conditions, has emerged. Although many studies utilize developed systems, data on how accurately these systems represent individual microbiota responses are scarce. Methods: In the present study, the Simulator of Human Intestinal Microbial Ecosystem (SHIME®) was exposed to experimental conditions mimicking the application of probiotics and dietary changes in the study participant. Next-generation 16S rRNA sequencing was used to reveal the structure of the microbial communities in the analyzed samples. Results: Analysis of 17 samples revealed that predominantly diet and, to a lesser extent, probiotics had a divergent effect on the microbiota’s fluctuations dependent on the culture environment. Despite this, results from both in vitro and in vivo conditions aligned well with previously published data on the expected impact of dietary changes on the intestinal microbial community. Conclusions: The anecdotal evidence presented in this study suggested that current in vitro technology enables the reproduction of some of the microbiota responses that are well known from in vivo research. However, further work is required to enable simulations of an individual microbiota

Metabolome analysis as a potential source of endometriosis biomarkers with the use of multiomics approach in its diagnosis

Endometriosis poses diagnostic challenges. This study aimed to analyze the metabolomic profiles of plasma and peritoneal fluid samples obtained from women with endometriosis compared to controls. Our multicenter study involved sample collection from women undergoing laparoscopic surgery. The metabolomic profiles of plasma samples obtained from 73 women with endometriosis and 35 controls, as well as peritoneal fluid samples from 53 women with endometriosis and 34 controls, were analysed using mass spectrometry techniques. Differences in lipid profiles were observed between the groups. Chemometric analyses identified a set of 20 metabolites present in peritoneal fluid and 26 compounds in plasma, which serve as potential diagnostic tools for endometriosis. Then, we used a simple approach to build a classification model based on the sets of metabolites in combination with autoantibodies selected using protein microarrays from our previous study. The classification performance obtained on the joined metabolomic and proteomic feature sets exceeds that achievable for separate assays (sensitivity/specificity for plasma and peritoneal fluid were respectively 0.98/0.86 and 0.92/0.82). Identified metabolites present promising candidates for biomarkers. Utilizing these metabolites in a diagnostic panel may enhance endometriosis detection. Moreover, we observed the potential benefits of a multi-omics approach based on integrated metabolomic and proteomic analysis to endometriosis research

Symmetric adenine methylation is an essential DNA modification in the early-diverging fungus Rhizopus microsporus

The discovery of N6-methyladenine (6mA) in eukaryotic genomes, typically found in prokaryotic DNA, has revolutionized epigenetics. Here, we show that symmetric 6mA is essential in the early diverging fungus Rhizopus microsporus, as the absence of the MT-A70 complex (MTA1c) responsible for this modification results in a lethal phenotype. 6mA is present in 70% of the genes, correlating with the presence of H3K4me3 and H2A.Z in open euchromatic regions. This modification is found predominantly in nucleosome linker regions, influencing the nucleosome positioning around the transcription start sites of highly expressed genes. Controlled downregulation of MTA1c reduces symmetric 6mA sites affecting nucleosome positioning and histone modifications, leading to altered gene expression, which is likely the cause of the severe phenotypic changes observed. Our study highlights the indispensable role of the DNA 6mA in a multicellular organism and delineates the mechanisms through which this epigenetic mark regulates gene expression in a eukaryotic genome