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Escherichia coli DNA replication: the old model organism still holds many surprises
Get PDFResearch on Escherichia coli DNA replication paved the groundwork for many breakthrough discoveries with important implications for our understanding of human molecular biology, due to the high level of conservation of key molecular processes involved. To this day, it attracts a lot of attention, partially by virtue of being an important model organism, but also because the understanding of factors influencing replication fidelity might be important for studies on the emergence of antibiotic resistance. Importantly, the wide access to high-resolution single-molecule and live-cell imaging, whole genome sequencing, and cryo-electron microscopy techniques, which were greatly popularized in the last decade, allows us to revisit certain assumptions about the replisomes and offers very detailed insight into how they work. For many parts of the replisome, step-by-step mechanisms have been reconstituted, and some new players identified. This review summarizes the latest developments in the area, focusing on (a) the structure of the replisome and mechanisms of action of its components, (b) organization of replisome transactions and repair, (c) replisome dynamics, and (d) factors influencing the base and sugar fidelity of DNA synthesis
A novel microRNA differentially expressed in patients with persistent and paroxysmal atrial fibrillation
Get PDFAtrial fibrillation (AF) is the most common cardiac arrhythmia in the general population. The estimated prevalence of this arrhythmia in adults ranges from 2% to 4%.1 AF is one of the leading causes of stroke, heart failure, other thromboembolic complications, and sudden death. On the basis of the duration of an arrhythmia episode, AF is classified as first-diagnosed, paroxysmal, persistent, long-standing persistent, or permanent.2 In recent years, there has been a growing body of evidence that microRNAs (miRNAs) play an important role in AF development and progression.3 Advances in next-generation sequencing technologies made it possible to identify and evaluate putative novel miRNAs associated with this arrhythmia. Hence, the main goal of this study was to identify novel circulating serum miRNAs that can differentiate between paroxysmal and persistent AF, and may serve as potential diagnostic biomarkers
The Role of Methanogenic Archaea in Inflammatory Bowel Disease—A Review
Get PDFMethanogenic archaea are a part of the commensal gut microbiota responsible for hydrogen sink and the efficient production of short-chain fatty acids. Dysbiosis of methanogens is suspected to play a role in pathogenesis of variety of diseases, including inflammatory bowel disease (IBD). Unlike bacteria, the diversity of archaea seems to be higher in IBD patients compared to healthy subjects, whereas the prevalence and abundance of gut methanogens declines in IBD, especially in ulcerative colitis. To date, studies focusing on methanogens in pediatric IBD are very limited; nevertheless, the preliminary results provide some evidence that methanogens may be influenced by the chronic inflammatory process in IBD. In this review, we demonstrated the development and diversity of the methanogenic community in IBD, both in adults and children
Comprehensive phenomic and genomic studies of the species, Pectobacterium cacticida and proposal for reclassification as Alcorniella cacticida comb. nov
Get PDFPectobacterium cacticida was identified as the causative agent of soft rot disease in cacti. Due to a high potential of spread in the face of global warming, the species poses a significant threat to horticultural and crop industry. The aim of this study was to revise the genomic, physiology and virulence characteristics of P. cacticida and update its phylogenetic position within the Pectobacterium genus
The UBP5 histone H2A deubiquitinase counteracts PRCs-mediated repression to regulate Arabidopsis development
Get PDFGeneration and characterization of single and multigene Arabidopsis thaliana mutants in LSU1-4 (RESPONSE TO LOW SULFUR) genes
Get PDFIn Arabidopsis thaliana, there are four members of the LSU (RESPONSE TO LOW SULFUR) gene family which are tandemly located on chromosomes 3 (LSU1 and LSU3) and 5 (LSU2 and LSU4). The LSU proteins are small, with coiled-coil structures, and they are able to form homo- and heterodimers. LSUs are involved in plant responses to environmental challenges, such as sulfur deficiency, and plant immune responses. Assessment of the role and function of these proteins was challenging due to the absence of deletion mutants. Our work fulfills this gap through the construction of a set of LSU deletion mutants (single, double, triple, and quadruple) by CRISPR/Cas9 technology. The genomic deletion regions in the obtained lines were mapped and the level of expression of each LSUs was assayed in each mutant. All lines were viable and capable of seed production. Their growth and development were compared at several different stages with the wild-type. No significant and consistent differences in seedlings’ growth and plant development were observed in the optimal conditions. In sulfur deficiency, the roots of 12-day-old wild-type seedlings exhibited increased length compared to optimal conditions; however, this difference in root length was not observed in the majority of lsu-KO mutants
A Multi-Faceted Analysis Showing CRNDE Transcripts and a Recently Confirmed Micropeptide as Important Players in Ovarian Carcinogenesis
Get PDFCRNDE is considered an oncogene expressed as long non-coding RNA. Our previous paper is the only one reporting CRNDE as a micropeptide-coding gene. The amino acid sequence of this micropeptide (CRNDEP) has recently been confirmed by other researchers. This study aimed at providing a mass spectrometry (MS)-based validation of the CRNDEP sequence and an investigation of how the differential expression of CRNDE(P) influences the metabolism and chemoresistance of ovarian cancer (OvCa) cells. We also assessed cellular localization changes of CRNDEP, looked for its protein partners, and bioinformatically evaluated its RNA-binding capacities. Herein, we detected most of the CRNDEP sequence by MS. Moreover, our results corroborated the oncogenic role of CRNDE, portraying it as the gene impacting carcinogenesis at the stages of DNA transcription and replication, affecting the RNA metabolism, and stimulating the cell cycle progression and proliferation, with CRNDEP being detected in the centrosomes of dividing cells. We also showed that CRNDEP is located in nucleoli and revealed interactions of this micropeptide with p54, an RNA helicase. Additionally, we proved that high CRNDE(P) expression increases the resistance of OvCa cells to treatment with microtubule-targeted cytostatics. Furthermore, altered CRNDE(P) expression affected the activity of the microtubular cytoskeleton and the formation of focal adhesion plaques. Finally, according to our in silico analyses, CRNDEP is likely capable of RNA binding. All these results contribute to a better understanding of the CRNDE(P) role in OvCa biology, which may potentially improve the screening, diagnosis, and treatment of this disease
Native and alien grasses as a hebitat for fungi
Get PDFBiological invasions are now seen as one of the main threats to the Antarctic ecosystem. An exam-ple of such an invasion is the recent colonization of the H. Arctowski Polish Antarctic Station area by the non-native grass Poa annua. This site was previously occupied only by native plants like the Antarctic hair grass Deschampsia antarctica. To adapt successfully to new conditions, plants interact with soil microorganisms, including fungi. The aim of this study was to determine how the newly introduced grass P. annua established interaction with fungi compared to resident grass D. antarc-tica. We found that fungal diversity in D. antarctica roots was significantly higher compared to P. annua roots. D. antarctica managed a biodiverse microbiome due to its ability to recruit fungal bi-ocontrol agents from soil and thus maintaining a beneficial nature of the endophyte community. P. annua relied on a set of specific fungal taxa which likely modulated its cold-response, increasing its competitiveness in Antarctic conditions. Cultivated endophytic fungi displayed strong chitinoly-sis, pointing towards their role as phytopathogenic fungi, nematode and insect antagonists. This is the first study to compare the root mycobiomes of both grass species by direct cul-ture-independent techniques as well as culture-based methods
The interplay between gingival crevicular fluid microbiome and metabolomic profile in intensively treated people with type 1 diabetes - a combined metagenomic/metabolomic approach cross-sectional study
Get PDFAims: This study aimed to assess the gingival crevicular fluid (GCF) microbiome and metabolome of adults with type 1 diabetes (T1D) treated with continuous subcutaneous insulin infusion (CSII).
Methods: In this cross-sectional study, the GCF of adults with T1D treated with CSII and non-diabetic controls were sampled, and metagenomic/metabolomic analyses were performed.
Results: In total, 65 participants with T1D and 45 healthy controls with a mean age of 27.05 ± 5.95 years were investigated. There were 22 cases of mild gingivitis (G) in the T1D group. There were no differences considering the Shannon and Chao indices and β-diversity between people with T1D and G, with T1D without G, and healthy controls. Differential taxa were identified, which were mainly enriched in people with T1D and G. Acetic acid concentration was higher in people with T1D, regardless of the presence of G, than in healthy controls. Propionic acid was higher in people with T1D and G than in healthy controls. Isobutyric and isovaleric acid levels were higher in individuals with T1D and G than in the other two subgroups. The concentration of valeric acid was lower and that of caproic acid was higher in people with T1D (regardless of gingival status) than in healthy controls.
Conclusions: The identification of early changes in periodontal tissues by targeting the microbiome and metabolome could potentially enable effective prevention and initial treatment of periodontal disease in people with T1D
Lactococcus lactis mutants resistant to lactococcin A and garvicin Q reveal missense mutations in the sugar transport domain of the mannose phosphotransferase system
Get PDFLactococcin A is a bacteriocin from Lactococcus lactis that permeabilizes the membrane of sensitive lactococcal cells and requires the presence of the membrane-bound components IIC and IID of the mannose phosphotransferase system (man-PTS). Recently, it was reported through cryo-electron microscopy analyses of man-PTS and several bacteriocins fused to a maltose-binding protein, including lactococcin A, that these bacteriocins create pores by inserting themselves between the Core and Vmotif domains of man-PTS. In our study, we obtained a dozen spontaneous mutants of L. lactis IL1403 resistant to lactococcin A. All but one of the mutants of IL1403 have mutations located in the genes encoding the IIC or IID proteins. These mutations also resulted in resistance to garvicin Q, a bacteriocin from Lactococcus garvieae with a broad inhibition spectrum and very little sequence homology to lactococcin A. Missense mutations were found in the sugar transport domain of man-PTS of bacteriocin-resistant IL1403 mutants, which also impeded the uptake of mannose. When lactococcin A, garvicin Q, or pediocin PA-1, an anti-listerial bacteriocin, were fused to a maltose-binding protein, we observed reduced or no antibacterial activity. Taken together, the precise mechanism of action of bacteriocins using the man-PTS remains to be fully understood