Accurate and accessible phylogenetic analysis is essential for understanding microbial taxonomy and evolution, which are integral to microbiology, ecology, and drug discovery, yet it remains a challenging task. AutoMLST2 https://automlst2.ziemertlab.com is a web server designed to facilitate automated phylogenetic reconstruction and microbial taxonomy analysis for bacterial and archaeal genomes. It builds on the foundation of AutoMLST, which remains widely used due to its user-friendly interface compared to similar tools. Given its continued popularity and utility, we have enhanced AutoMLST to leverage newer reference databases and computational tools. AutoMLST2 integrates the Genome Taxonomy Database, extends support to archaeal genomes, and improves analytical flexibility. Key improvements include more customizable processing modes, containerization to prevent queue accumulations, and parallel computing for large-scale studies. By incorporating up-to-date databases and workflows, AutoMLST2 continues to provide an accessible and efficient platform for researchers in microbiology, evolutionary ecology, and natural product discovery.

Rheumatoid arthritis (RA) is characterized by massive intra-articular infiltration of pro-inflammatory macrophages, leading to articular immune dysfunction, severe synovitis, and ultimately joint erosion. Comprehensive remodeling of articular immune homeostasis and bone homeostasis is essential for alleviating RA. Here we report on Spirulina platensis (SP), a natural microorganism commercially farmed worldwide as a food, as an efficient regulator of both synovial inflammation and osteoclast differentiation in male RA mouse models. SP reduces excessive reactive oxygen species and downregulates pro-inflammatory cytokines in synovial macrophages. Moreover, SP reprograms pro-inflammatory M1-like macrophages to anti-inflammatory M2-like phenotype, suppressing synovitis and remodeling redox balance. Notably, SP inhibits osteoclast activation effectively and blocks the progression of bone erosion. SP is then engineered with macrophage membranes (SP@M) to enable immune evasion and RA-targeting in vivo. SP@M increases LC3-mediated autophagy as well as strengthens ubiquitin-mediated proteasomal degradation toward KEAP1, which promotes the expression and nuclear translocation of NRF2. The NRF2 further activates antioxidant enzymes to terminate macrophages-initiated pathological cascades and reestablish intra-articular immune homeostasis, conferring a bone recovery and chondroprotective effect in collagen-induced arthritis mouse models. This work shows the therapeutic activity of FDA-approved functional food of SP in suppressing synovial inflammation and osteoclast differentiation, offering an off-the-shelf strategy for RA treatment. Treating rheumatoid arthritis remains challenging as the pathological development involves multiple cells. Here, the authors develop an engineered microalgae to combat rheumatoid arthritis by suppressing osteoclasts for bone remodeling, and inhibiting macrophages for restoring immune homeostasis.

Bacteria rely on an arsenal of weapons to challenge their opponents in highly competitive environments. To specifically counter closely related bacteria, specialized weapons with a narrow activity spectrum are deployed, particularly contractile phage tail-like particles or R-tailocins. Their production leads to the lysis of the producing cells, indicating that their expression must be carefully orchestrated so that only a small percentage of cells produce R-tailocins for the benefit of the entire population. In this study, we set out to better understand how the production of these phage tail-like weapons is regulated in environmental pseudomonads using the competitive plant root colonizer and environmental model strain Pseudomonas protegens CHA0. Using an RNA sequencing (RNA-seq) approach, we found that genes involved in DNA repair, particularly the SOS response program, are upregulated following exposure of the pseudomonad to the DNA-damaging agents mitomycin C and hydrogen peroxide, while genes involved in cell division and primary metabolism are downregulated. The R-tailocin and prophage gene clusters were also upregulated in response to these DNA damaging agents. By combining reverse genetics, transcriptional reporters and chromatin immunoprecipitation sequencing (ChIP-seq), we show that the R-tailocin locus-specific LexA-like regulator PrtR1 represses R-tailocin gene expression by binding directly to the promoter region of the cluster, while the histone-like nucleoid structuring (H-NS) proteins MvaT and MvaV act as master regulators that indirectly regulate R-tailocin cluster expression. Our results suggest that at least these three regulators operate in concert to ensure tight control of R-tailocin expression and cell lytic release in environmental Pseudomonas protegens strains.

Protein–protein interactions are one of the pillars of all life processes. Many signalling molecules work by promoting and stabilizing these interactions. These molecular ‘glues’ bind simultaneously to two proteins inducing their interaction, which would be otherwise less favorable or non-favorable. Importantly, they can be harnessed for a clinical purpose, but, despite advances in medicine, the wealth of natural molecular glues in plants have only rarely been commercially utilized. These molecular glues may be plant-endogenous or plant-exogenous small molecules or peptides, and they may be involved in many different processes, such as growth promotion or stress response, opening new opportunities for crop protection, along with other applications. In this Review, we analyse the underlying structural motives and molecular interactions in detail, classifying the modes of actions based on their nature (small ligands versus peptides) and receptor classes. We discuss both natural metabolites and mimetics of such compounds, highlighting similarities and differences between signalling pathways and comparing them with relevant mechanisms in mammals. In this Review we discuss the fascinating molecular details of the small molecules and peptides promoting plant protein–protein interactions, and their relevance for plant development and environmental responses.

Circular dichroism (CD) spectroscopy is a widely used technique to characterize the secondary structure composition of proteins. We have developed the Beta Structure Selection (BeStSel) method (PNAS, 112, E3095), which solves the main problem of protein CD spectroscopy—namely, the spectral variability of β-structures. The BeStSel web server utilizes this method to provide tools to the community for CD spectrum analysis. BeStSel uniquely provides information on eight secondary structure components, including parallel β-structure and antiparallel β-sheets with three different twist groups. It outperforms all available methods in accuracy and information content, and is also able to predict protein folds down to the topology/homology level of the CATH classification. The algorithm has been further developed, and the accuracy of the estimation of the secondary structure elements is improved by 0.7% as an average on the reference dataset. A new module of the web server calculates protein stability from the thermal denaturation profile followed by CD. Secondary structure calculations of uploaded PDB and mmcif files support the experimental verification of MD simulations and AlphaFold models by CD spectroscopy. Well-proven modules for disorder–order classification and extinction coefficient calculation continue to work. The BeStSel server is freely accessible at https://bestsel.elte.hu.

CRISPR-Cas technologies facilitate routine genome engineering of one or a few genes at a time. However, large-scale CRISPR screens with guide RNA libraries remain challenging in plants. Here, we have developed a comprehensive all-in-one CRISPR toolbox for Cas9-based genome editing, cytosine base editing, adenine base editing (ABE), Cas12a-based genome editing and ABE, and CRISPR-Act3.0-based gene activation in both monocot and dicot plants. We evaluated all-in-one T-DNA expression vectors in rice (Oryza sativa, monocot) and tomato (Solanum lycopersicum, dicot) protoplasts, demonstrating their broad and reliable applicability. To showcase the applications of these vectors in CRISPR screens, we constructed guide RNA (gRNA) pools for testing in rice protoplasts, establishing a high-throughput approach to select high-activity gRNAs. Additionally, we demonstrated the efficacy of sgRNA library screening for targeted mutagenesis of ACETOLACTATE SYNTHASE in rice, recovering novel candidate alleles for herbicide resistance. Furthermore, we carried out a CRISPR activation screen in Arabidopsis thaliana, rapidly identifying potent gRNAs for FLOWERING LOCUS T activation that confer an early-flowering phenotype. This toolbox contains 61 versatile all-in-one vectors encompassing nearly all commonly used CRISPR technologies. It will facilitate large-scale genetic screens for loss-of-function or gain-of-function studies, presenting numerous promising applications in plants.

With only a fraction of plastic waste being recovered and the majority incinerated, landfilled or released into the environment, plastic is increasingly accumulating in aquatic and terrestrial ecosystems, leading to widespread pollution. Biocatalysis offers a route to the sustainable recycling of synthetic polyesters, such as polyethylene terephthalate (PET), which is commonly used in textiles, food and beverage packaging, representing a major source of plastic waste. In particular, polyester hydrolases can deconstruct recalcitrant synthetic polymers at scale. This Review discusses the role of biocatalysis in a circular economy of plastics, outlining enzymatic modification and deconstruction strategies for synthetic polyesters. Moreover, protein engineering and computational approaches are examined to design and optimize polyester hydrolases for large-scale recycling in key industrial applications. Finally, the importance of economic viability is highlighted, including strategies to make biocatalysis a cost-effective and sustainable plastics recycling strategy. Plastic pollution could be partly addressed through the biocatalytic recycling of plastic waste streams. This Review discusses the identification and optimization of polyester-degrading enzymes for the large-scale recycling of plastic waste. industry

Circular RNAs (circRNAs) are a class of non-coding RNAs generated through back splicing. High expression of circRNAs is often associated with numerous abnormal cellular biological processes. However, the regulatory factors of circRNAs are not fully understood. In this study, we identified PTBP1 as a crucial regulator of circRNA biogenesis through a comprehensive analysis of the whole transcriptome profiles across 10 diverse cell lines. Knockdown of PTBP1 led to a significant decrease in circRNA expression, concomitant with a distinct reduction in cell proliferation. To investigate the regulatory mechanism of PTBP1 on circRNA biogenesis, we constructed a minigene reporter based on SPPL3 gene. The results showed that PTBP1 can bind to the flanking introns of circSPPL3, and the mutation of PTBP1 motif impedes the back splicing of circSPPL3. Subsequently, to demonstrate that this observation is not an exception, the comprehensive regulatory effects of PTBP1 on circRNAs were confirmed by miniGFP, reflecting the necessity of the binding site in the flanking introns. Analysis of data from clinical samples showed that both PTBP1 and circRNAs exhibited substantial upregulation in acute myeloid leukemia, further demonstrating a potential role for PTBP1 in promoting circRNA biogenesis under in vivo conditions. Competitive endogenous RNA (ceRNA) network revealed that PTBP1-associated circRNAs participated in biological processes associated with cell proliferation. In summary, our study is the first to identify the regulatory effect of PTBP1 on circRNA biogenesis and indicates a possible link between PTBP1 and circRNA expression in leukemia.