Cell-Free Systems to Mimic and Expand Metabolism.

Cell-free synthetic biology incorporates purified components and/or crude cell extracts to carry out metabolic and genetic programs. While protein synthesis has historically been the primary focus, more metabolism researchers are now turning toward cell-free systems either to prototype pathways for cellular implementation or to design new-to-nature reaction networks that incorporate environmentally relevant substrates or new energy sources. The ability to design, build, and test enzyme combinations has accelerated efforts to understand metabolic bottlenecks and engineer high-yielding pathways.

Engineering the future of medicine: Natural products, synthetic biology and artificial intelligence for next-generation therapeutics.

The eXchange Unit between Thiolation domains approach and artificial intelligence (AI)-driven tools like Synthetic Intelligence are transforming nonribosomal peptide synthetase and polyketide synthase engineering, enabling the creation of novel bioactive compounds that address critical challenges like antibiotic resistance and cancer. These innovations expand chemical space and optimize biosynthetic pathways, offering precise and scalable therapeutic solutions. Collaboration across synthetic biology, AI, and clinical research is essential to translating these breakthroughs into next-generation treatments and revolutionizing drug discovery and patient care.

A Global Relationship Between Genome Size and Encoded Carbon Metabolic Strategies of Soil Bacteria.

Microbial traits are critical for carbon sequestration and degradation in terrestrial ecosystems. Yet, our understanding of the relationship between carbon metabolic strategies and genomic traits like genome size remains limited. To address this knowledge gap, we conducted a global-scale meta-analysis of 2650 genomes, integrated whole-genome sequencing data, and performed a continental-scale metagenomic field study.

A truncated variant of the ribosome-associated trigger factor specifically contributes to plant chloroplast ribosome biogenesis.

Molecular chaperones are essential throughout a protein's life and act already during protein synthesis. Bacteria and chloroplasts of plant cells share the ribosome-associated chaperone trigger factor (Tig1 in plastids), facilitating maturation of emerging nascent polypeptides. While typical trigger factor chaperones employ three domains for their task, the here described truncated form, Tig2, contains just the ribosome binding domain.

Engineering carbon assimilation in plants.

Carbon assimilation is a crucial part of the photosynthetic process, wherein inorganic carbon, typically in the form of CO, is converted into organic compounds by living organisms, including plants, algae, and a subset of bacteria. Although several carbon fixation pathways have been elucidated, the Calvin-Benson-Bassham (CBB) cycle remains fundamental to carbon metabolism, playing a pivotal role in the biosynthesis of starch and sucrose in plants, algae, and cyanobacteria. However, Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the key carboxylase enzyme of the CBB cycle, exhibits low kinetic efficiency, low substrate specificity, and high temperature sensitivity, all of which have the potential to limit flux through this pathway.

A Novel Lineage of Endosymbiotic Actinomycetales: Genome Reduction and Acquisition of New Functions in Bifidobacteriaceae Associated With Termite Gut Flagellates.

Cellulolytic flagellates are essential for the symbiotic digestion of lignocellulose in the gut of lower termites. Most species are associated with host-specific consortia of bacterial symbionts from various phyla. 16S rRNA-based diversity studies and taxon-specific fluorescence in situ hybridization revealed a termite-specific clade of Actinomycetales that colonise the cytoplasm of Trichonympha spp.

Bacteria use exogenous peptidoglycan as a danger signal to trigger biofilm formation.

For any organism, survival is enhanced by the ability to sense and respond to threats in advance. For bacteria, danger sensing among kin cells has been observed, but the presence or impacts of general danger signals are poorly understood. Here we show that different bacterial species use exogenous peptidoglycan fragments, which are released by nearby kin or non-kin cell lysis, as a general danger signal.

Swarming bacteria exhibit developmental phase transitions to establish scattered colonies in new regions.

The collective surface motility and swarming behavior of microbes play a crucial role in the formation of polymicrobial communities, shaping ecosystems as diverse as animal and human microbiota, plant rhizospheres, and various aquatic environments. In the human oral microbiota, T9SS-driven gliding bacteria transport non-motile microbes and bacteriophages as cargo, thereby influencing the spatial organization and structural complexity of these polymicrobial communities. However, the physical rules governing the dispersal of T9SS-driven bacterial swarms are barely understood.

Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks.

Metabolic variation across pathogenic bacterial strains can impact their susceptibility to antibiotics and promote the evolution of antimicrobial resistance (AMR). However, little is known about how metabolic mutations influence metabolism and which pathways contribute to antibiotic susceptibility. Here, we measured the antibiotic susceptibility of 15,120 Escherichia coli mutants, each with a single amino acid change in one of 346 essential proteins.

In situ architecture of a nucleoid-associated biomolecular co-condensate that regulates bacterial cell division.

In most bacteria, cell division depends on the tubulin-homolog FtsZ that polymerizes in a GTP-dependent manner to form the cytokinetic Z-ring at the future division site. Subsequently, the Z-ring recruits, directly or indirectly, all other proteins of the divisome complex that executes cytokinesis. A critical step in this process is the precise positioning of the Z-ring at the future division site.

Plant Species Richness and the Root Economics Space Drive Soil Fungal Communities.

Trait-based approaches have been increasingly used to relate plants to soil microbial communities. Using the recently described root economics space as an approach to explain the structure of soil-borne fungal communities, our study in a grassland diversity experiment reveals distinct root trait strategies at the plant community level. In addition to significant effects of plant species richness, we show that the collaboration and conservation gradient are strong drivers of the composition of the different guilds of soil fungi.

Light-Controlled Secretion and Injection of Proteins into Eukaryotic Cells by Optogenetic Control of the Bacterial Type III Secretion System.

Gram-negative bacteria can use the type III secretion system (T3SS) to inject effector proteins into eukaryotic target cells. In this chapter, we describe the application of a light-controlled T3SS, based on the targeted sequestration of an essential dynamic T3SS component with the help of optogenetic interaction switches. This method enables to control the secretion or injection into eukaryotic cells for a wide range of protein cargos with high temporal and spatial precision.

Symbiotic bacteria associated with entomopathogenic nematodes showed molluscicidal activity against Biomphalaria glabrata, an intermediate host of Schistosoma mansoni.

Background: Biomphalaria glabrata acts as the intermediate host of schistosomes that causes human schistosomiasis. Symbiotic bacteria, Xenorhabdus and Photorhabdus associated with Steinernema and Heterorhabditis, produce secondary metabolites with several biological activities. Controlling B.

Increased methane production associated with community shifts towards Methanocella in paddy soils with the presence of nanoplastics.

Background: Planetary plastic pollution poses a major threat to ecosystems and human health in the Anthropocene, yet its impact on biogeochemical cycling remains poorly understood. Waterlogged rice paddies are globally important sources of CH. Given the widespread use of plastic mulching in soils, it is urgent to unravel whether low-density polyethylene (LDPE) will affect the methanogenic community in flooded paddy soils.

A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide.

Subsurface environments are among Earth's largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface and subsurface microbiomes. Here, we analyzed 478 archaeal and 964 bacterial metabarcoding datasets and 147 metagenomes from diverse and widely distributed environments.

Enhanced sensitivity of TAPscan v4 enables comprehensive analysis of streptophyte transcription factor evolution.

Transcription-associated proteins (TAPs) fulfill multiple functions in regulatory and developmental processes and display lineage-specific evolution. TAPscan is a comprehensive and highly reliable tool for genome-wide TAP annotation via domain profiles. Here, we present TAPscan v4, including an updated web interface (https://tapscan.

Structural and kinetic insights into tRNA promoter engagement by yeast general transcription factor TFIIIC.

Transcription of transfer RNA (tRNA) genes by RNA polymerase (Pol) III requires the general transcription factor IIIC (TFIIIC), which recognizes intragenic A-box and B-box DNA motifs of type II gene promoters. However, the underlying mechanism has remained elusive, in part due to missing structural information for A-box recognition. In this study, we use single-particle cryogenic electron microscopy (cryo-EM) and single-molecule fluorescence resonance energy transfer (smFRET) to reveal structural and real-time kinetic insights into how the 520-kDa yeast TFIIIC complex engages A-box and B-box DNA motifs in the context of a tRNA gene promoter.

A conserved cell-pole determinant organizes proper polar flagellum formation.

The coordination of cell cycle progression and flagellar synthesis is a complex process in motile bacteria. In γ-proteobacteria, the localization of the flagellum to the cell pole is mediated by the SRP-type GTPase FlhF. However, the mechanism of action of FlhF, and its relationship with the cell pole landmark protein HubP remain unclear.

Frequent transitions in self-assembly across the evolution of a central metabolic enzyme.

Many enzymes assemble into homomeric protein complexes comprising multiple copies of one protein. Because structural form is usually assumed to follow function in biochemistry, these assemblies are thought to evolve because they provide some functional advantage. In many cases, however, no specific advantage is known and, in some cases, quaternary structure varies among orthologs.

- & : plasmid toolboxes for scarless transcription unit and modular Golden Gate acceptor plasmid assembly.

Golden Gate cloning has become one of the most important DNA assembly strategies. The construction of standardized and reusable part libraries, their assembly into transcription units, and the subsequent assembly of multigene constructs is highly reliable and sustainable. Researchers can quickly construct derivatives of their assemblies or entire pathways, and importantly, the standardization of Golden Gate assemblies is compatible with laboratory automation.

New-to-nature CO-dependent acetyl-CoA assimilation enabled by an engineered B-dependent acyl-CoA mutase.

Acetyl-CoA is a key metabolic intermediate and the product of various natural and synthetic one-carbon (C1) assimilation pathways. While an efficient conversion of acetyl-CoA into other central metabolites, such as pyruvate, is imperative for high biomass yields, available aerobic pathways typically release previously fixed carbon in the form of CO. To overcome this loss of carbon, we develop a new-to-nature pathway, the Lcm module, in this study.

Layered entrenchment maintains essentiality in the evolution of Form I Rubisco complexes.

Protein complexes composed of strictly essential subunits are abundant in nature and often arise through the gradual complexification of ancestral precursor proteins. Essentiality can arise through the accumulation of changes that are tolerated in the complex state but would be deleterious for the standalone complex components. While this theoretical framework to explain how essentiality arises has been proposed long ago, it is unclear which factors cause essentiality to persist over evolutionary timescales.

The emergence of Sox and POU transcription factors predates the origins of animal stem cells.

Stem cells are a hallmark of animal multicellularity. Sox and POU transcription factors are associated with stemness and were believed to be animal innovations, reported absent in their unicellular relatives. Here we describe unicellular Sox and POU factors.