Evolutionary flexibility and rigidity in the bacterial methylerythritol phosphate (MEP) pathway

Integration of HDS and HSFA1 Functions in MEcPP-Mediated Thermotolerance and Growth Regulation in Physcomitrium patens

Land plants evolved mechanisms to cope with terrestrial challenges. The methylerythritol phosphate (MEP) pathway intermediate 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEcPP) plays a central role in chloroplast retrograde signalling (CRS) and stress responses in Arabidopsis. However, its regulation in nonvascular plants remains underexplored. This study characterizes the 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate synthase (HDS) gene family in Physcomitrium patens, uncovering unique evolutionary patterns with multiple HDS copies compared to the single-copy HDS in most angiosperms. We demonstrate that HDS catalyses a key step in MEP and interacts with heat shock transcription factor A1 (HSFA1) to modulate thermotolerance. CRISPR/LbCas12a-edited hds mutants exhibited enhanced thermotolerance and elevated MEcPP levels, with exogenous MEcPP mimicking this effect. Transcriptomic analysis identified upregulated stress-responsive genes, including small heat shock proteins, which prepare the plant for heat stress. This priming effect depends on HSFA1, which regulates MEP pathway genes, including HDS, thereby influencing MEcPP accumulation and thermotolerance. Furthermore, HDS and HSFA1 synergistically regulate growth in P. patens, with hds2 hds3 hsfa1 triple mutant displaying reduced size, lower IAA levels, and altered non-photochemical quenching. These findings highlight a novel HDS-HSFA1 regulatory module, expanding CRS paradigms and offering new insights into the evolution of stress adaptation in bryophytes, bridging gaps in understanding HDS function across species.

Identifying Opportunity Targets in Gram-Negative Pathogens for Infectious Disease Mitigation

Antimicrobial drug resistance (AMR) is a pressing global human health challenge. Humans face one of their grandest challenges as climate change expands the habitat of vectors that bear human pathogens, incidences of nosocomial infections rise, and new antibiotics discovery lags. AMR is a multifaceted problem that requires a multidisciplinary and an "all-hands-on-deck" approach. As chemical microbiologists, we are well positioned to understand the complexities of AMR while seeing opportunities for tackling the challenge. In this Outlook, we focus on vulnerabilities of human pathogens and posit that they represent "opportunity targets" for which few modulatory ligands exist. We center our attention on proteins in Gram-negative organisms, which are recalcitrant to many antibiotics because of their external membrane barrier. Our hope is to highlight such targets and explore their potential as "druggable" proteins for infectious disease mitigation. We posit that success in this endeavor will introduce new classes of antibiotics that might alleviate some of the current pressing AMR concerns.

A review on comparative analysis of marine and freshwater fish gut microbiomes: insights into environmental impact on gut microbiota

The gut microbiota, which includes prokaryotes, archaea, and eukaryotes such as yeasts, some protozoa, and fungi, significantly impacts fish by affecting digestion, metabolism, and the immune system. In this research, we combine various tasks carried out by various bacteria in the gut of fish. This study also examines the gut microbiome composition of marine and freshwater fish, identifying important bacterial species linked to different biological functions. The diversity within fish species highlights the importance of considering nutrition, habitat, and environmental factors in microbiological research on fish. The ever-changing gut microbiome of the fish indicates that microbial communities are specifically adapted to meet the needs of both the host and its environment. This indicates that the fish can adjust to a specific environment with the help of gut microbiota. This important research is crucial for comprehending the complex relationships between fish and their gut bacteria in different aquatic environments. These discoveries have implications for aquaculture practices, fisheries administration, and the broader ecological processes of both freshwater and marine environments. With further progress in this area of study, the knowledge acquired would offer a valuable standpoint to enhance our comprehension of aquatic microbiology and enhance the sustainability and nutrition of fish resources.

Biogenic volatile organic compounds (BVOCs) emissions and physiological changes in Pinus densiflora and Quercus acutissima seedlings under elevated particulate matter (PM)

Urban trees effectively reduce air pollution, including particulate matter (PM), which is a major concern in East Asia. While acting as biofilters, urban trees can be affected by PM exposure, which hinders their growth and physiological functions, thereby reducing their pollution mitigation ability. Trees absorb pollutants but also emit biogenic volatile organic compounds (BVOCs), which can act as precursors to other forms of air pollution. To better understand the effects of PM on urban trees, this study examined how two tree species, Pinus densiflora and Quercus acutissima, respond to elevated PM levels under controlled conditions at a concentration of 300 μg m-3. The aim was to investigate how increased PM levels affect BVOCs emissions and physiological responses in seedlings, and how these physiological changes influence BVOCs emission pattern. The results revealed species-specific responses in BVOCs emissions under PM stress with being especially oxygenated monoterpenes more than non‑oxygenated monoterpenes. Increased PM adsorption was found to reduce photosynthetic abilities, including photosynthesis (Anet), carboxylation capacity (Vcmax), and electron transport rate (J). This reduction in photosynthetic efficiency was further evidenced by decreased chlorophyll content and light absorption, which were assessed through chlorophyll fluorescence measurements. Additionally, the study evaluated oxidative stress indicators, such as lipid peroxidation and the accumulation of reactive oxygen species (ROS), to provide a comprehensive understanding of the species' responses to elevated PM conditions. The study found that elevated PM conditions were closely linked to an increase in oxygenated monoterpenes, which was associated with both oxidative stress and impaired physiological function. These observations emphasize the need for strategic urban tree selection to enhance air quality and suggest that understanding species-specific BVOCs emissions in response to PM is crucial for optimizing urban green spaces for health and environmental benefits.

An evolutionarily conserved metabolite inhibits biofilm formation in Escherichia coli K-12

Methylerythritol cyclodiphosphate (MEcPP) is an intermediate in the biosynthesis of isoprenoids in plant plastids and in bacteria, and acts as a stress signal in plants. Here, we show that MEcPP regulates biofilm formation in Escherichia coli K-12 MG1655. Increased MEcPP levels, triggered by genetic manipulation or oxidative stress, inhibit biofilm development and production of fimbriae. Deletion of fimE, encoding a protein known to downregulate production of adhesive fimbriae, restores biofilm formation in cells with elevated MEcPP levels. Limited proteolysis-coupled mass spectrometry (LiP-MS) reveals that MEcPP interacts with the global regulatory protein H-NS, which is known to repress transcription of fimE. MEcPP prevents the binding of H-NS to the fimE promoter. Therefore, our results indicate that MEcPP can regulate biofilm formation by modulating H-NS activity and thus reducing fimbriae production. Further research is needed to test whether MEcPP plays similar regulatory roles in other bacteria.

Reconstructing Early Microbial Life

For more than 3.5 billion years, life experienced dramatic environmental extremes on Earth. These include shifts from oxygen-less to overoxygenated atmospheres and cycling between hothouse conditions and global glaciations. Meanwhile, an ecological revolution took place. Earth evolved from one dominated by microbial life to one containing the plants and animals that are most familiar today. Many key cellular features evolved early in the history of life, collectively defining the nature of our biosphere and underpinning human survival. Recent advances in molecular biology and bioinformatics have greatly improved our understanding of microbial evolution across deep time. However, the incorporation of molecular genetics, population biology, and evolutionary biology approaches into the study of Precambrian biota remains a significant challenge. This review synthesizes our current knowledge of early microbial life with an emphasis on ancient metabolisms. It also outlines the foundations of an emerging interdisciplinary area that integrates microbiology, paleobiology, and evolutionary synthetic biology to reconstruct ancient biological innovations.

Expanded Archaeal Genomes Shed New Light on the Evolution of Isoprenoid Biosynthesis

Isoprenoids and their derivatives, essential for all cellular life on Earth, are particularly crucial in archaeal membrane lipids, suggesting that their biosynthesis pathways have ancient origins and play pivotal roles in the evolution of early life. Despite all eukaryotes, archaea, and a few bacterial lineages being known to exclusively use the mevalonate (MVA) pathway to synthesize isoprenoids, the origin and evolutionary trajectory of the MVA pathway remain controversial. Here, we conducted a thorough comparison and phylogenetic analysis of key enzymes across the four types of MVA pathway, with the particular inclusion of metagenome assembled genomes (MAGs) from uncultivated archaea. Our findings support an archaeal origin of the MVA pathway, likely postdating the divergence of Bacteria and Archaea from the Last Universal Common Ancestor (LUCA), thus implying the LUCA's enzymatic inability for isoprenoid biosynthesis. Notably, the Asgard archaea are implicated in playing central roles in the evolution of the MVA pathway, serving not only as putative ancestors of the eukaryote- and Thermoplasma-type routes, but also as crucial mediators in the gene transfer to eukaryotes, possibly during eukaryogenesis. Overall, this study advances our understanding of the origin and evolutionary history of the MVA pathway, providing unique insights into the lipid divide and the evolution of early life.