Essays in biochemistry最新文献

Forest trees are ecologically and economically vital, contributing to carbon sequestration, biodiversity conservation, pollution mitigation, and renewable bioenergy. However, forests worldwide are increasingly threatened by interacting biotic and abiotic stressors, including pathogens, insect pests, drought, heat, and extreme weather events driven by climate change. Drought and heat stress trigger complex physiological and metabolic responses in trees that can reshape their resistance to pathogens. While moderate stress may activate protective mechanisms, severe stress can cause cellular damage, dehydration, and reactive oxygen species accumulation, weakening defense capacity. Emerging evidence highlights additional layers of regulation, including epigenetic mechanisms and the role of beneficial microbiomes in enhancing tree resilience under combined environmental and pathogen pressures. Breeding and genetic improvement are also essential for strengthening adaptation and resistance to emerging diseases. Although advances in forest genetics, long-term field studies, and tree genomics are improving our predictive capacity, major knowledge gaps remain. Addressing how forest trees respond to pathogens under climate change will require multidisciplinary approaches integrating molecular biology, multiomics, big data analytics, remote sensing, ecology, and climate modelling.

Nuclear receptors (NRs) are ligand-regulated transcription factors that control many physiological processes, from metabolism and inflammation to development and circadian rhythms. Beginning in the 1990s, systematic chemical probe development transformed many 'orphan' NRs with unknown endogenous ligands into chemically tractable, well-studied molecular targets, uncovering their physiological functions and potential for therapeutic development. The present review examines how small molecule ligands for peroxisome proliferator-activated receptors, liver X receptors, farnesoid X receptor, pregnane X receptor, and constitutive androstane receptor enabled the scientific community to connect orphan NR activation to specific transcriptional programs, metabolic phenotypes, and disease processes-while emerging tools for liver receptor homolog-1/steroidogenic factor-1, Rev-Erbs, nerve growth factor-induced clone Bs, HNF4, and transcription factor tailless hold promise to do likewise. These tools not only had widespread impact on NR biology but also established many design principles for chemical probes that continue to guide the field today. The NR field demonstrates how systematic chemical probe discovery can enable basic research and de-risk therapeutic hypotheses, providing a roadmap for other chemical probe initiatives in the human proteome.

Although the study of microbes started with type strains and reference genomes, advances in sequencing technology and new interest in mixed microbial communities have made us aware that a single genome cannot and does not reflect the diversity of a given bacterial species. Bacteria rarely occupy an environmental or host niche alone and quickly diversify into strains upon colonization of a new niche. The genetic diversity present within a phylogenetically related set of bacterial strains (the 'pangenome') is influenced by the niche that they occupy and how they interact with the other microorganisms that they share that niche with. In this review, I examine how the social lives of bacteria can affect their genetic diversity and the bioinformatic techniques that we use to detect that diversity.

Antimicrobial peptide research has long centred on host defence molecules, yet microbiomes themselves encode a diverse and increasingly important repertoire of peptide-based antimicrobials. These microbiome-derived antimicrobial peptides include bacteriocins, ribosomally synthesised and post-translationally modified peptides, cryptic short open reading frame-encoded peptides, embedded antimicrobial regions within larger proteins, and selected peptide antibiotics recovered from human, animal, plant and environmental microbiomes. Recent advances in genome mining, metagenomics, and machine learning have greatly expanded the scale of discovery, moving the field from a handful of landmark exemplars to large candidate catalogues spanning the global microbiome. In the clearest cases, these molecules are not only anti-infective leads but ecological effectors: they mediate microbial competition, enforce colonisation resistance, and influence community structure within densely occupied niches. The present review synthesises the field across discovery classes, microbiome sources, ecological roles, and translational bottlenecks, emphasizing a central limitation of the field: candidate catalogues are expanding at extraordinary scale, while evidence for native expression, producer assignment, ecological function, and in vivo relevance remains limited for the vast majority of predicted molecules. Progress will depend on workflows that connect sequence level prediction to biological context through expression support, producer assignment, community level validation, and perturbation-based approaches that distinguish ecological association from causal function. Microbiome-derived antimicrobial peptides are best understood not only as promising therapeutic leads, but also as molecular mediators of microbial social life whose ecological origins are central to their interpretation and future application.

In nature, microorganisms exist in multispecies microbial communities containing bacteria, fungi, archaea, and viruses. The organisation, behaviour, and ecological impact of these communities are very much defined by the various interactions between bacteria and fungi within the community, with physical associations, chemical communication, metabolic exchange, and genetic regulation collectively shaping how these interkingdom communities assemble, adapt, and influence their hosts and habitats. Methods of interaction are widely shared across the microbiota of plants, animals, and the built environment; however, interkingdom microbial communities have environmentally specific outcomes, meaning it is critically important to understand bacterial-fungal interactions (BFIs) within the host or environmental context. With recent advances in BFI analysis now providing increasingly detailed resolution of BFIs and their function in the dialogue between interkingdom microbial communities and their growth environment, we can now gain better insight into these fundamental processes. In the present mini-review, we detail the main BFIs observed in these interkingdom microbial communities, and their implications in the context of plant, human, and the health of the built environment. We also discuss tools and methodologies for their analysis and potential use in the development of microbially derived technologies to improve health and well-being. Finally, we endorse the perspective that interkingdom microbial communities should be considered as structured, interdependent networks with analogy to multicellular organisation.

Horizontal gene transfer, mediated by mobile genetic elements such as conjugative plasmids, is recognised as a major driver of bacterial innovation. While predominantly explored in the context of change within individual strains and species, the broad host ranges of many plasmids mean that they can invade not just lineages but communities. This has far-reaching implications for both the fate of the plasmid and our understanding of bacterial adaptation, as well as applications for the functional engineering of microbial communities. In comparison to single-strain systems, in which plasmid invasion is largely determined by a now well-defined set of parameters-conjugation rate, fitness cost of carriage, and segregation loss-the spread of plasmids into communities is vastly more complex: governed by the wide range of dynamics within strains, but also by community dynamics, spatial heterogeneity, and the interactions between strain- and community-level selection. Here, we review the processes by which plasmids can invade communities and discuss how community complexity both constrains and facilitates plasmid spread. We further explore how this mechanistic understanding can be harnessed to enhance microbial community function.

Biofilms are challenging samples for microscopy, because they are usually large samples with small features of interest, a fragile nature due to their high water content, and they may be grown on a variety of substrates. Cryo-scanning electron microscopy (cryo-SEM) has long been used to image microbiological components in plant-pathogen interactions, food products, and soil. The main advantage, compared with the more widely available room temperature SEM, is that the rapid sample preparation results in a native-like structure. It has been used to study environmental biofilms, but rarely for medically relevant biofilms. The cryo-SEM workflow starts with freezing the sample, either by high-pressure freezing, plunge-freezing, or slush nitrogen freezing. This is followed by fracture, sublimation, and coating, before the cryo-SEM imaging takes place. The present review aims to give new potential users an overview of the workflow and give examples of the equipment available, while discussing advantages and limitations of specific steps and their suitability for the research of various biofilms.

Microbial communities deliver essential functions in ecosystems. In plant environments, the plant microbiome facilitates nutrient uptake, supports plants during abiotic stress, and counteracts disease. As implementation of synthetic microbial communities becomes more of a realistic strategy for mitigating the effects of biotic and abiotic stressors on plant productivity, it is increasingly important to understand how interactions between microbes, which are essential for ecosystem function (hub microbes), are maintained. Recent research highlights the ecological role of bacteriophages, the viruses of bacteria, in host-associated microbial communities. Current evidence demonstrates the influence of the phageome on microbiomes, ranging from effects on an individual (transduction, lysogenic conversion, and evolutionary pressure) to entire populations and communities, such as Kill-the-Winner dynamics. These dynamics appear to affect the overall function of microbial communities and support plant growth. In this review, we lay out recent insights on the role of bacteriophages in plant-associated microbiomes through an eco-evolutionary lens and future directions of research to broaden our understanding of the ecological implications of bacteriophages.

The human gut microbiome-predominantly in the colon-comprises vastly more genetic material than that contained in human cells. Three papers in this journal highlight the functional consequences of imbalance (dysbiosis) of the gut microbiome regarding neurodegenerative conditions, cancer chemotherapy, and the wide-reaching consequences of aberrant metabolism of complex carbohydrates and amino acids in the gut.

Members of the genus Streptomyces are prolific producers of antibiotics and bioactive natural products, whose biosynthesis is intricately linked to complex social and ecological interactions. Understanding how these bacteria adaptively regulate development and natural product biosynthesis in response to diverse environmental cues remains incomplete. Here, recent advances are synthesised revealing that phenotypic plasticity in Streptomyces is underpinned by regulatory networks integrating physiological and social signals, enabling multicellular differentiation, division of labour, and alternative growth modes such as exploration and foraging. These dynamic responses allow colonies to balance competition, cooperation, and reproduction in fluctuating environments. Our insights highlight the ecological and evolutionary significance of plasticity in shaping Streptomyces biology, with implications for natural product discovery and understanding microbial community dynamics.