The microRNA pathway regulates obligatory aestivation in the cabbage stem flea beetle Psylliodes chrysocephala.

Aestivation, or summer diapause, is a dormancy strategy that enables animals to survive hot and dry summer conditions. Despite its ecological importance, the gene regulatory mechanisms underlying aestivation remain poorly understood. MicroRNAs (miRNAs) are post-transcriptional regulators involved in various biological processes, including development.

Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid-protein interaction sites by mass spectrometry.

Ultraviolet (UV) crosslinking with mass spectrometry (XL-MS) has been established for identifying RNA- and DNA-binding proteins along with their domains and amino acids involved. Here, we explore chemical XL-MS for RNA-protein, DNA-protein, and nucleotide-protein complexes in vitro and in vivo. We introduce a specialized nucleotide-protein-crosslink search engine, NuXL, for robust and fast identification of such crosslinks at amino acid resolution.

Microbial metacommunity of salt marshes rebuilds along an elevational gradient after initial disturbance.

Salt marshes are ecologically important ecosystems with dynamic nutrient exchange between land and sea. Their zonation along an elevation gradient supports specific communities exhibiting successional patterns. Previous studies have mainly focused on individual domains, with limited attempts to explore interdependencies of community assemblies across domains.

A roadmap to developing unified streptophyte algal model systems.

Over the last decade, collaborative efforts in plant evolutionary research have elucidated the phylogenetic relationships in the green plant lineage and provided insights into the emergence of land plants from a group of terrestrial and freshwater streptophyte algae. A foremost finding was that the genetic underpinnings of several key traits emerged much earlier than land plants - they were present in their streptophyte algal progenitors. Currently, the field is at a crossroads, transitioning from genomics-informed descriptions of streptophyte algae to a functional understanding of molecular mechanisms underlying their unique physiology, as well as to understanding their origin and evolution.

Nucleotide-bound crystal structures of the SARS-CoV-2 helicase NSP13.

Nucleotide-bound crystal structures of SARS-CoV-2 NSP13 in ADP- and ATP-bound states were resolved to 1.8 and 1.9 Å, respectively.

Algal origins of core land plant stress response subnetworks.

We computed co-expression networks from more than 2200 samples of nine species across 600 million years of divergent streptophyte evolution and infer that the streptophyte algal ancestors of land plants already had a remarkable fraction of the embryophytic stress response system. Despite its phytohormone-independent origin, homologs of all core components of the drought hormone abscisic acid (ABA) subnetwork are present, and we find that most are co-expressed in streptophyte algae and land plants; this subnetwork was thus co-opted in embryophytes by bringing it under the regime of ABA. The last common ancestor of embryophytes and Zygnematophyceae algae had ancient stress-responsive pathways, enabling it to face the stresses typical of the land environment - even before the origin of land plants - while evolution on land led to the adaptive refinement of these responses.

The Aspergillus nidulans velvet domain containing transcription factor VeA is shuttled from cytoplasm into nucleus during vegetative growth and stays there for sexual development, but has to return into cytoplasm for asexual development.

Survival of multicellular organisms requires the coordinated interplay between networks regulating gene expression and controlled intracellular transport of respective regulators. Velvet domain proteins are fungal transcription factors, which form various heterodimers and play key roles in controlling early developmental decisions towards more either asexual or sexual differentiation. VeA is the central subunit of the trimeric velvet complex VelB-VeA-LaeA, which links transcriptional to epigenetic control for the coordination of fungal developmental programs to specific secondary metabolite synthesis.

Protist genomics: key to understanding eukaryotic evolution.

All eukaryotes other than animals, plants, and fungi are protists. Protists are highly diverse and found in nearly all environments, with key roles in planetary health and biogeochemical cycles. They represent the majority of eukaryotic diversity, making them essential for understanding eukaryotic evolution.

proximity-labeling with TurboID to screen for protein-protein interactions in the filamentous ascomycete .

The Biotin Identification (BioID) method applies proximity-dependent labeling of co-localizing proteins to screen for protein-protein interactions . Therefore, the protein of interest (POI) is fused to a promiscuous biotin ligase. This ligase covalently biotinylates proximal proteins, which allows their specific enrichment and subsequent identification by mass spectrometry.

What can we learn from the ecophysiology of plants inhabiting extreme environments?: from 'sherplants' to 'shercrops'.

Already in the 19th Century it was proposed that ecophysiology could be best studied in regions with extreme climatic conditions. In the present perspective, we argue that perhaps this is timelier than ever. The main reason is the need to improve crops to be simultaneously more productive - due to increased population - and more stress-tolerant - due to climate change.

Myricetin-bound crystal structure of the SARS-CoV-2 helicase NSP13 facilitates the discovery of novel natural inhibitors.

The SARS-CoV-2 helicase NSP13 is a highly conserved and essential component of the viral replication machinery, making it a promising target for antiviral drug development. Here, we present the 2 Å resolution crystal structure of NSP13 bound to the natural flavonoid myricetin, revealing a conserved allosteric binding site. Guided by these structural findings, a virtual screening campaign identified the caffeic acid derivatives rosmarinic acid and chlorogenic acid as potential novel natural inhibitors, which were experimentally validated to inhibit RNA-unwinding activity.

Sexual reproduction in land plants: an evolutionary perspective.

We link key aspects of land plant reproductive evolution and detail how successive molecular changes leading to novel tissues and organs require co-evolution of communication systems between tissues. The transition of water-dependent reproduction of algae to mechanisms with very limited water dependence in many land plant lineages allowed plants to colonize diverse terrestrial environments, leading to the vast variety of extant plant species. The emergence of modified cell types, novel tissues, and organs enabled this transition; their origin is associated with the co-evolution of novel or adapted molecular communication systems and gene regulatory networks.

Adaptations in development and secondary metabolism of Aspergillus nidulans isolates from the Erbil province in Iraq.

Aspergillus nidulans is a common soil fungus, distributed worldwide. Adaptations in development and secondary metabolism of so far uncharacterized isolates from the Erbil province of Iraq were compared to each other and the commonly in laboratory work used strain A4 from Europe was used as a reference. Erb strains showed an increase in conidia formation during asexual development at 37°C when compared to A4.

Identification of an a-factor-like pheromone secreted by the heterothallic ascomycete Aspergillus fumigatus.

Members of the fungal kingdom serve as models for numerous cellular processes, among them sexuality. In heterothallic ascomycetes, mating-type systems ensure that only compatible isolates fuse to enter the sexual phase. This includes reciprocal secretion and recognition of pheromones, commonly termed α-factor and a-factor, which are processed from peptide precursors.

Isolation and characterization of sp. nov.: a carboxydotrophic hydrogenogen in the genus of isolated from a charcoal-burning pile.

A Gram-negative bacterial strain, designated ACPt, was isolated from the top of the covering soil of an active charcoal-burning pile. The cells of ACPt were strictly anaerobic, rod-shaped and grew optimally at 40 °C and pH 7. The substrates ribose, glucose, sucrose, raffinose, melezitose, pyruvate, vanillate, syringate, methanol and CO were utilized for growth.

Enhanced discovery of bacterial laccase-like multicopper oxidase through computer simulation and metagenomic analysis of industrial wastewater.

Laccases belong to the superfamily of multicopper oxidases (MCO), a group of enzymes with the ability to reduce oxygen to water in a reaction without producing harmful byproducts. Laccase activity is influenced by many factors, such as structure; the number, location and binding status of copper ions; and the substrate-binding status. A large number of sequences that have not been experimentally characterized yet have been annotated as laccases.

Soil bacterial community composition of different tropical land use systems in Jambi province, Indonesia.

We sequenced the V3-V4 region of 16S rRNA genes and transcripts to assess entire (DNA) and active (RNA) soil bacterial communities in four different Indonesian land use systems (jungle rubber, rubber, oil palm, and rainforest). and were dominant, with higher relative abundances at active community level.

Resolving the fungal velvet domain architecture by VelB.

Velvet transcription factors are found throughout the fungal kingdom and share a common velvet domain with a fold similar to that of animal NF-κB. They act as homodimeric or heterodimeric master regulators of fungal secondary metabolism, development, and differentiation. A comparison of velvet domains from 4,999 fungal velvet proteins revealed a conserved overall architecture, including an N-terminal DNA-binding region of approximately 30 amino acids and a C-terminal dimerization region of about 100 amino acids.

Rationally designed peptides inhibit the formation of α-synuclein fibrils and oligomers.

Parkinson's Disease (PD) is characterized by the pathological aggregation of α-synuclein (αSyn) into oligomers and amyloid fibrils, making αSyn aggregation a key target for drug development. Peptides have gained recent attention as potential agents to inhibit aggregation. Two previously identified peptide inhibitors, discovered through large-scale yeast screening, were used as templates for in silico mutagenesis aimed at designing novel peptides with improved efficacy in inhibiting αSyn aggregation and cytotoxicity.

Toward Antibody Production in Genome-Minimized Strains.

is a bacterial cell factory with outstanding protein secretion capabilities that has been deployed as a workhorse for the production of industrial enzymes for more than a century. Nevertheless, the production of other proteins with , such as antibody formats, has thus far been challenging due to specific requirements that relate to correct protein folding and disulfide bond formation upon export from the cytoplasm. In the present study, we explored the possibility of producing functional antibody formats, such as scFvs and scFabs, using the genome-reduced - and strain lineage.

Time-resolved oxidative signal convergence across the algae-embryophyte divide.

The earliest land plants faced a significant challenge in adapting to environmental stressors. Stress on land is unique in its dynamics, entailing swift and drastic changes in light and temperature. While we know that land plants share with their closest streptophyte algal relatives key components of the genetic makeup for dynamic stress responses, their concerted action is little understood.

Insights into the lemon (Citrus limon) epiphytic microbiome: impact of the biocontrol yeast Clavispora lusitaniae 146.

Background: Postharvest lemons are affected by several fungal infections, and as alternatives to chemical fungicides for combating these infections, different microbial biocontrol agents have been studied, with the Clavispora lusitaniae 146 strain standing out. Although strain 146 has proven to be an effective agent, the influence of a microbial biological control agent on the postharvest lemon microbiome has not been studied until now. Thus, this study aimed to evaluate how the epiphytic microbiome of postharvest lemons is affected by the application of the biocontrol yeast C.

Pan-phylum genomes of hornworts reveal conserved autosomes but dynamic accessory and sex chromosomes.

Hornworts, one of the three bryophyte phyla, show some of the deepest divergences in extant land plants, with some families separated by more than 300 million years. Previous hornwort genomes represented only one genus, limiting the ability to infer evolution within hornworts and their early land plant ancestors. Here we report ten new chromosome-scale genomes representing all hornwort families and most of the genera.

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.