Search Results (362)

Background: Hemiboea yongfuensis is a recently discovered critically endangered species. It is exclusive to the limestone regions of Yongfu County, Guilin, Guangxi. Currently, there is a lack of mitogenome data for Hemiboea species, hindering the potential of disclosing the evolutionary processes of the mitochondrial genome, which has been far less assembled and shown to be complex in the plant kingdom. Moreover, it prevents potential applications of mitochondrial genome data in phylogenetics and plant adaption, breeding, and conservation. Results: In order to reveal the mitochondrial features and variations and explore the usefulness of mitochondrial genes in phylogenetics, in this study, we assembled the complete mitogenome of H. yongfuensis using PacBio HiFi long reads, and analyzed its codon usage bias, RNA editing sites, repetitive sequences, sequence lateral transfer, phylogenetic relationships, and synteny. The linear mitochondrial genome assembly we obtained has a length of 619,997 bp and a GC content of 43.63%. The assembly encompasses 61 genes, which include 37 protein-coding genes (PCGs), 21 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Importantly, our analysis uncovered a significant presence of repetitive sequences with a high proportion of forward repeats in the mitogenome and significant transposition of sequences from the chloroplast to mitochondrion. Additionally, we revealed the codon usage characteristics of protein-coding genes and identified numerous RNA editing events. Furthermore, we assessed the collinearity of the species in the Gesneriaceae family and found rampant reorganizations. The phylogenetic analyses based on the mitochondrial PCGs for the entire Lamiales order show the monophyly of Gesneriaceae as well as other families and a general high phylogenetic resolution. Conclusions: Our study provides the first mitogenome data for H. yongfuensis and the genus Hemiboea, expanding the rapidly increasing but yet limited plant mitogenome resources. It enhances our understanding of the mitogenome and Lamiales evolution, whereas more potentials of the mitogenome data, such as its possible functions in adaptation to limestone habitats, conservation, and germplasm breeding, remain under-exploited. This first reported Hemiboea mitogenome in addition to more mitogenomes from the same and related species would shed further light on these unresolved issues in future studies. Full article

It has been known for decades that eukaryotic cellular mRNAs are frequently translated by multiple ribosomes organized into polysomes of diverse topology, including circular arrangements. The closed-loop model, in which the 5′ cap and 3′ poly(A) tail are bridged by initiation factors, provided a mechanistic basis for mRNA circularization and suggested that the spatial proximity of termini facilitates ribosome recycling. Various biochemical, structural, and imaging approaches—including electron microscopy, atomic force microscopy, cryo-electron tomography, and single-molecule fluorescence—have since demonstrated that polysomes indeed adopt compact and heterogeneous conformations, with circular assemblies representing a significant fraction. Although direct visualization of ribosome recycling remains technically challenging, ribosome turnover experiments, kinetic analyses and modeling support the concept of closed-loop-assisted reinitiation (CLAR), whereby terminating ribosomes are re-utilized to sustain translation efficiency. Together, the findings suggest that mRNA circularization is a dynamic and regulated state that enhances protein synthesis under specific conditions, while linear or modular polysome architectures may dominate in others. Understanding the balance between these modes of translation remains central to elucidating the interplay between mRNA topology, ribosome dynamics, and translational control. Full article

Yi’an Reservoir is located on a major tributary of the Baoquan River and hosts abundant aquatic resources, with Cyprinus carpio, Carassius auratus, and Hemiculter leucisculus as the dominant fish species. Water quality parameters significantly shape fish gut microbiota, which in turn plays a crucial role in host physiological functions. This study aimed to characterize the water quality parameters in Yi’an Reservoir and identify the microbial communities in both the aquatic environment and fish guts (C. carpio, C. auratus, and H. leucisculus) through 16S ribosomal RNA sequencing. The objective was to examine the associations of water quality parameters and aquatic environmental microbiota with the assembly of gut microbial communities in fish inhabiting this reservoir system. The water quality parameters showed significant site-specific differences, of which temperature and dissolved oxygen were highest at Location B, while pH was highest at Location A. The Cyanobium_PCC-6307 was identified as a major differentially abundant taxon at the genera level across different sampling sites. Furthermore, the gut microbiota of the same fish species exhibited substantial variation across different sampling sites. Redundancy analysis identified distinct environmental drivers at each location. Specifically, pH, conductivity, and total dissolved solids (TDS) showed positive correlations with the gut microbiota at Location A. In contrast, temperature, dissolved oxygen (DO), and the environmental abundance of Cyanobium PCC-6307 were positively correlated with the gut microbiota at Locations B and C. This study provides important insights for the conservation and management of aquatic resources in reservoir ecosystems. Full article

Orbea is a morphologically diverse lineage within the subtribe Stapeliinae, yet plastome evolution in Arabian taxa remains insufficiently characterized. This study reports the first complete chloroplast genomes of Orbea sprengeri subsp. commutata and O. wissmannii var. eremastrum and investigates plastome structure, sequence variability, and phylogenetic relationships across tribe Ceropegieae. Chloroplast genomes were assembled, annotated, and compared with 13 published plastomes representing major Ceropegieae lineages. Both Arabian plastomes displayed the typical quadripartite structure and identical gene content of 114 unique genes, including 80 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. However, O. wissmannii var. eremastrum exhibited pronounced structural divergence, possessing the largest plastome recorded for the tribe (170,054 bp), an 8.9 kb expansion of the inverted repeat regions, and an 8.4 kb inversion spanning the ndhG–ndhF region. Comparative analyses revealed conserved gene order across Ceropegieae but identified six highly variable loci (accD, clpP, ndhF, ycf1, psbM–trnD, and rpl32–trnL) as potential DNA barcodes. Selection pressure analyses indicated strong purifying selection across most genes, with localized adaptive signals in accD, ndhE, ycf1, and ycf2. Phylogenomic reconstruction consistently resolved the two Arabian Orbea taxa as a distinct clade separate from the African O. variegata. This study fills a gap in Ceropegieae plastid genomics and underscores the importance of sequencing additional Orbea species to capture the full extent of genomic variation within this diverse genus. Full article

Choy sum (Brassica rapa var. parachinensis) is an important vegetable crop in Brassicaceae. However, its mitochondrial genome has not been well studied. In this study, Illumina and Nanopore sequencing technologies were combined to assemble the complete mitochondrial genome of choy sum. The mitochondrial genome is a circular molecule of 219,775 bp, with a GC content of 45.23%. A total of 60 genes were annotated, including 33 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, 3 ribosomal RNA (rRNA) genes, and one pseudogene. A total of 466 RNA editing sites were identified in the PCGs. Codon usage analysis revealed that leucine (leu) was the most frequently used amino acid. Twenty-nine codons showed a relative synonymous codon usage (RSCU) value greater than 1. Most of these preferred codons ended with A or U. A total of 308 repetitive sequences were detected, including 136 dispersed repeats, 17 tandem repeats, and 55 simple sequence repeats (SSRs). Evolutionary analysis indicated that most mitochondrial genes are under negative selection. The highest nucleotide diversity detected in the cox2 gene suggests that this gene could serve as a valuable molecular marker for mitochondrial research in the species. Homology analysis found 22 homologous fragments between the mitochondrial and chloroplast genomes of choy sum. These fragments total 13,325 bp, representing 6.06% of the mitochondrial genome. Phylogenetic analysis showed that choy sum is most closely related to B. rapa var. purpuraria. This study offers a genomic resource for genetic improvement and breeding of choy sum. It also provides molecular insights into the evolution of Brassica species. Full article

Background/Objectives: Rapid cellular proliferation, a hallmark of malignancy, requires sustained and elevated protein synthesis, which in turn requires efficient ribosome biogenesis. The aim of this study was to evaluate the expression levels of TP53, C-MYC, FBL, and NCL in pre-B ALL and neuroblastoma tissues compared to healthy bone marrow samples—factors that may carry prognostic significance in pediatric malignancies. Materials and methods: The cohort included 45 pre-B ALL patients, 19 neuroblastoma patients, and 12 healthy bone marrow donors as controls. Total RNA was extracted from bone marrow or tumor samples and cDNA synthesis was performed with the Bio-Rad iScript kit. Quantitative PCR was conducted using SYBR Green chemistry, with GAPDH as the reference gene. Primers targeted TP53, C-MYC, FBL, and NCL, and gene expression was calculated using the 2^−ΔCt method. Results: The expression of C-MYC and FBL was found to be significantly decreased in patients with pre-B ALL in comparison to the healthy control group. NCL expression was highest in healthy donors, intermediate in pre-B ALL, and lowest in neuroblastoma. In addition to intergroup comparisons, correlations between gene expression levels were assessed within each diagnostic group. In the pre-B ALL group, a positive correlation was observed between TP53 and C-MYC expression, as well as between TP53 and both FBL and NCL. Furthermore, a significant positive correlation was found between FBL and NCL. In the neuroblastoma group, a statistically significant positive correlation was identified between C-MYC and FBL expression. In the control group, TP53 expression was positively correlated with NCL, and FBL expression showed a significant positive correlation with NCL. Conclusions: This study suggests the altered expression of ribosome biogenesis-related genes in pediatric pre-B acute lymphoblastic leukemia and neuroblastoma. The reported dysregulation suggests a disease-associated disruption in nucleolar function and translational regulation and may contribute to oncogenesis through altered ribosomal assembly, protein synthesis, or proliferative signaling. Full article

The function of the highly conserved GTPase LepA, a homolog of elongation factor EF-G, remains unknown in translation. However, there is biochemical data that it implicates in the 30S ribosomal subunit biogenesis. Here, using cryo-electron microscopy, we characterized 30S subunits isolated from an Escherichia coli strain with a deleted lepA gene. The cryo-EM maps for ∆lepA 30S particles were divided into classes corresponding to consecutive assembly intermediates: from particles characterized by unformed helices h44/h45 of the central decoding center (CDR) and highly flexible head, through intermediates with a distorted CDR and a partial stabilization of the head, to near-mature 30S subunits with correctly docked h44 in the CDR, accessible 3′ end of 16S rRNA for translation but significant flexibility in head domain. Cryo-EM analysis of ΔlepA 30S intermediates revealed that they predominantly proceed to nearly mature functional state and exhibit suboptimal flexibility in the head domain. This finding suggests that LepA likely contributes to the final proper stabilization of the 3′ domain of the 30S subunit during ribosome assembly. Full article

Background: The global incidence of multidrug-resistant and extensively drug-resistant tuberculosis continues to rise. The ribosome serves as a target for multiple antimicrobials, making functional research on it hold great significance. Methods: Using homologous recombination combined with a multiple serine integrase-mediated site-specific recombination system, we replaced the two endogenous rRNA operons in Mycobacterium smegmatis MC² 155 with a single copy of the single rRNA operon from Mycobacterium tuberculosis H37Rv, constructing the M. smegmatis BRkoA strain. We assessed growth kinetics at 37 °C, cold sensitivity at lower temperatures, transcriptional levels by RT-qPCR, 70S ribosome integrity through cryo-EM, and antimicrobial susceptibility by microdilution assays. Results: The BRkoA strain was successfully constructed. It exhibited markedly slower growth compared to the wild-type strain. Cold-sensitivity assays indicated potential ribosome assembly defects, while transcriptional analysis suggested altered rRNA processing and modification. Cryo-EM analysis further demonstrated the absence of specific ribosomal proteins in the BRkoA 70S ribosome. Moreover, BRkoA displayed reduced susceptibility tendency to several ribosome-targeting antibiotics, including kanamycin, amikacin, paromomycin, gentamicin, and linezolid. Conclusions: Replacement of the two endogenous rrn operons in M. smegmatis with a single copy of the single M. tuberculosis rrn operon using a serine integrase-mediated recombination system caused growth impairment and decreased sensitivity tendency to several ribosome-targeting antimicrobials. These findings suggest that ribosome structural variation contributes to intrinsic drug resistance mechanisms. Full article

Upon transcription, most mRNAs associate with the small ribosomal subunit, after which a fully translating ribosome assembles. Under starvation or stress, however, mRNA–ribosome associations are blocked and many mRNAs are instead sequestered with specific RNA-binding proteins into stress granules or other subcellular condensates, a process that has been extensively studied. In contrast, much less attention has been paid to the fate of ribosomes under these same conditions. Ribosomes can remain fully assembled but unbound to mRNA, entering an inactive, dormant state. Dormancy is often supported by specific protein factors which protect ribosomes from degradation and facilitate reactivation once growth conditions improve. In this review, we highlight that dormant ribosome states are well defined in prokaryotes, in part because they possess distinct and experimentally tractable features, such as stable vacant 100S dimers. In eukaryotes, by contrast, analogous disomes are largely absent, making their discovery more indirect and method-dependent. We therefore focus on how evidence for eukaryotic dormant ribosomes has been assembled through multiple independent findings and how their interpretation depends critically on the experimental approaches used to study them. Finally, we consider atypical ribosomal states, such as translationally inactive polysomes in neurons, which underscore the context-dependent nature of ribosome activity. Full article

Bacteriophages are powerful drivers of microbial evolution and are increasingly explored as alternatives to antibiotics against multidrug-resistant pathogens such as Pseudomonas aeruginosa. Here, we describe the isolation, phenotypic characterization and genomic, structural and evolutionary analysis of Pseudomonas phage Adele, a lytic myovirus representing a novel species within the genus Pakpunavirus (family Vandenendeviridae). Phage Adele exhibits a short latent period of 20 min, a burst size of 59 ± 11 virions per infected cell and a high virulence index, efficiently lysing non-O11 Pseudomonas aeruginosa strains and reducing biofilm biomass. In vivo, Adele confers marked protection in a Galleria mellonella infection model. Phylogenetic reconstruction, synteny analysis and structural modeling demonstrate the relatedness of Vandenendeviridae to phages of the Andersonviridae and Vequintavirinae clades, pointing to a stable, ancestral virion architecture that has undergone lineage-specific elaborations, including the duplication and divergence of tail tube proteins. The tail assembly chaperone gene employs a conserved −1 programmed ribosomal frameshift. Phage Adele encodes an elaborate set of metabolic reprogramming and anti-defense systems, reflecting extensive horizontal gene transfer. The combination of a conserved structural architecture and mosaic genome establishes Adele as an exemplary system for studying modular evolution in phages, alongside its demonstrated therapeutic efficacy. Full article

Microinflammation serves as a central mechanism linking metabolic diseases and cancer. This study integrates gene expression profiles from irritable bowel syndrome (IBS), obesity, type 2 diabetes (T2D), colorectal cancer (CRC), renal cell carcinoma (RCC), and pancreatic cancer (PC) to identify shared molecular drivers of inflammation-mediated pathology. Weighted gene co-expression network analysis (WGCNA) revealed three highly preserved modules (blue, brown, turquoise) enriched in RNA processing, spliceosome assembly, ribosome biogenesis, and proteostasis regulation. Key hub genes, along with regulatory miRNAs have interconnected networks that modulate transcription, mRNA maturation, protein synthesis, and inflammatory signaling. Although classical inflammatory pathways were not directly enriched, their activity appears to be indirectly shaped by disruptions in RNA-processing and proteostasis machinery. Additionally, gut microbiota-derived products and altered metabolic states may further reinforce these transcriptional and post-transcriptional imbalances. Collectively, these findings reveal conserved molecular signatures that bridge microinflammation, metabolic disease, and oncogenesis, and highlight potential diagnostic and therapeutic targets centered on RNA regulation, proteostasis, and miRNA-mediated control Full article

Musk deer (Moschidae), a primitive lineage within Ruminantia, are distributed across East Asia and have long been of interest in molecular phylogenetic research. The spotted forest musk deer from Huanglong (HL) Mountain in Shaanxi, China, has long been morphologically classified as Moschus moschiferus (Siberian musk deer). However, its true taxonomic status has remained uncertain due to the lack of comprehensive molecular evidence. Moreover, studies on mitochondrial genome (mitogenome) variation within Moschidae, particularly at the intraspecific level, remain limited. To date, few phylogenetic analyses of Moschidae have incorporated all available complete mitochondrial genomes from public databases. In this study, we sequenced and assembled the complete mitogenomes of two spotted musk deer individuals from Huanglong Mountain, Shaanxi, China, and identified them as M. berezovskii (forest musk deer) by phylogenetic analysis. All available complete mitochondrial genomes of Moschidae were also included in the phylogenetic reconstruction. The average complete mitogenome length of M. berezovskii distributed in HL was 16,355 bp, and comprises 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. Phylogenetic analysis and genetic distance indicate that the taxonomic identity of the HL Mountain population as M. berezovskii supports the monophyly of M. berezovskii and provides a robust phylogenetic framework for clarifying evolutionary relationships within the family. Full article

Background: Semisulcospiridae is a family of freshwater gastropods with over 100 species, primarily distributed in East Asia and North America. They play crucial ecological roles and are of medical importance as intermediate hosts for parasites. However, their phylogenetic relationship remains unclear. Most previous studies, which focused on fewer molecular markers (e.g., COI, 16S, 28S), have shown limitations in resolving relationships with low resolution. Mitochondrial genomes, with their richer phylogenetic information, offer a promising tool to infer the evolutionary relationships within this family. Methods: This study sequenced, assembled, and annotated the complete mitochondrial genomes of three Semisulcospiridae species from China: Koreoleptoxis friniana, Hua textrix, and Hua yangi. Phylogenetic analyses were conducted using Maximum Likelihood (ML) and Bayesian Inference (BI) methods on five distinct datasets derived from the mitochondrial genomes, including nucleotide sequences of protein-coding genes (with and without third codon positions), amino acid sequences, and combinations with two ribosomal RNA genes. Results: The complete (or near-complete) mitochondrial genomes of K. friniana, H. textrix, and H. yangi were 15,474 bp, 15,660 bp, and 15,744 bp in length, respectively, showing typical gene content and an A+T bias. The gene order was highly conserved. Phylogenetic analyses consistently recovered the family Semisulcospiridae as monophyletic and revealed three well-supported, distinct clades corresponding to the genera Semisulcospira, Koreoleptoxis, and Hua. While the overall tree topologies were robust for Semisulcospiridae, some incongruences were observed in the placements of other cerithioidean families depending on the dataset used. Evolutionary rate analysis (Ka/Ks) indicated strong purifying selection across all protein-coding genes, with COX1 being the most conserved. Conclusions: This study provided three new mitochondrial genomes for Semisulcospiridae: K. friniana, H. textrix, and H. yangi. Phylogenetic analysis based on mitochondrial genome datasets offers new evidence that supports the monophyly of the three Asian genera of Semisulcospiridae. Future research should include broader taxonomic sampling, particularly of the North American genus Juga and the atypical Japanese Semisulcospira lineages, to achieve a comprehensive phylogenetic framework. Full article

Microproteins are small polypeptides translated from short open reading frames (sORFs) that typically encode < 100 amino acids. Advances in ribosome profiling, mass spectrometry, and computational prediction have revealed a growing number of microproteins that play important roles in cellular metabolism, organelle function, and stress adaptation; however, these were considered non-coding or functionally insignificant. At the mitochondrial level, microproteins, such as MTLN (also known as mitoregulin/MOXI) and BRAWNIN, contribute to lipid oxidation, oxidative phosphorylation efficiency, and respiratory chain assembly. Other microproteins at the endoplasmic reticulum–mitochondria interface, including PIGBOS and several muscle-resident regulators of calcium cycling, show diverse biological contexts in which these microproteins act. A subset of microproteins responds to nutrient availability. For example, SMIM26 modulates mitochondrial complex I translation under serine limitation, and non-coding RNA expressed in mesoderm-inducing cells encoded with peptides facilitates glucose uptake during differentiation, indicating that some microproteins can affect metabolic adaptation through localized translational- or organelle-level mechanisms. Rather than functioning as primary nutrient sensors, these microproteins complement classical nutrient-responsive pathways such as AMP-activated protein kinase-, peroxisome proliferator-activated receptor-, and carbohydrate response element binding protein-mediated signaling. As the catalog of microproteins continues to expand, integrating proteogenomics, nutrient biology, and functional studies will be central to defining their physiological relevance; these integrative approaches will also help reveal their potential applications in metabolic health. Full article

This study presents the complete assembly and analysis of the mitochondrial genome (mitogenome) of Medicago lupulina L. var. vulgaris Koch, cultivar-population VIK32, line MlS-1, which forms an effective symbiosis not only with arbuscular mycorrhiza but also with the root nodule bacteria Sinorhizobium meliloti. The assembly, generated using a hybrid sequencing approach, revealed sequences of putative horizontal origin. These include a highly conserved open reading frame (ORF), orf279, encoding a protein structurally homologous to maturase K, yet bearing remote similarity to bacterial reverse transcriptases and CRISPR-associated proteins. We also identified sequences homologous to mitovirus RNA-dependent RNA polymerases and a fragment of the chloroplast 23S ribosomal RNA (rRNA), suggesting historical gene transfers from viruses and plastids. This work establishes a foundation for investigating the role of mitochondrial genome variation in key plant’s phenotypic traits, such as the enhanced responsiveness to arbuscular mycorrhiza observed in this agronomically valuable line. Full article