Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

Genetic Basis of Reproductive Isolation in Torrey Pine (Pinus torreyana Parry): Insights From Hybridization and Adaptation

Tree species are often locally adapted to their environments, but the extent to which environmental adaptation contributes to incipient speciation is unclear. One of the rarest pines in the world, Torrey pine (Pinus torreyana Parry), persists naturally across one island and one mainland population in southern California. The two populations are morphologically and genetically differentiated but experience some connectivity, making it an ideal system for assessing the evolution of reproductive isolation. Previous work has found evidence of heterosis in F1 mainland-island hybrids, suggesting genetic rescue could be beneficial in the absence of reproductive barriers. Using ddRADseq and GWAS for a common garden experiment of island, mainland, and F1 individuals, we identified candidate loci for environmentally driven reproductive isolation, their function, and their relationship to fitness proxies. By simulating neutral evolution and admixture between the two populations, we identified loci that exhibited reduced heterozygosity in the F1s, evidence of selection against admixture. SNPs with reduced F1 heterozygosity were enriched for growth and pollination functions, suggesting genetic variants that could be involved in the evolution of reproductive barriers between populations. One locus with reduced F1 heterozygosity exhibited strong associations with growth and reproductive fitness proxies in the common garden, with the mainland allele conferring increased fitness. If this locus experiences divergent selection in the two natural populations, it could promote their reproductive isolation. Finally, although hybridization largely reduced allele fixation in the F1s initially, indicating heterosis is likely due to the masking of deleterious alleles, the emergence of reproductive isolation between populations may diminish the longer-term benefits of genetic rescue in F2 or advanced-generation hybrids. As Torrey pine is a candidate for interpopulation genetic rescue, caution is warranted where longer-term gene flow between diverged populations may result in reduced fitness if barriers have evolved.

Phylogenomics as baseline for taxonomy description: Amphibiibacter pelophylacis gen. nov., sp. nov., a novel taxon of the family Sphaerotilaceae, class Betaproteobacteria, isolated from the skin microbiota of Pelophylax perezi from different populations

Bacterial strain SL12-8T was characterized and isolated from the skin microbiota of Pelophylax perezi, the Perez's frog. Strain SL12-8T stained Gram-negative and formed rod-shaped cells that grew optimally at 25 °C and pH 7.0-7.5. The G+C content of the DNA was 66.2 mol%. Ubiquinone 8 was the respiratory quinone identified in the studied strain and the most closely related taxon. The major fatty acids were summed in feature 3 and summed in feature 8 and C16:0, representing 84% of the total fatty acids. Phylogenetic analyses based on the 16S rRNA gene sequence placed strain SL12-8T within the order Burkholderiales in a distinct lineage. The 16S rRNA gene sequence similarities of strain SL12-8T to that of Rubrivivax albus, Scleromatobacter humisilvae, Piscinibacter aquaticus, Azohydromonas caseinilytica and Aquincola agrisoli were 94.41, 94.08, 93.72, 93.72 and 93.64%, respectively. The draft genome sequence of strain SL12-8T comprises 3,115,197 bases with a 313-fold mapped genome coverage. The assembled genome consists of 53 large contigs with more than 500 bp, and the genome encodes 2,814 putative coding sequences. The analysis of the available genomes from the closest genera showed 124 core genes that reveal a novel genus-level clade including the strain SL12-8T. Analysis of the SL12-8T genome revealed the presence of the beta-lactone and terpene biosynthetic gene clusters. The phylogenomic, phylogenetic, phenotypic and chemotaxonomic data showed that strain SL12-8T (=UCCCB 131T=CECT 30762T) represents the type of a novel species and genus, for which we propose the name Amphibiibacter pelophylacis gen. nov., sp. nov.

Engineering archaeal membrane-spanning lipid GDGT biosynthesis in bacteria: Implications for early life membrane transformations

Eukaryotes are hypothesized to be archaeal-bacterial chimeras. Given the different chemical structures of membrane phospholipids in archaea and bacteria, transformations of membranes during eukaryogenesis that led to the bacterial-type membranes of eukaryotic cells remain a major conundrum. One of the possible intermediates of eukaryogenesis could involve an archaeal-bacterial hybrid membrane. So far, organisms with hybrid membranes have not been discovered, and experimentation on such membranes has been limited. To generate mixed membranes, we reconstructed the archaeal membrane lipid biosynthesis pathway in Escherichia coli, creating three strains that individually produced archaeal lipids ranging from simple, such as DGGGOH (digeranylgeranylglycerol) and archaeol, to complex, such as GDGT (glycerol dialkyl glycerol tetraether). The physiological responses became more pronounced as the hybrid membrane incorporated more complex archaeal membrane lipids. In particular, biosynthesis of GDGT induced a pronounced SOS response, accompanied by cellular filamentation, explosive cell lysis, and ATP accumulation. Thus, bacteria seem to be able to incorporate simple archaeal membrane lipids, such as DGGGOH and archaeol, without major fitness costs, compatible with the involvement of hybrid membranes at the early stages of cell evolution and in eukaryogenesis. By contrast, the acquisition of more complex, structurally diverse membrane lipids, such as GDGT, appears to be strongly deleterious to bacteria, suggesting that this type of lipid is an archaeal innovation.

The first two human infections with Helicobacter zhangjianzhongii, a new Helicobacter closely related to Helicobacter canis

PURPOSE

In 2023, Helicobacter zhangjianzhongii was proposed as a new species in the Helicobacter genus. We here describe two human cases of H. zhangjianzhongii bacteremia.

METHODS

Four clinical strains from the Helicobacter genus isolated from blood culture between 2017 and 2023 were studied. They were initially identified as H. canis by MALDI-TOF and 16S rDNA sequencing. The strains were biochemically characterized and tested at different temperatures and atmospheres. Two databases were used to characterize the isolates: the Bruker® MBT compass Version 4.1.1 database and a in-house spectrum-enriched database. After bacterial DNA extraction the genomes were sequenced on NovaSeq 6000 (Illumina) and analyzed using an in-house pipeline.

RESULTS

Case 1 involved a 58-year-old woman who was hospitalized in a thoracic oncology unit because her general condition deteriorated in a setting of small-cell carcinoma. She presented with abdominal pain associated with significant hepatomegaly. Case 2 involved a 78-year-old woman on rituximab who was hospitalized to treat chest pain, anemia, and inflammatory syndrome. Both strains exhibited very similar microbiological and genomic characteristics, thus growth in a microaerobic atmosphere at 37°C and 42°C, oxidase-positivity, and urease- and catalase-negativity. Both were formally identified by whole-genome sequencing as H. zhangjianzhongii (ANI > 99% and DDH > 94%).

CONCLUSION

This proposed species is associated with bacteremia in humans. It is thus likely to be a novel human pathogen. Dogs may have been the source of infection.

Diatom heterotrophy on brown algal polysaccharides emerged through horizontal gene transfer, gene duplication, and neofunctionalization

A major goal of evolutionary biology is to identify the genetic basis for the emergence of complex adaptive traits. Diatoms are ancestrally photosynthetic microalgae. However, in the genus Nitzschia, loss of photosynthesis led to a group of free-living secondary heterotrophs whose manner of acquiring chemical energy is unclear. Here, we sequence the genome of the non-photosynthetic diatom Nitzschia sing1 and identify the genetic basis for its catabolism of the brown algal cell wall polysaccharide alginate. N. sing1 obtained an endolytic alginate lyase enzyme by horizontal gene transfer (HGT) from a marine bacterium. Subsequent gene duplication through unequal crossing over and transposition led to 91 genes in three distinct gene families. One family retains the ancestral endolytic enzyme function. By contrast, the two others underwent domain duplication, gain, loss, rearrangement, and mutation to encode novel functions that can account for oligosaccharide import through the endomembrane system and the exolytic production of alginate monosaccharides. Together, our results show how a single HGT event followed by substantial gene duplication and neofunctionalization led to alginate catabolism and access to a new ecological niche.

A premature termination codon mutation in the onion AcCER2 gene is associated with both glossy leaves and thrip resistance

Plant epicuticular waxes (EW) play a critical role in defending against biotic and abiotic stresses. Notably, onions (Allium cepa L.) present a distinctive case where the mutant with defect in leaf and stalk EW showed resistance to thrips compared with the wild type with integral EW. We identified a premature stop codon mutation in the AcCER2 gene, an ortholog of CER2 gene in Arabidopsis thaliana that has been proved essential for the biosynthesis of very long-chain fatty acids (VLCFAs), in the onions with glossy leaf and stalks in our experiments. The data hinted at the possibility that this mutation might impede the elongation process of VLCFAs from C28 to C32, thereby hindering the production of 16-hentriacontanone, a primary constituent of onion EW. Transcriptomic analysis revealed substantial alterations in expression of genes in the pathways related not only to lipid synthesis and transport but also to signal transduction and cell wall modification in glossy mutants. Meanwhile, metabolomic profiling indicates a remarkable increase in flavonoid accumulation and a significant reduction in soluble sugar content in glossy mutants. These findings suggested that the enhanced resistance of glossy mutants to thrips might be a consequence of multiple physiological changes, and our integrated multiomics analysis highlighting the regulatory role of AcCER2 in these processes. Our study has yielded valuable insights into the biosynthesis of onion EW and has provided an initial hypothesis for the mechanisms underlying thrip resistance. These findings hold significant promise for the breeding programs of thrip-resistant onion.

Meniscomyces senecionis sp. nov., a novel anamorphic basidiomycete yeast species

A novel basidiomycete yeast, designated as NYNU 2211380, was isolated from a leaf of Senecio scandens collected in the Baotianman Nature Reserve, Henan Province, central China. Phylogenetic analyses of the D1/D2 domain of the LSU rRNA gene and the internal transcribed spacer (ITS) region revealed its close relationship to Meniscomyces layueensis, differing by 3.4% mismatches (14 substitutions and 6 gaps) in the D1/D2 domain and 12.4% mismatches (35 substitutions and 37 gaps) in the ITS region. The novel strain also exhibits distinct physiological traits, including an inability to assimilate maltose and cellobiose and the ability to utilize d-xylose, d-ribose, glycerol, ribitol, d-mannitol, dl-lactate and d-gluconate. Based on phylogenetic and phenotypic data, the strain represents a new species in the genus Meniscomyces, for which the name Meniscomyces senecionis sp. nov. (Holotype: CICC 33585; MycoBank: MB 857392) is proposed.

PBAN regulates sex pheromone biosynthesis by Ca2+/CaN/ACC and Ca2+/PKC/HK2 signal pathways in Spodoptera litura

Sex pheromones emitted by female moths play important roles in mate attraction. The molecular mechanism underlying pheromone biosynthesis activating neuropeptide (PBAN)-regulated sex pheromone biosynthesis has been well elucidated in many moth species, although this mechanism is species-dependent. Spodoptera litura, an important pest, has caused serious economic losses to agricultural production, yet the mechanism for its sex pheromone biosynthesis has not been fully identified. The present study investigates in detail mechanism underlying PBAN-regulated sex pheromone biosynthesis in S. litura. The transcriptome sequencing of S. litura pheromone glands (PGs) was analysed to identify a serial of candidate genes potentially involved in sex pheromone biosynthesis. Further investigation revealed a bimodal pattern in both sex pheromone release and mating frequency. PBAN was found to regulate sex pheromone biosynthesis via its receptor by using Ca2+ as a secondary messenger, as demonstrated by RNA interference and the application of pharmacological inhibitors. Furthermore, PBAN/Ca2+ signalling activated calcineurin (CaN) and acetyl-CoA carboxylase (ACC), which mediated sex pheromone biosynthesis in response to PBAN stimulation. Mostly importantly, hexokinase 2 (HK2) was confirmed to be activated by PBAN/PBANR /Ca2+/PKC signalling via phosphorylation at two specific sites (ser423 and ser434 sites of HK2). Overall, our findings shed light on the intricate processes involved in sex pheromone production in S. litura, in which PBAN regulates sex pheromone biosynthesis through PBAN/PBANR/Ca2+/CaN/ACC and PBAN/PBANR/Ca2+/PKC/HK2 signalling pathways. These insights significantly contribute to our comprehension of the specific mechanisms underlying sex pheromone biosynthesis in this moth species.

Initial Characterization of 12 New Subtypes and Variants of Type V CRISPR Systems

Type V CRISPR systems are highly diverse in sequence, mechanism, and function. Although recent efforts have greatly expanded our understanding of their evolution, the diversity of type V systems remains to be completely explored, and many clades have not been experimentally characterized. In this work, we mined metagenomic databases to identify three new subtypes and nine new variants of Cas12, the effector of Type V systems, and provide experimental and computational characterization of their Protospacer-Adjacent Motif (PAM), interference activity, loci architecture, and tracrRNA dependence. Half of the new Cas12s are found in phages or prophages. New subtypes Cas12o and Cas12p lack the canonical RuvC catalytic residues, suggesting they interfere with the target without cleavage, possibly by blocking transcription or replication. One variant, Cas12f10, displays substantial activity on PAM-less targets. Our work expands the diversity of the functionally characterized Cas12 effectors and provides some promising candidates for genome engineering tools.

Deciphering bacterial protein functions with innovative computational methods

Bacteria colonize every niche on Earth and play key roles in many environmental and host-associated processes. The sequencing revolution revealed the remarkable bacterial genetic and proteomic diversity and the genomic content of cultured and uncultured bacteria. However, deciphering functions of novel proteins remains a high barrier, often preventing the deep understanding of microbial life and its interaction with the surrounding environment. In recent years, exciting new bioinformatic tools, many of which are based on machine learning, facilitate the challenging task of gene and protein function discovery in the era of big genomics data, leading to the generation of testable hypotheses for bacterial protein functions. The new tools allow prediction of protein structures and interactions and allow sensitive and efficient sequence- and structure-based searching and clustering. Here, we summarize some of these recent tools which revolutionize modern microbiology research, along with examples for their usage, emphasizing the user-friendly, web-based ones. Adoption of these capabilities by experimentalists and computational biologists could save resources and accelerate microbiology research.

Archaean green-light environments drove the evolution of cyanobacteria's light-harvesting system

Cyanobacteria induced the great oxidation event around 2.4 billion years ago, probably triggering the rise in aerobic biodiversity. While chlorophylls are universal pigments used by all phototrophic organisms, cyanobacteria use additional pigments called phycobilins for their light-harvesting antennas-phycobilisomes-to absorb light energy at complementary wavelengths to chlorophylls. Nonetheless, an enigma persists: why did cyanobacteria need phycobilisomes? Here, we demonstrate through numerical simulations that the underwater light spectrum during the Archaean era was probably predominantly green owing to oxidized Fe(III) precipitation. The green-light environments, probably shaped by photosynthetic organisms, may have directed their own photosynthetic evolution. Genetic engineering of extant cyanobacteria, simulating past natural selection, suggests that cyanobacteria that acquired a green-specialized phycobilin called phycoerythrobilin could have flourished under green-light environments. Phylogenetic analyses indicate that the common ancestor of modern cyanobacteria embraced all key components of phycobilisomes to establish an intricate energy transfer mechanism towards chlorophylls using green light and thus gained strong selective advantage under green-light conditions. Our findings highlight the co-evolutionary relationship between oxygenic phototrophs and light environments that defined the aquatic landscape of the Archaean Earth and envision the green colour as a sign of the distinct evolutionary stage of inhabited planets.

Targeted discovery of diterpene compounds ostamycins with anti-influenza a viral activity from a deepsea-derived Streptomyces strain

Heterologous expression of a nonconventional terpene biosynthetic gene cluster from the deepsea-derived Streptomyces amphotericinicus DS22-01 led to the production of a novel cyclic diterpene, ostamycin A (1). Anti-influenza A virus activity evaluation revealed that compound 1 showed significant activity with an IC50 value of 4.72 μM, which was much stronger than that of the positive control ribavirin (IC50 = 20.80 μM). Inspired by its intriguing activity, yield optimization was achieved through a combined approach involving promoter engineering and codon modification in a stepwise manner. This strategy led to a ∼ 13-fold increase in the production of ostamycin A (1), as well as the concurrent accumulation of another novel cyclic diterpene, ostamycin B (2), which also displayed anti-influenza A virus activity with an IC50 value of 195.59 μM. The planar structures and stereochemistry of compounds 1 and 2 were established through extensive MS and NMR spectroscopic analyses together with ECD calculations. Further investigations revealed that compound 1 inhibits the influenza A virus (A/Puerto Rico/8/34) replication by directly targeting the nucleoprotein (NP). These findings highlight compound 1 as a promising lead for the development of novel influenza virus inhibitors.

Rodentibacter abscessus sp. nov. isolated from pet hamster subcutaneous abscess

Five strains related to the genus Rodentibacter were isolated from five pet hamsters kept in Japan. Isolates were genotypically and phenotypically distinct from previously described species within the genus Rodentibacter (family Pasteurellaceae). The five strains were the most genetically similar to Rodentibacter haemolyticus 1625-19T, exhibiting a 16S rRNA gene sequence similarity of 96.5%, an average nucleotide identity value of 90.8% and a digital DNA-DNA hybridization value of 42.7%. Phenotypic characteristics further distinguish the isolated strains from other Rodentibacter species. Although they share β-haemolysis capacity with R. haemolyticus, the novel strains are differentiated by their positive reactions for α-glucosidase, l-arabinose and trehalose, as well as negative reactions for β-glucuronidase, mannose, inositol and glycerol. Genotypic and phenotypic differences between the novel strains and closely related known strains suggested that we have identified a new Rodentibacter species. We propose the name Rodentibacter abscessus sp. nov. The type strain is THUN1654T with a G+C DNA content of 40.6 mol%, and it is deposited in the DSMZ Germany (DSM 118002T), KCTC Korea (KCTC 8595T) and JCM Japan (JCM 37054T).

α/β Hydrolases: Toward Unraveling Entangled Classification

α/β Hydrolase-like enzymes form a large and functionally diverse superfamily of proteins. Despite retaining a conserved structural core consisting of an eight-stranded, central β-sheet flanked with six α-helices, they display a modular architecture allowing them to perform a variety of functions, like esterases, lipases, peptidases, epoxidases, lyases, and others. At the same time, many α/β hydrolase-like families, even enzymatically distinct, share a high degree of sequence similarity. This imposes several problems for their annotation and classification, because available definitions of particular α/β hydrolase-like families overlap significantly, so the unambiguous functional assignment of these superfamily members remains a challenging task. For instance, two large and important peptidase families, namely S9 and S33, blend with lipases, epoxidases, esterases, and other enzymes unrelated to proteolysis, which hinders automatic annotations in high-throughput projects. With the use of thorough sequence and structure analyses, we newly annotate three protein families as α/β hydrolase-like and revise current classifications of the realm of α/β hydrolase-like superfamily. Based on manually curated structural superimpositions and multiple sequence and structure alignments, we comprehensively demonstrate structural conservation and diversity across the whole superfamily. Eventually, after detailed pairwise sequence similarity assessments, we develop a new clustering of the α/β hydrolases and provide a set of family profiles allowing for detailed, reliable, and automatic functional annotations of the superfamily members.

Viral piracy of host RNA phosphatase DUSP11 by avipoxviruses

Proper recognition of viral pathogens is an essential part of the innate immune response. A common viral replicative intermediate and chemical signal that cells use to identify pathogens is the presence of a triphosphorylated 5' end (5'ppp) RNA, which activates the cytosolic RNA sensor RIG-I and initiates downstream antiviral signaling. While 5'pppRNA generated by viral RNA-dependent RNA polymerases (RdRps) can be a potent activator of the immune response, endogenous RNA polymerase III (RNAPIII) transcripts can retain the 5'ppp generated during transcription and induce a RIG-I-mediated immune response. We have previously shown that host RNA triphosphatase dual-specificity phosphatase 11 (DUSP11) can act on both host and viral RNAs, altering their levels and reducing their ability to induce RIG-I activation. Our previous work explored how experimentally altered DUSP11 activity can impact immune activation, prompting further exploration into natural contexts of altered DUSP11 activity. Here, we have identified viral DUSP11 homologs (vDUSP11s) present in some avipoxviruses. Consistent with the known functions of host DUSP11, we have shown that expression of vDUSP11s: 1) reduces levels of endogenous RNAPIII transcripts, 2) reduces a cell's sensitivity to 5'pppRNA-mediated immune activation, and 3) restores virus infection defects seen in the absence of DUSP11. Our results identify a context where DUSP11 activity has been co-opted by viruses to alter RNA metabolism and influence the outcome of infection.

Evidence for the Existence of Mating Subtypes Within the Schizophyllum commune: Mating Behavior and Genetic Divergence

Schizophyllum commune, a Basidiomycota fungus with a tetrapolar mating system, serves as a key model for studying sexual reproduction. In this study, two distinct mating subtypes (I and II) were identified in strain 20R-7-ZF01, isolated from subseafloor sediment, which exhibited eight different mating interaction phenotypes. Intra-subtypes exhibited colony-symmetric tetrapolar interactions (G1), whereas inter-subtype crosses yielded colony-asymmetric phenotypes (G2) and a reduced number of fruiting bodies. Nuclear migration analysis revealed that both subtypes follow the same sexual reproductive process, suggesting functional similarities despite the different reproductive outcomes. Gene silencing of mating-type loci identified the genes bbp2-9 and bbp2-7 within the B locus as key factors in determining mating subtype identity. Additionally, a similar pattern of mating subtype differentiation was observed in five other S. commune strains from both subseafloor and terrestrial environments. These findings highlight the genetic diversity within S. commune, challenge the classical understanding of fungal mating systems, and provide new insights into the genetic evolutionary mechanisms governing fungi with tetrapolar mating systems.

Modulation of peptidoglycan recognition protein expression alters begomovirus vectoring efficiency and fitness of Bemisia tabaci

Peptidoglycan recognition proteins (PGRPs) are evolutionarily conserved molecules. Their role in the immune response to invading pathogens makes them a natural target for viral defence study in a wide range of organisms. Silverleaf whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is one of the invasive insect pests and transmits begomoviruses in a circulative and persistent manner to vegetables, legumes, fibres and ornamentals. The virus entry, retention, circulation, and release process involve interactions with several proteins in B. tabaci and evade innate immunity to avoid the antiviral mechanisms. The present study investigated the role of BtPGRP in chilli leaf curl virus (ChiLCV, Begomovirus capsica) transmission by B. tabaci. Silencing of BtPGRP using double-stranded (ds) RNA led to the loss of innate immunity to ChiLCV resulting in increased virus titre in B. tabaci. DsBtPGRP was orally administered to adults of B. tabaci at a concentration of 1, 3, and 5 μg/mL. The expression of BtPGRP was downregulated up to 4.67-fold. The virus titre in B. tabaci increased 90.05 times post-exposure to dsBtPGRP at 5 μg/mL. The test plants inoculated with ChiLCV by dsBtPGRP-exposed B. tabaci expressed severe curling symptoms with a higher virus load and transmission ratio than the control. Besides, the silencing of BtPGRP also induced up to 56.67% mortality in treated B. tabaci. The active site pocket of BtPGRP was found to interact directly with the ChiLCV-CP in computational analyses. Key residues of BtPGRP, including Tyr45, Asp84, His86, Trp87, and Asn119 exhibited critical interactions with the ChiLCV-CP. To our knowledge, this is the first report on the effect of PGRP silencing on ChiLCV acquisition and transmission efficiency and fitness of B. tabaci Asia II I.

Transcriptome sequencing on different ages of Saraca asoca bark: Insights from tannin biosynthetic pathways and EST-SSR marker design

The bark of Saraca asoca is extensively used for treating gynecological issues, primarily due to its tannin content. This study focused on transcriptome sequencing of young (BY; 0-6 years), middle-aged (BM; 6-12 years), and old (BO; >12 years) Ashoka barks. The de novo assembly produced 1,37,451 unigenes of 1,31,647,800 bp from BY, 1,16,825 unigenes of 1,15,283,571 bp from BM, and 81,825 unigenes of 68,553,092 bp from BO samples. These transcripts closely matched with Glycine max and Cajanus cajan. Transcriptome analysis identified key genes and enzymes in the tannin biosynthetic pathway, with higher levels of phenylpropanoid and flavonoid pathways observed in middle-aged samples, followed by young and old samples. Pathway enrichment analysis indicated that the Differentially Expressed Genes (DEGs) were predominantly in the biosynthetic pathways of flavonoids, isoflavonoids, anthocyanins, terpenoids, and isoquinoline alkaloids. The study also examined the up-regulated and down-regulated DEGs involved in tannin production across the different sample comparisons, revealing the flavonoid pathway to be the most regulated. Additionally, 9612, 8053, and 4659 simple sequence repeats (SSRs) were identified from BY, BM, and BO transcripts, respectively. Fourteen EST-SSR markers specific to tannins were designed and validated, with one found to be polymorphic. This research represents the first report on transcriptome sequencing and EST-SSR markers from various ages of Saraca asoca bark, providing a foundation for future genetic mapping and conservation efforts of this vulnerable species.

Single-Cell Transcriptomic Analysis of Kaposi Sarcoma

Kaposi Sarcoma (KS) is a complex tumor caused by KS-associated herpesvirus 8 (KSHV). Histological analysis reveals a mixture of "spindle cells", vascular-like spaces, extravasated erythrocytes, and immune cells. In order to elucidate the infected and uninfected cell types in KS tumors, we examined twenty-five skin and blood samples from sixteen subjects by single cell RNA sequence analyses. Two populations of KSHV-infected cells were identified, one of which represented a CD34-negative proliferative fraction of endothelial cells, and the second representing CD34-positive cells expressing endothelial genes found in a variety of cell types including high endothelial venules, fenestrated capillaries, and endothelial tip cells. Although both infected clusters contained cells expressing lytic and latent KSHV genes, the CD34+ cells expressed more K5 and less K12. Novel cellular biomarkers were identified in the KSHV infected cells, including the sodium channel SCN9A. The number of KSHV positive cells was found to be less than 10% of total tumor cells in all samples and correlated inversely with tumor-infiltrating immune cells. T-cell receptor clones were expanded in KS tumors and blood, although in differing magnitudes. Changes in cellular composition in KS tumors after treatment with antiretroviral therapy alone, or immunotherapy were noted. These studies demonstrate the feasibility of single cell analyses to identify prognostic and predictive biomarkers.

Carbapenem-resistant Morganella morganii carrying blaKPC-2 or blaNDM-1 in the clinic: one-decade genomic epidemiology analysis

Carbapenem-resistant Morganella morganii (CRMM) isolates, particularly those producing Klebsiella pneumoniae carbapenemase-2 (KPC-2) or New Delhi metallo-β-lactamase-1 (NDM-1), are increasingly being recognized as causative agents of nosocomial infections. However, systematic phylogeography and genetic characterization of these isolates worldwide are still lacking. Here, through seven years of surveillance of CRMM in a tertiary hospital, we analyzed the genomic characteristics of blaKPC-2- or blaNDM-1-positive CRMM isolates. Furthermore, we conducted a global genomic epidemiological study of Morganella spp. harboring blaKPC or blaNDM using the NCBI database over the past decade. By combining the timeline of isolate collection with the structural analysis of the plasmids, we traced the evolution of the IncL/M plasmid, which acquired the blaKPC-2 gene. Our findings indicate that horizontal transfer of Tn6296 based on IS26 is crucial for the transmission of blaKPC in CRMM isolates. Additionally, the Tn125 transposon appears to have played an important role in early plasmid-mediated dissemination of blaNDM; however, it has been surpassed in recent years by other elements, including IS26 and ISCR. In summary, through phylogeographic analysis of Morganella spp. globally, we elucidated their spatial-temporal distribution and revealed the evolutionary characteristics of KPC- or NDM-producing CRMM isolates as the predominant "epidemic" clone.

IMPORTANCE

Currently, infections attributable to carbapenem-resistant Morganella morganii (CRMM) isolates harboring blaKPC or blaNDM are on the rise, highlighting the increasing severity of acquired antimicrobial resistance. However, systematic phylogeographic and genetic characterization of these isolates worldwide is still lacking. In this study, we elucidated the spatial-temporal distribution and evolutionary trajectory of blaKPC and blaNDM genes within their core genetic environments. We emphasize the necessity of strengthening surveillance and controlling these organisms in clinical settings to prevent the generation of so-called "superbug" isolates.

Single-cell transcriptional footprint for pseudogene SsCLEC9A is associated with antigen processing and presentation in Sus scrofa

The C-type lectin domain family 9 member A (CLEC9A) is widely recognized as the most critical receptor protein for cross presentation of dead cell associated antigens in animal dendritic cells (DCs). Surprisingly, we revealed for the first time that the sole CLEC9A (SsCLEC9A) in pigs becomes a pseudogene due to three causal mutations that occurred approximately 29.8-44.7 million years ago, challenging the significance of CLEC9A in immune cross-presentation across mammals. Interestingly, we found that SsCLEC9A can transcribe a mutated transcript encoding a truncated protein. Through fluorescence-activated cell sorting and single-cell RNA sequencing, we observed that SsCLEC9A mutant transcript is mainly expressed in DCs and correlated with the expression of its homolog CLEC7A. Further data showed that DCs with SsCLEC9A mutant transcripts exhibited reduced cellular interaction ability and downregulation of antigen presentation function, displaying the characteristics of mature DCs. In addition, introducing the conserved sequence of CLEC9A gene into FLT3L-induced bone marrow hematopoietic cells significantly increased the expression of genes involved in antigen processing and presentation. This study presents a natural mutation model of pseudogenes to understand its transcriptional adation, and provides a fundamental basis for rescuing SsCLEC9A to promote immunity in pigs in the future.

Ultrastructural Architecture and Morphological Examination of Hirudo verbana (Annelida, Hirudinea)

In this study, the morphological characteristics of the medicinal leech Hirudo verbana (Annelida, Hirudinea) were examined. Mitochondrial CO1 gene sequences of representative specimens were recorded in GenBank, and macroscopic, histological, and SEM analyses of remaining representatives were made. The species had trignathous jaws, each half-moon in shape. There were 75-80 denticles on the left jaw with their tips medially, while the right jaw had 30-34 equilateral triangular denticles, all arranged in a single row. The anterior jaw had 35-40 blunt-tipped denticles similarly arranged in a single row. Salivary papillae of varying sizes were scattered along the edges of the jaws, with salivary pores appearing as irregularly distributed round openings. Five pairs of dorsal eyes appeared round under a stereomicroscope but oval under SEM. Seventeen pairs of round nephridial pores were symmetrically located on every fifth annulus of the ventral side. Grape-cluster-like cells containing granules were observed between the crop and the muscle layer. Bean-shaped testisacs and coiled vas deferens canals were bilaterally arranged near the crop. Thread-like extensions and sensilla were identified across the ventral annuli. Beneath the epidermis, circular, oblique, and longitudinal muscle layers and three types of secretory cells between them were identified. As a result, this study has identified differences in the denticle morphology of H. verbana and has contributed these findings to the literature. Additionally, it was found that there are differences in the shape of the examined structures between stereomicroscope and SEM images in small and complexly structured organisms.

MVGNN-PPIS: A novel multi-view graph neural network for protein-protein interaction sites prediction based on Alphafold3-predicted structures and transfer learning

Protein-protein interactions (PPI) are crucial for understanding numerous biological processes and pathogenic mechanisms. Identifying interaction sites is essential for biomedical research and targeted drug development. Compared to experimental methods, accurate computational approaches for protein-protein interaction sites (PPIS) prediction can save significant time and costs. In this study, we propose a novel model named MVGNN-PPIS. To the best of our knowledge, it is the first to utilize predicted structures generated by AlphaFold3, and combined with transfer learning techniques, for predicting PPIS. This approach addresses the limitations of traditional methods that depend on native protein structures and multiple sequence alignments (MSA). Additionally, we introduced a multi-view graph framework based on two types of graph structures: the k-nearest neighbor graph and the adjacency matrix. By alternately employing a Graph Transformer and Graph Convolutional Networks (GCN) to aggregate node information, this framework effectively captures both local and global dependencies of each residue in the predicted structures, thereby significantly enhancing the model's sensitivity to binding sites. This framework further integrates direction, distances and angular information between the 3D coordinates of side-chain atom centroids to construct a relative coordinate system, generating enhanced edge features that ensure the model's equivariance to molecular translations and rotations in space. During training, the Focal Loss function is employed to effectively address the class imbalance in the dataset. Experimental results demonstrate that MVGNN outperforms the current state-of-the-art methods across multiple PPIS benchmark datasets. To further validate the model's generalization capability, we extended MVGNN to the domain of predicting protein-nucleic acid interaction sites, where it also achieved superior performance.

Discovery and In Silico Characterization of Anatolian Water Buffalo Rumen-Derived Bacterial Thermostable Xylanases: A Sequence-Based Metagenomic Approach

This study involved shotgun sequencing of rumen metagenomes from three Anatolian water buffalos, an exploration of the relationship between microbial flora and xylanases, and in silico analyses of thermostable xylanases, focusing on their sequence, structure, and dynamic properties. For this purpose, the rumen metagenome of three Anatolian water buffalos was sequenced and bioinformatically analyzed to determine microbial diversity and full-length xylanases. Analyses of BLAST, biophysicochemical characteristics, phylogenetic tree, and multiple sequence alignment were performed with Blastp, ProtParam, MEGA11 software, and Clustal Omega, respectively. Three-dimensional homology models of three xylanases (AWBRMetXyn5, AWBRMetXyn10, and AWBRMetXyn19) were constructed by SWISS-MODEL and validated by ProSA, ProCheck, and Verify3D. Also, their 3D models were structurally analyzed by PyMOL, BANΔIT, thermostability predictor, What If, and Protein Interaction Calculator (PIC) software. Protein-ligand interactions were examined by docking and MD simulation. Shotgun sequence and Blastp analyses showed that Clostridium (Clostridiales bacterial order), Ruminococcus (Oscillospiraceae bacterial family), Prevotella (Bacteroidales bacterial order), and Butyrivibrio (Lachnospiraceae bacterial family) were found as dominant potential xylanase-producer genera in three rumen samples. Furthermore, the biophysicochemical analysis indicated that three xylanases exhibited an aliphatic index above 80, an instability index below 40, and melting temperatures (T m) surpassing 65 °C. Phylogenetic analysis placed three xylanases within the GH10 family, clustering them with thermophilic xylanases, while homology modeling identified the optimal template as a xylanase from a thermophilic bacterium. The structural analysis indicated that three xylanases possessed the number of salt bridges, hydrophobic interactions, and T m score higher than 50, 165, and 70 °C, respectively; however, the reference thermophilic XynAS9 had 43, 145, and 54.41 °C, respectively. BANΔIT analysis revealed that three xylanases exhibited lower B'-factor values in the β3-α1 loop/short-helix at the N-terminal site compared to the reference thermophilic XynAS9. In contrast, six residues (G79, M123, D150, T199, A329, and G377) possessed higher B'-factor values in AWBRMetXyn5 and their aligned positions in AWBRMetXyn10 and AWBRMetXyn19, relative to XynAS9 including Gln, Glu, Ile, Lys, Ser, and Val at these positions, respectively. MD simulation results showed that the β9-η5 loop including catalytic nucleophile glutamic acid in the RMSF plot of three xylanases had a higher fluctuation than the aligned region in XynAS9. The distance analysis from the MD simulation showed that the nucleophile residue in AWBRMetXyn5 and AWBRMetXyn10 remained closer to the ligand throughout the simulation compared with XynAS9 and AWBRMetXyn19. The most notable difference between AWBRMetXyn5 and AWBRMetXyn10 was the increased amino acid fluctuations in two specific regions, the η3 short-helix and the η3-α3 loop, despite a minimal sequence difference of only 1.24%, which included three key amino acid variations (N345, N396, and T397 in AWBRMetXyn5; D345, K396, and A397 in AWBRMetXyn10). Thus, this study provided computational insights into xylanase function and thermostability, which could inform future protein engineering efforts. Additionally, three xylanases, especially AWBRMetXyn5, are promising candidates for various high-temperature industrial applications. In a forthcoming study, three xylanases will be experimentally characterized and considered for potential industrial applications. In addition, the amino acid substitutions (G79Q, M123E, D150I, T199K, A329S, and G377V) and the residues in the β3-α1 loop will be targeted for thermostability improvement of AWBRMetXyn5. The amino acids (N345, N396, and T397) and the residues on the β9-η5 loop, η3 short-helix, and η3-α3 loop will also be focused on development of the catalytic efficiency.

The wheat NLR pair RXL/Pm5e confers resistance to powdery mildew

Powdery mildew poses a significant threat to global wheat production and most cloned and deployed resistance genes for wheat breeding encode nucleotide-binding and leucine-rich repeat (NLR) immune receptors. Although two genetically linked NLRs function together as an NLR pair have been reported in other species, this phenomenon has been relatively less studied in wheat. Here, we demonstrate that two tightly linked NLR genes, RXL and Pm5e, arranged in a head-to-head orientation, function together as an NLR pair to mediate powdery mildew resistance in wheat. The resistance function of the RXL/Pm5e pair is validated by mutagenesis, gene silencing, and gene-editing assays. Interestingly, both RXL and Pm5e encode atypical NLRs, with RXL possessing a truncated NB-ARC (nucleotide binding adaptor shared by APAF-1, plant R proteins and CED-4) domain and Pm5e featuring an atypical coiled-coil (CC) domain. Notably, RXL and Pm5e lack an integrated domain associated with effector recognition found in all previously reported NLR pairs. Additionally, RXL and Pm5e exhibit a preference for forming hetero-complexes rather than homo-complexes, highlighting their cooperative role in disease resistance. We further show that the CC domain of Pm5e specifically suppresses the hypersensitive response induced by the CC domain of RXL through competitive interaction, revealing regulatory mechanisms within this NLR pair. Our study sheds light on the molecular mechanism underlying RXL/Pm5e-mediated powdery mildew resistance and provides a new example of an NLR pair in wheat disease resistance.

Expanding kinetoplastid genome annotation through protein structure comparison

Kinetoplastids belong to the Discoba supergroup, an early divergent eukaryotic clade. Although the amount of genomic information on these parasites has grown substantially, assigning gene functions through traditional sequence-based homology methods remains challenging. Recently, significant advancements have been made in in-silico protein structure prediction and algorithms for rapid and precise large-scale protein structure comparisons. In this work, we developed a protein structure-based homology search pipeline (ASC, Annotation by Structural Comparisons) and applied it to transfer biological information to all kinetoplastid proteins available in TriTrypDB, the reference database for this lineage. Our pipeline enabled the assignment of structural similarity to a substantial portion of kinetoplastid proteins, improving current knowledge through annotation transfer. Additionally, we identified structural homologs for representatives of 6,700 uncharacterized proteins across 33 kinetoplastid species, proteins that could not be annotated using existing sequence-based tools and databases. As a result, this approach allowed us to infer potential biological information for a considerable number of kinetoplastid proteins. Among these, we identified structural homologs to ubiquitous eukaryotic proteins that are challenging to detect in kinetoplastid genomes through standard genome annotation pipelines. The results (KASC, Kinetoplastid Annotation by Structural Comparison) are openly accessible to the community at kasc.fcien.edu.uy through a user-friendly, gene-by-gene interface that enables visual inspection of the data.

From Genes to Molecules: The Fusarium PKS16 Gene Cluster Facilitates the Biosynthesis of Proliferapyrones

Ascomycete fungi of the genus Fusarium are found in manifold ecological niches and thus pursue several lifestyles. On average, individual Fusarium species have the genetic capability to produce 50 natural products (NPs), which are in general thought to improve the fungus's fitness in defined environments. This also includes NPs with toxic potential (mycotoxins) contaminating food and feed sources. Recent research has shown that the production of NPs is tightly regulated on the transcriptional level and depends on the delicate balance between the deposition and removal of histone marks. Within this study, we show that the expression of the prior cryptic Fusarium PKS16 biosynthetic gene cluster (BGC) greatly depends on modifications at histone H3 lysine 27 (H3K27). By combining molecular-, chemical-, and bioinformatic analyses we show that the PKS16 BGC from F. fujikuroi B14 (FfB14) consists of nine genes, including a positively acting pathway-specific transcription factor, which although absent in some fusaria, functions in activating other PKS16 cluster genes. Moreover, we linked the PKS16 BGC to the biosynthesis of proliferapyrone (PRO) E, an isomer of the recently isolated PRO A.

Understanding a point mutation signature D54K in the caspase activation recruitment domain of NOD1 capitulating concerted immunity via atomistic simulation

Point mutation D54K in the human N-terminal caspase recruitment domain (CARD) of nucleotide-binding oligomerization domain -1 (NOD1) abrogates an imperative downstream interaction with receptor-interacting protein kinase (RIPK2) that entails combating bacterial infections and inflammatory dysfunction. Here, we addressed the molecular details concerning conformational changes and interaction patterns (monomeric-dimeric states) of D54K by signature-based molecular dynamics simulation. Initially, the sequence analysis prioritized D54K as a pathogenic mutation, among other variants, based on a sequence signature. Since the mutation is highly conserved, we derived the distant ortholog to predict the sequence and structural similarity between native and mutant. This analysis showed the utility of 33 communal core residues associated with structural-functional preservation and variations, concurrently served to infer the cryptic hotspots Cys39, Glu53, Asp54, Glu56, Ile57, Leu74, and Lys78 determining the inter helical fold forming homodimers for putative receptor interaction. Subsequently, the atomistic simulations with free energy (MM/PB(GB)SA) calculations predicted structural alteration that takes place in the N-terminal mutant CARD where coils changed to helices (45 α3- L4-α4-L6- α683) in contrast to native (45T2-L4-α4-L6-T483). Likewise, the C-terminal helices 93T1-α7105 connected to the loops distorted compared to native 93α6-L7105 may result in conformational misfolding that promotes functional regulation and activation. These structural perturbations of D54K possibly destabilize the flexible adaptation of critical homotypic NOD1CARD-CARDRIPK2 interactions (α4Asp42-Arg488α5 and α6Phe86-Lys471α4) is consistent with earlier experimental reports. Altogether, our findings unveil the conformational plasticity of mutation-dependent immunomodulatory response and may aid in functional validation exploring clinical investigation on CARD-regulated immunotherapies to prevent systemic infection and inflammation.

Effects of Rainfall and Drought on the Functional and Taxonomic Diversity of Cultivable Yeasts Associated With Bromelia laciniosa From a Brazilian Tropical Dryland

The phyllosphere is a crucial interface for plant-environment interactions, hosting a diverse microbial community, including yeasts. This community affects the host's fitness and can act as a plant resilience booster. Nonetheless, abiotic factors can have a significant impact on the microbial community. Therefore, this work aims to investigate the potential effects of rain and drought on the taxonomic and functional diversity of epiphytic yeasts associated with Bromelia laciniosa leaves in the Caatinga, a tropical dryland in South America. A total of 262 isolates were obtained. Based on their D1/D2 region of the LSU gene rRNA sequences, the isolates were identified as belonging to 76 species of yeasts and yeast-like fungi, including 53 Basidiomycetes and 23 Ascomycetes. Furthermore, 23 species (ca. 30% of the total) are possible new species. Most of the variables related to rainfall and drought did not affect the yeast taxonomic diversity. Furthermore, the impact of rain and drought on the community composition differs between functional and taxonomic diversities, which may suggest a decoupling between these dimensions. The functional and taxonomic structure of the yeast community in the Caatinga is complex, and rain and drought alone are not the absolute factors governing its dynamics. Additionally, the functional traits may provide valuable insights into the behavior of the yeast community in bromeliads and help predict the effects of dry-wet cycles on the leaf-inhabiting yeast community, as well as potential impacts on the host.

High-Altitude Open-Pit Coal Mining has Changed the Sulfur Cycle and Ecological Network of Plant Rhizosphere Microorganisms

Ecological restoration of mining sites has a considerable effect on microbial community dynamics; however, its impact on sulfur cycling is unclear. This study explored the changes in functional genes related to sulfur cycling and microbial diversity during different stages of succession following the ecological restoration of a mining site in a cold arid area. A total of three succession stages were selected-natural, secondary, and artificial. The expression of sulfur cycle-related genes and associated microbial drivers was investigated using metagenomics and network analysis. The dominant bacteria in the secondary succession were found to be r-strategy-adopting Proteobacteria and Cyanobacteria. Natural succession primarily comprised Aspergillus and Thermus, whereas artificial succession comprised Proteobacteria, Chlorophyta, and Actinobacteria. Mining disturbances were determined to significantly reduce the abundance of sulfur-cycling archaea. Secondary succession was primarily influenced by soil total phosphorus in the sulfur-cycle gene network. The key bacteria and archaea involved in the sulfur cycle were found to be Bradyrhizobium and Nitrosopumilus, respectively. The abundance of Streptomyces was significantly higher in natural succession than in artificial or secondary succession. Burkholderia, which has biological control and bioremediation effects, was abundant during artificial succession. These results provide a theoretical basis for restoring the sulfur cycle and promoting a positive succession of ecosystems in mining areas.

Independent evolution of satellite DNA sequences in homologous sex chromosomes of Neotropical armored catfish (Harttia)

The Neotropical armored catfish Harttia is a valuable model for studying sex chromosome evolution, featuring two independently evolved male-heterogametic systems. This study examined satellitomes-sets of satellite DNAs-from four Amazonian species: H. duriventris (X1X2Y), H. rondoni (XY), H. punctata (X1X2Y), and H. villasboas (X1X2Y). These species share homologous sex chromosomes, with their satellitomes showing a high number of homologous satellite DNAs (satDNAs), primarily located on centromeres or telomeres, and varying by species. Each species revealed a distinct satDNA profile, with independent amplification and homogenization events occurring, suggesting an important role of these repetitive sequences in sex chromosome differentiation in a short evolutionary time, especially in recently originated sex chromosomes. Whole chromosome painting and bioinformatics revealed that in Harttia species without heteromorphic sex chromosomes, a specific satDNA (HviSat08-4011) is amplified in the same linkage group associated with sex chromosomes, suggesting an ancestral system. Such sequence (HviSat08-4011) has partial homology with the ZP4 gene responsible for the formation of the egg envelope, in which its role is discussed. This study indicates that these homologous sex chromosomes have diverged rapidly, recently, and independently in their satDNA content, with transposable elements playing a minor role when compared their roles on autosomal chromosome evolution.

Genome-Wide Characterization of CaM/CML Gene Family in Cabbage (Brassica oleracea var. capitata): Expression Profiling and Functional Implications During Hyaloperonospora parasitica Infection

Calmodulin (CaM) and calmodulin-like proteins (CMLs) are crucial for calcium signal transduction in plants. Although CaM/CML genes have been extensively studied in various plant species, research on these genes in Brassica oleracea is still limited. In this study, 14 BoCaM and 75 BoCML genes were identified in the B. oleracea genome through a genome-wide search. Phylogenetic analysis categorized these genes, along with their homologs in Arabidopsis and rice, into six distinct groups. All BoCaM/BoCML genes were unevenly distributed across the nine chromosomes of B. oleracea, with 52 of them lacking introns. Collinearity analysis revealed that CaM/CML genes in Arabidopsis are present in multiple copies in the B. oleracea genome. Moreover, the majority of BoCaM/BoCML genes exhibited distinct expression patterns across the different tissues, indicating their role in the growth and development of B. oleracea. A clustering heatmap of BoCaM/BoCML gene expression showed distinct patterns before and four days after Hyaloperonospora parasitica infection, dividing the genes into five groups based on their expression patterns. Notably, BoCML46-2 is significantly downregulated in both susceptible and resistant materials, suggesting that it plays an important role in responding to H. parasitica infection. This study conducted a comprehensive survey of the BoCaM/BoCML gene family in B. oleracea. It could serve as a theoretical foundation for further functional identification and utilization of family members and their role in the interaction between B. oleracea and H. parasitica.

Discovery of a phylogenetically novel tropical marine Gammaproteobacteria elucidated from assembled genomes and the proposed transfer of the genus Umboniibacter from the family Cellvibrionaceae to Umboniibacteraceae fam. nov

Marine heterotrophic bacteria in coastal waters respond to the influx of carbon from natural and anthropogenic sources. We identified two nearly identical, (99.9% average nucleotide identity; 100% amino acid identity; same DNA G + C content of 52.3 mol%) high-quality (≥99% CheckM completeness and ≤ 1.3% contamination) draft metagenome-assembled genomes (MAGs; SJ0813 and SJ0972) from seawater microbiomes of a southern island of Singapore that is in a protected marine park. The MAGs were only assigned to the Cellvibrionaceae family according to Genome Taxonomy Database. Overall genome related indices to Pseudomaricurvus alkylphenolicus KU41GT as the closest phylogenetic relative revealed no more than 70.45% average nucleotide identity (ANIcutoff < 95%), below the 50% percentage of conserved proteins (POCPcutoff = 43.54%) for genera cutoff and low digital DNA-DNA hybridization values (DDH = 20.6 and 20.8%). The major respiratory quinone is predicted to be ubiquinone-9 from the annotation of 3-demethylubiquinone-9 3-methyltransferase (ubiG, K00568) involved in the last step of the ubiquinone biosynthesis pathway (M00117), which differed from the ubiquinone-8 utilized by known members of Cellvibrionaceae. Both MAGs contained a complete pathway for dissimilatory nitrate reduction to ammonia, which increases bioavailability of nitrogen in seawater. An identical choline dehydrogenase found in both MAGs have a low amino-acid identity (≤64.47%) compared to existing GMC family oxidoreductases, expanding on the diversity of this family of enzymes. The MAGs meet nearly all the minimum requirements but lack a 16S rRNA gene of sufficient length required for the proposed novel genus and species under SeqCode. Nevertheless, phylogenetic trees based on core-genome and RpoB as an alternative phylogenetic marker are congruent with the taxon standing as a monophyletic clade to other taxa of the order Cellvibrionales. Taken together, the MAGs (SJ0813 and SJ0972) represent an uncultured, undescribed genus and species in which we tentatively propose the name Candidatus Pelagadaptatus aseana gen. nov., sp. nov. and strain SJ0813TS (=BAABNI000000000.1TS) as type sequence. Phylogenetic inference from core-genome and RpoB phylogenetic trees placed Umboniibacter marinipuniceus KMM 3891T outside Cellvibrionaceae. We, therefore, propose the transfer of the genus Umboniibacter from the family Cellvibrionaceae to a new family Umboniibacteraceae according to the International Code of Nomenclature of Prokaryotes.

Low-biomass pyruvate production with engineered Vibrio natriegens is accompanied by parapyruvate formation

BACKGROUND

Pyruvate is a precursor for various compounds in the chemical, drug, and food industries and is therefore an attractive target molecule for microbial production processes. The fast-growing bacterium Vibrio natriegens excels with its specific substrate uptake rate as an unconventional chassis for industrial biotechnology. Here, we aim to exploit the traits of V. natriegens for pyruvate production in fermentations with low biomass concentrations.

RESULTS

We inactivated the pyruvate dehydrogenase complex in V. natriegens Δvnp12, which harbors deletions of the prophage regions vnp12. The resulting strain V. natriegens Δvnp12 ΔaceE was unable to grow in minimal medium with glucose unless supplemented with acetate. In shaking flasks, the strain showed a growth rate of 1.16 ± 0.03 h- 1 and produced 4.0 ± 0.3 gPyr L- 1 within 5 h. We optimized the parameters in an aerobic fermentation process and applied a constant maintenance feed of 0.24 gAc h- 1 which resulted in a maximal biomass concentration of only 6.6 ± 0.4 gCDW L- 1 and yielded highly active resting cells with a glucose uptake rate (qS) of 3.5 ± 0.2 gGlc gCDW-1 h- 1. V. natriegens Δvnp12 ΔaceE produced 41.0 ± 1.8 gPyr L- 1 with a volumetric productivity of 4.1 ± 0.2 gPyr L- 1 h- 1. Carbon balancing disclosed a gap of 30%, which we identified partly as parapyruvate. Deletion of ligK encoding the HMG/CHA aldolase in V. natriegens Δvnp12 ΔaceE did not impact biomass formation but plasmid-based overexpression of ligK negatively affected growth and led to a 3-fold higher parapyruvate concentration in the culture broth. Notably, we also identified parapyruvate in supernatants of a pyruvate-producing Corynebacterium glutamicum strain. Cell-free bioreactor experiments mimicking the biological process also resulted in parapyruvate formation, pointing to a chemical reaction contributing to its synthesis.

CONCLUSIONS

We engineered metabolically highly active resting cells of V. natriegens producing pyruvate with high productivity at a low biomass concentration. However, we also found that pyruvate production is accompanied by parapyruvate formation in V. natriegens as well as in a pyruvate producing C. glutamicum strain. Parapyruvate formation seems to be a result of chemical pyruvate conversion and might be supported biochemically by an aldolase reaction.

Identification of Enoyl-CoA Hydratase EchA19 in Mycolicibacterium neoaurum Involved in the First β-Oxidation Pathway of Phytosterols for Key Steroidal Intermediate Synthesis

Microbial transformation has enabled phytosterols as readily available and bio-renewable starting materials for the industrial synthesis of steroidal active pharmaceutical ingredients (APIs). Editing the phytosterol side chain would create various steroidal compounds with a specific C17-side chain, which will greatly facilitate the synthesis of steroidal APIs. Precise cleavage of the phytosterol side chain requires identification of the key enzymes and the reaction pathways of phytosterol side chain metabolism. In this study, a hydratase EchA19 was identified in Mycolicibacterium neoaurum NRRL B-3805, a strain which was engineered by traditional mutation and screening or genetic manipulation, generating recombinant strains for the industrial-scale production of androstenedione (AD), androstadienedione (ADD), and 9α-hydroxy-androstenedione (9α-OH-AD) from phytosterols. It was found that EchA19 is the key hydratase affecting the first β-oxidation pathway of phytosterol side chain metabolism. The previously proposed carboxylation at the C28 position might occur after the cleavage of the C24 branched alkyl side chain, rather than after the dehydrogenation reaction. This study has provided us with new insights and a deeper understanding of the metabolic pathways of phytosterol side chain, and laid a foundation for synthesizing valuable steroid drug intermediates from phytosterols through metabolic regulation by precisely editing the side chain.

Development of a Novel mRNA Vaccine Against Shigella Pathotypes Causing Widespread Shigellosis Endemic: An In-Silico Immunoinformatic Approach

Shigellosis remains a major global health concern, particularly in regions with poor sanitation and limited access to clean water. This study used immunoinformatics and reverse vaccinology to design a potential mRNA vaccine targeting Shigella pathotypes out of 4071 proteins from Shigella sonnei str. Ss046, 4 key antigenic candidates were identified: putative outer membrane protein (Q3YZL0), PapC-like porin protein (Q3YZM5), putative fimbrial-like protein (Q3Z3I2), and lipopolysaccharide (LPS)-assembly protein LptD (Q3Z5V5), ensuring broad pathotype coverage. A multitope vaccine was designed incorporating cytotoxic T lymphocyte, helper T lymphocyte, and B-cell epitopes, linked with suitable linkers and adjuvants to enhance immunogenicity. Computational analyses predicted vaccine's favorable antigenicity, solubility, and stability, while molecular docking and dynamic simulations demonstrated strong binding affinity and stability with Toll-like receptor 4 (TLR-4), indicating potential for robust immune activation. Immune simulations predicted strong humoral and cellular immune responses, characterized by significant cytokine production and long-term immune memory. Structural evaluations of the complex, including radius of gyration, root mean square deviation, root mean square fluctuation, and solvent accessibility, confirmed the vaccine's structural integrity, and stability under physiological conditions. This research contributes to the ongoing effort to alleviate the global burden of Shigella infections, providing a foundation for future wet laboratory investigations aimed at vaccine development.

A wheat tandem kinase and NLR pair confers resistance to multiple fungal pathogens

Tandem kinase proteins underlie the innate immune systems of cereal plants, but how they initiate plant immune responses remains unclear. This report identifies wheat protein wheat tandem NBD 1 (WTN1), a noncanonical nucleotide-binding leucine-rich repeat (NLR) receptor featuring tandem nucleotide binding adaptor shared by APAF-1, plant R proteins, and CED-4 (NB-ARC) domains, required for WTK3-mediated disease resistance. Both WTK3 and its allelic variant Rwt4-known for conferring resistance to wheat powdery mildew and blast, respectively-are capable of recognizing the blast effector PWT4. They activate WTN1 to form calcium-permeable channels, akin to ZAR1 and Sr35. Thus, tandem kinase proteins and their associated NLRs operate as "sensor-executor" pairs against fungal pathogens. Additionally, evolutionary analyses reveal a coevolutionary trajectory of the tandem kinase-NLR module, highlighting their cooperative role in triggering plant immunity.

Isolation and cultivation of a novel freshwater magnetotactic coccus FCR-1 containing unchained magnetosomes

Magnetotactic bacteria are ubiquitous aquatic prokaryotes that have the ability to biomineralize magnetite (Fe3O4) and/or greigite (Fe3S4) nanoparticles called magnetosomes. Magnetotactic cocci belonging to the class "Ca. Magnetococcia" are most frequently identified in freshwater habitats, but remain uncultivated. Here, we report for the first time axenic cultivation of freshwater magnetotactic coccus FCR-1 isolated from Chichijima, Japan. Strain FCR-1 grows microaerophilically in a semi-solid gellan gum medium. We find that strain FCR-1 biomineralizes Fe3O4 nanoparticles, which are not chained, into a cell. Based on phylogenomic analysis, compared with strains of the class "Ca. Magnetococcia", strain FCR-1 represents a novel genus of candidate family "Ca. Magnetaquicoccaceae" within the class "Ca. Magnetococcia" and we tentatively name this novel genus "Ca. Magnetaquiglobus chichijimensis". Our isolate provides a promising tool for elucidating the functions of unchained magnetosomes, the global distribution of magnetotactic bacteria and the origin of magnetotaxis.

Strictly G-Specific Alginate Lyase Aly7Sa for Efficient Preparation of Unsaturated Guluronate Oligosaccharides

Alginate is a commercially valuable polysaccharide consisting of β-d-mannuronate (M) and its C5 epimer, α-l-guluronate (G). Alginate lyases are efficient tools for the degradation of alginate and the preparation of oligosaccharides. In this research, an endolytic alginate lyase Aly7Sa with strict G specificity was expressed and characterized with the optimum reaction conditions at 30 °C and pH 6.5. The main degradation products of Aly7Sa for alginate were trisaccharide to octasaccharide, and those of PolyG were disaccharide to heptasaccharide. By utilizing HPAEC-PAD/MS and NMR methods, we identified the structure of products obtained from alginate. Interestingly, the trisaccharide to hexasaccharide products of Aly7Sa contained only unsaturated guluronate oligosaccharides, which were different from all of the characterized G-specific alginate lyases. The absence of oligosaccharide products with M residues demonstrated the strict G specificity of Aly7Sa. The targeted preparation was carried out based on the regular oligosaccharide pattern of Aly7Sa. By single-step purification employing gel-permeation chromatography, 4.8 mg of ΔGG, 6.8 mg of ΔGGG, and 3.7 mg of ΔGGGG were obtained with 100 mg of alginate as substrate. The strictly G-specific alginate lyase Aly7Sa provided an efficient tool for the preparation of unsaturated guluronate oligosaccharides, and the unique substrate specificity of the enzyme could also serve the research and development of alginate.

Interfacial extracellular electron uptake is linked to nitrate respiration in the marine heterotroph, Thalassospira xiamenensis SN3

Thalassospira species are ubiquitous marine bacteria with poorly understood ecology, and some have been implicated in iron corrosion. To better elucidate the mechanisms and ecological implications of extracellular electron transfer (EET) in oxidative processes, we conducted genomic and bioelectrochemical characterization of Thalassospira xiamenensis strain SN3, an obligate heterotroph isolated from coastal marine sediment cathode-oxidizing enrichments. Physiologic and genomic analyses indicate that SN3 lacks the capacity for lithoautotrophic growth and lacks homologs to genes canonically involved in EET. Bioelectrochemical characterization of SN3 cells shows that inward EET requires a terminal electron acceptor (respiration). Deletion of nitrate reductase catalytic subunit napA abolished current consumption and catalytic activity under nitrate-reducing conditions. Media exchange experiments demonstrate that inward EET in SN3 is facilitated by direct contact with the electrode, with a formal midpoint potential of -153 ± 16 mV vs. SHE. Through deletion of the formate dehydrogenase fdhABCD and electrochemical characterization of mutant cells, we show that inward EET is not a function of Fdh enzyme sorption to the electrode, as has been demonstrated for other organisms. This provides further evidence of a cell-mediated and contact-dependent EET mechanism. This work provides a foundation for investigating this metabolically versatile organism's yet uncharacterized mechanism of EET.

High-quality genome assembly of the azooxanthellate coral Tubastraea coccinea (Lesson, 1829)

Coral reefs are among the most biodiverse and economically significant ecosystems globally, yet they are increasingly degrading due to global climate change and local human activities. The sun coral Tubastraea coccinea (T. coccinea) an obligate heterotroph lacking symbiotic zooxanthellae, exhibits remarkable tolerance to conditions that cause bleaching and mortality in zooxanthellate species. With its extensive low-latitude distribution across multiple oceans, T. coccinea has become a highly invasive species, adversely impacting native species, degrading local ecosystems, and causing significant socio-economic challenges that demand effective management. Despite substantial research efforts, the molecular biology of T. coccinea remains insufficiently characterized. To address this gap, we generated a draft genome assembly for T. coccinea using PacBio Hi-Fi long-read sequencing. The assembly spans 875.9 Mb with a scaffold N50 of 694.3 kb and demonstrates high completeness, with a BUSCO score of 97.4%. A total of 37,307 protein-coding sequences were identified, 95.2% of which were functionally annotated through comparisons with established protein databases. This reference genome provides a valuable resource for understanding the genetic structure of T. coccinea, advancing research into its adaptive mechanism to environmental changes, and informing conservation and management strategies to mitigate its invasive impact.

Insights into membrane-bound fatty acid desaturase genes in tigernut (Cyperus esculentus L.), an oil-rich tuber plant in Cyperaceae

BACKGROUND

Tigernut (Cyperus esculentus L.), an oil-rich tuber plant of the Cyperaceae family, is typical for the naturally high content of oleic acid. However, to date, genes contributing to oil composition have not been well characterized.

RESULTS

In this study, the first genome-wide analysis of tigernut genes encoding membrane-bound fatty acid desaturases (FADs), the key contributors to oil composition, is presented. According to phylogenetic analysis, ten members identified from the tigernut genome were assigned into seven out of eight evolutionary groups as defined in Arabidopsis thaliana, i.e., FAD2 (3), FAD6 (1), FAD3 (1), FAD7 (1), FAD4 (1), DES (1), and SLD (2). In contrast to the absence of an FAD5 homolog, FAD2 and SLD in tigernut were shown to have expanded via tandem and dispersed duplications, respectively. Comparison of 285 members from 29 representative plant species resulted in 11 orthogroups, where FAD2a, FAD6, FAD7, FAD3, FAD4, FAD5, DES, and SLD1 were shown to have already appeared in the ancestor of seed plants. Significantly, orthologous and syntenic analyses revealed that loss of FAD5 and expansion of SLD in tigernut are lineage-specific, occurred sometime before the radiation of core monocots, in contrast to species-specific expansion of FAD2. Moreover, though no syntenic relationship was observed between CeFAD genes, our comparative genomics analyses indicated that FAD3 and -7 are more likely to arise from segmental duplication. Structural variation and expression divergence of CeFAD genes were also observed. Gain of introns in CeFAD4, CeSLD1, and CeSLD2 was shown to be lineage-specific, occurred sometime before Cyperaceae-Juncaceae split. Tissue-specific expression analysis revealed that CeFAD2-1, CeFAD6, and CeFAD7 were constitutively expressed, whereas others were tissue-specific. Among five paralogs identified, CeFAD2-1 and CeSLD1 have evolved to be two dominant members. Putative roles of CeFAD2-1 in oil accumulation are supported by 1) exhibited an expression pattern positively associated with oil accumulation during tuber development; 2) were expressed more in tubers than their orthologs in C. rotundus. Additionally, in contrast to high expression of CrFAD3, transcript levels of CeFAD3 in tubers were fairly low, which may explain the distinct α-linolenic acid content between these two close species.

CONCLUSIONS

Our findings provide a global view of CeFAD genes, which not only highlights lineage-specific evolution of the family, but also provides valuable information for further functional analysis and genetic improvement in tigernut.

Fine-tuning of conditional Transformers improves in silico enzyme prediction and generation

We introduce Finenzyme, a Protein Language Model (PLM) that employs a multifaceted learning strategy based on transfer learning from a decoder-based Transformer, conditional learning using specific functional keywords, and fine-tuning for the in silico modeling of enzymes. Our experiments show that Finenzyme significantly enhances generalist PLMs like ProGen for the in silico prediction and generation of enzymes belonging to specific Enzyme Commission (EC) categories. Our in silico experiments demonstrate that Finenzyme generated sequences can diverge from natural ones, while retaining similar predicted tertiary structure, predicted functions and the active sites of their natural counterparts. We show that embedded representations of the generated sequences obtained from the embeddings computed by both Finenzyme and ESMFold closely resemble those of natural ones, thus making them suitable for downstream tasks, including e.g. EC classification. Clustering analysis based on the primary and predicted tertiary structure of sequences reveals that the generated enzymes form clusters that largely overlap with those of natural enzymes. These overall in silico validation experiments indicate that Finenzyme effectively captures the structural and functional properties of target enzymes, and can in perspective support targeted enzyme engineering tasks.

Characterization and host range prediction of Staphylococcus aureus phages through receptor-binding protein analysis

Bacteriophages are crucial in bacterial communities and can be used for therapy of multidrug-resistant pathogens such as Staphylococcusaureus. However, the host range of new phages remains difficult to predict. We identified the receptor-binding proteins (RBPs) of 335 S. aureus-infecting phages, yielding 8 distinct RBP clusters. Recombinant representative RBPs of all clusters, including several subclusters, were analyzed for binding to S. aureus strains differing in potential phage receptor structures. Notably, most of the phages encoded two separate RBPs, and all RBPs used S. aureus wall teichoic acid (WTA) polymers as receptors, albeit with varying preference for WTA glycosylation patterns and backbone structures. Based on these findings, a sequence-based tool for predicting the adsorption of new phages was developed. Moreover, one of the RBPs proved useful for identifying S. aureus-type WTA in other bacterial species. These findings facilitate the characterization of phage and bacterial isolates and the development of phage therapies.

Developmental Regulation of Corazonin, Eclosion Hormone, and Bursicon Messages and RNAi Suppression of Corazonin in Adult, Female American Dog Ticks, Dermacentor variabilis

The insect molting process is critical to growth and development and is regulated in part by the neuropeptides corazonin, eclosion hormone, and α and β bursicon. We found messages in a synganglion transcriptome from adult, female American dog ticks, Dermacentor variabilis (that do not molt), with a high similarity to the larval insect neuropeptides that control molting. The phylogenetic analysis of the tick putative neuropeptides compared to other arthropods is discussed in detail. The relative gene expression of these peptides was determined by quantitative PCR during the following adult developmental stages: (i) virgin, unfed 0-24 h after entering the adult stage (non-host-seeking), (ii) host-seeking, unfed, and not mated (3 d after emergence), (iii) part-fed (unmated, attached to host; 1st and 3rd day after emergence), (iv) mated (females are part-fed; allowed to mate for ≤1 day, 7th day after emergence), (v) mated repletes (completion of blood feeding but still attached to host), and (vi) post-drop-off (from host) with egg laying starting within 1 d of detachment. Eclosion hormone transcript levels peaked at mating and at drop-off. Bursicon α levels were highest just after molting into adults, with a second smaller peak in replete females. Bursicon β levels were highest (32-fold) post-drop-off. Corazonin message levels peaked in part-feds and were much higher (40-fold) in repletes compared to 0-24 h after emergence. RNAi suppression of the corazonin message by injection in newly molted ticks reduced oviposition and the number of vitellogenic eggs in the ovaries at drop-off but had no apparent effect on host-seeking, partial feeding, mating, feeding to repletion, and drop-off. The possible roles of these transcripts in adult, female tick development are discussed.

Targets for the diagnosis of Acanthamoeba eye infections include four cyst wall proteins and the mannose-binding domain of the trophozoite mannose-binding protein

Acanthamoebae, which are free-living amoebae, cause corneal inflammation (keratitis) and blindness, if not quickly diagnosed and effectively treated. The walls of Acanthamoeba cysts contain cellulose and have two layers connected by conical ostioles. Cysts are identified by in vivo confocal microscopy of the eye or calcofluor-white- or Giemsa-labeling of corneal scrapings, both of which demand great expertise. Trophozoites, which use a mannose-binding protein to adhere to keratinocytes, are identified in eye cultures that delay diagnosis and treatment. We recently used structural and experimental methods to characterize cellulose-binding domains of Luke and Leo lectins, which are abundant in the inner layer and ostioles. However, no antibodies have been made to these lectins or to a Jonah lectin and a laccase, which are abundant in the outer layer. Here, confocal microscopy of rabbit antibodies (rAbs) to recombinant Luke, Leo, Jonah, and laccase supported localizations of GFP-tagged proteins in walls of transfected Acanthamoebae. rAbs efficiently detected calcofluor white-labeled cysts of 10 of the 11 Acanthamoeba isolates tested, including six T4 genotypes that cause most cases of keratitis. Further, laccase shed into the medium during encystation was detected by an enzyme-linked immunoassay. Structural and experimental methods identified the mannose-binding domain (ManBD) of the Acanthamoeba mannose-binding protein, while rAbs to the ManBD efficiently detected DAPI-labeled trophozoites from all 11 Acanthamoeba isolates tested. We conclude that antibodies to four cyst wall proteins and the ManBD efficiently identify Acanthamoeba cysts and trophozoites, respectively.IMPORTANCEFree-living amoeba in the soil or water cause Acanthamoeba keratitis, which is diagnosed by identification of unlabeled cysts by in vivo confocal microscopy of the eye or calcofluor-white (CFW) labeled cysts by fluorescence microscopy of corneal scrapings. Alternatively, Acanthamoeba infections are diagnosed by the identification of trophozoites in eye cultures. Here, we showed that rabbit antibodies (rAbs) to four abundant cyst wall proteins (Jonah, Luke, Leo, and laccase) each efficiently identify CFW-labeled cysts of 10 of the 11 Acanthamoeba isolates tested. Further, laccase released into the medium by encysting Acanthamoebae was detected by an enzyme-linked immunoassay. We also showed that rAbs to the mannose-binding domain (ManBD) of the Acanthamoeba mannose-binding protein, which mediates adherence of trophozoites to keratinocytes, efficiently identify DAPI-labeled trophozoites of all 11 Acanthamoeba isolates tested. In summary, four wall proteins and the ManBD appear to be excellent targets for the diagnosis of Acanthamoeba cysts and trophozoites, respectively.

Computational insights into host-pathogen protein interactions: unveiling penaeid shrimp and white spot syndrome virus interplay

White spot syndrome virus (WSSV) has been a major threat in shrimp farming system especially for penaeid shrimps. The lack of effective control measures for WSSV makes this disease a significant threat to aquaculture. This study seeks to explore the mechanisms of WSSV infection and its impact on shrimp by examining host-pathogen interactions (HPI) through in silico approach, which can offer valuable insights into the processes of infection and disease progression. The investigation focused on five Penaeus species, including Penaeus vannamei, Penaeus chinensis, Penaeus monodon, Penaeus japonicus, and Penaeus indicus, studying their interaction with the WSSV. This study employed orthology-based and domain-driven analyses to reveal protein-protein interactions (PPIs) between the host and the pathogen. The combined strategies were found to be effective in detecting shared molecular mechanisms in pathogenesis, unveiling intricate PPI networks critical for virulence and host response. Most interacting proteins in WSSV are immediate early proteins involved in DNA replication and proliferation, and are crucial for ubiquitination, transcription regulation, and nucleotide metabolism. A large number of host proteins interact with WSSV across species (2360-11,704 interactions), with P. chinensis (11,704) and P. japonicus (11,458) exhibiting the highest counts, suggesting greater susceptibility or response. Host hub proteins are crucial in signaling, cellular processes, and metabolism, interacting across the cytoplasm, nucleus, and membrane, highlighting their role in WSSV pathogenesis. This study provides essential insights into host-pathogen interactions, offering a foundation for future research aimed at improving WSSV control in shrimp aquaculture.

A mesophilic Argonaute from Clostridium formicaceticum with efficient DNA cleavage activity guided by small DNA

We characterized a new Argonaute protein (pAgo), CfAgo, from the mesophilic bacterium Clostridium formicaceticum. CfAgo possesses DNA-guided DNA endonuclease activity and cleaves DNA targets at the canonical site. It is active from 28°C to 75°C and prefers DNA guides with a 5'-phosphate group and thymidine as the first nucleotide. Cleavage activity is reduced by single-nucleotide mismatches in the seed, central, and 3'-supplementary regions of guides, with stronger mismatch discrimination observed for 5'hydroxylated (5'OH) guides compared to 5'phosphorylated (5'P) guides. Moreover, structural analysis suggests that the MID domain of CfAgo is crucial for recognizing the 5' guide and it influences the binding specificity. CfAgo catalyzes programmable cleavage of double-stranded DNA in AT-rich regions in the presence of Mn2+ and Mg2+ ions at appropriate salt concentrations. These properties could make CfAgo a promising tool for DNA manipulation such as nucleic acid detection and cleavage.

In-cell architecture of the mitochondrial respiratory chain

Mitochondria regenerate adenosine triphosphate (ATP) through oxidative phosphorylation. This process is carried out by five membrane-bound complexes collectively known as the respiratory chain, working in concert to transfer electrons and pump protons. The precise organization of these complexes in native cells is debated. We used in situ cryo-electron tomography to visualize the native structures and organization of several major mitochondrial complexes in Chlamydomonas reinhardtii cells. ATP synthases and respiratory complexes segregate into curved and flat crista membrane domains, respectively. Respiratory complexes I, III, and IV assemble into a respirasome supercomplex, from which we determined a native 5-angstrom (Å) resolution structure showing binding of electron carrier cytochrome c. Combined with single-particle cryo-electron microscopy at 2.4-Å resolution, we model how the respiratory complexes organize inside native mitochondria.

Genome-wide analysis of CHYR gene family and BnA03.CHYR.1 functional verification under salt stress in Brassica napus L

Brassica napus, an allotetraploid used as an oilseed crop, vegetable, or feed crop, possesses significant economic and medicinal value. Although the CHYR gene family has been functionally characterised in various aspects of plant growth, development, and stress responses, its systematic investigation in B. napus is lacking. In contrast to the seven CHYR genes (AtCHYR1-AtCHYR7) identified in Arabidopsis thaliana, nine CHYR orthologues were detected in B. rapa and B. oleracea, while 24 were found in B. napus. This discrepancy is consistent with the established triplication events that occurred during the Brassicaceae family evolution. Phylogenetic analysis indicated that the 24 CHYRs identified in B. napus could be categorised into three distinct groups. Among these, 24 BnCHYRs contained conserved domains, including the CHY-zinc finger, C3H2C3-type RING finger and zinc ribbon domains. Group III members featured an additional one to three hemerythrin domains in their N-terminal regions. Each BnCHYR group shared similar patterns in the distribution of conserved domains. Our results revealed that the selected eight BnCHYRs were up-regulated following heat treatment, exhibiting varying expression patterns in response to salt, cold, and drought stress during the seedling stage. Expression analysis revealed that several BnCHYRs were significantly induced by one or more abiotic stressors. BnA03.CHYR.1 was significantly induced by salt and heat stress and repressed by polyethylene glycol treatment. BnA03.CHYR.1 was localised in the nucleus and cytoplasm, and its overexpression in A. thaliana enhanced tolerance to salt stress. Our results provide a comprehensive analysis of the CHYR family in B. napus, elucidating the biological role of BnA03.CHYR.1 in adaptive responses of plants to salt stress.