Sequence Similarity Research Articles

Functional analysis of MS-based proteomics data: from protein groups to networks

Mass-spectrometry-based proteomics allows the quantification of thousands of proteins, protein variants, and their modifications, in many biological samples. These are derived from the measurement of peptide relative quantities, and it is not always possible to distinguish proteins with similar sequences due to the absence of protein-specific peptides. In such cases, peptide signals are reported in protein groups that can correspond to several genes. Here, we show that multi-gene protein groups have a limited impact on GO-term enrichment, but selecting only one gene per group affects network analysis. We thus present the Cytoscape app Proteo Visualizer (https://apps.cytoscape.org/apps/ProteoVisualizer) that is designed for retrieving protein interaction networks from STRING using protein groups as input and thus allows visualisation and network analysis of bottom-up MS-based proteomics data sets.

Assessing the transcriptional landscape of Pseudomonas phage 201ϕ2-1: Uncovering the small regulatory details of a giant phage.

The transcriptional architecture of phages can deepen our understanding of the phage-host infection process and can be of key importance for phage engineering and biotechnological applications. Here, we applied ONT-cappable-sequencing, a long-read RNA-sequencing technique, to study the regulatory mechanisms of Pseudomonas infecting giant phage 201ϕ2-1. We identified 67 promoters and 132 terminators that together represent 92 transcriptional units. A full comparison of these data to the transcriptome of model Pseudomonas phage ϕKZ confirmed that the transcriptional programs of these prototypes of the Serwervirus and Phikzvirus genera are largely conserved, despite some subtle regulatory differences. Evidence supporting these shared mechanisms include the identification of highly similar sequence motifs for regulatory elements in both phages and the conservation of regulatory elements loci relative to homologous genes in each phage. Moreover, we discovered a sRNA in 201ϕ2-1 that is highly conserved among prototype members of different giant phage genera. Sequencing of the 201ϕ2-1 host genome resulted in its reclassification as Pseudomonas atacamensis, a close relative of the important agricultural biocontrol agent Pseudomonas chlororaphis. Finally, we conducted invivo assays of eight 201ϕ2-1 terminators and found them to strongly terminate transcription in P. chlororaphis. Control elements from phage transcriptional programs have a rich history for applications in biotechnology. In these studies, we demonstrate new insight into the transcriptional program of 201ϕ2-1 and demonstrate the potential of its regulatory elements for novel and useful tools for synthetic biology circuitry.

First Report of Uromyces aecidiiformis Causing Rust Disease on Fritillaria unibracteata in China.

Fritillaria unibracteata Hsiao et K. C. Hsia is a recognized source of 'Chuanbeimu' in the 'Chinese Pharmacopoeia'. In China, its bulbs have been used as a traditional herbal cough remedy for about 2,000 years. Surveys for fungal diseases were conducted in Xiaojin and Songpan, Sichuan Province, the primary cultivation region of F. unibracteata, with an area of 150 acres, in May and July 2022. Rust was found in almost all areas and incidence ranged from 5% to 80% in all study areas. Diseased leaves displayed yellow spots on the upper side, and raised buff, golden, or fuscous waxy pustules on the lower side. In severe cases, the infection extended to the stems and petioles, leading to wilting and death of plant. Spermogonia, aecia, and telia were mainly found on the underside of leaves. Spermogonia were scattered among the aecia and exhibited a range of colors from honey-yellow to chestnut-brown. They had a cross-sectional diameter of 94.4 to 214.3 µm height and 94.2 to 197.5 µm in width (n=30). They were nearly spherical, embedded in the host tissue, and had distinct periphysis at the pores. Aecia were hemispherical, initially white, with the peridium later turning yellowish-brown and opening via a central pore. Aeciospores were pale yellow, finely and closely verrucose, measuring 20.6 to 34.1 × 18.4 to 30.1 µm with a cell wall thickness of 1.5 to 2.4 µm (n=51). Prior to plants wilting, elongated telia were observed, gradually exposed, then finally opening through longitudinal cracks in the epidermis. Teliospores were unicellular, dark brown, oblong to oval, and solitary on stems, measuring 24.7 to 38.2 × 19.2 to 27.8 µm (n=130) with a wall thickness of 1.6 to 3.1 µm, with a low hyaline papilla at the apex and were moderately rugose with longitudinal parallel ridges. The characteristics align with previous descriptions of Uromyces aecidiiformi (Rees, 1917, Zhuang, 2005). The primer pair LR0R (Moncalvo et al., 1995)/LR5 (Vilgalys & Hester, 1990) was utilized for amplifying and sequencing the large subunit of the nuclear ribosomal RNA genes from strains IS909-3 and IS1816 (GenBank PQ008482, PQ008483). The obtained sequences showed a high similarity of 99.9% to 100% similarity to strains U1023 and UBC19 of U. aecidiiformis in RustHubb (KR0014142 and PUN23000)( Kaishian et al., 2024). Through examination of morphology, host range, and sequence similarity, we determined the rust species to be U. aecidiiformis. Pathogenicity testing was conducted by spraying a suspension of aeciospores (1×105 spores/mL in 0.05% Tween 20 solution) on six healthy four-year-old F. unibracteata plants indoors in May 2023. The plants were allowed to grow under natural conditions, where the diurnal temperature ranged from 9 to 20℃, with an average temperature of 14℃, which is conducive to the growth of F. unibracteata. Another six seedlings were sprayed with 0.05% Tween 20 solution as controls. After three weeks, all infected plants showed symptoms similar to those seen in the field, while control plants remained symptom-free. Microscopic examination and sequencing confirmed that the pathogen morphology was consistent between the field and the inoculation, meeting Koch's postulates. Although U. aecidiiformis has been previously reported to cause rust of F. pallidiflora and F. ussuriensis(Zhuang, 1989, Zhuang, 2005), this is the first report of U. aecidiiformis causing rust on F. unibracteata in China. This pathogen significantly reduces the yield and quality of Chuanbeimu, highlighting the importance of effectively identifying and controlling it.

Discovery of <i>Brevibacterium</i> predominating in fecal samples from three children with persistent diarrhea negative for common pathogens

Acute diarrhea is a common disease in children under 5 years old and can develop into persistent diarrhea, greatly affecting the children's health. Although advanced techniques had been used to diagnose and detect common pathogens in hospitals, however, 40% of cases are negative for the pathogens. In this study, to investigate dominant bacteria in stool samples of three persistent-diarrheal children with unidentified pathogenic agents, the V3 and V68 regions of the 16S rRNA gene were amplified from fecal bacterial metagenomic DNA, separated on DGGE gel, and the dominant DNA bands were sequenced. As a result, the V3 and V68 regions of bacteria in persistent diarrheal children were less diverse and different from the corresponding DNA bands of the indicator strains. Sequence analysis and similarity comparison of six DNA bands of V3 regions and seven DNA bands of V68 regions showed that two V3 sequences (of 160 bp) derived from two samples were novel and did not match any genes from the non-redundant database, but they shared 93.75% similarity to each other. The four V3 sequences left derived from all three samples were the most similar (94.53-100%) with the corresponding genes of Brevibacterium. Six of the seven V68 sequences derived from dominant DNA bands of all three samples were the most similar (from 99.4% to 100%) to the corresponding genes of referent strains belonging to the genus Enterococcus. In sample D3, a sequence of the V68 region possessed 100% identity to the E. faecalis ATCC 19433 strain. This is the first study report that Brevibacterium was the dominant bacteria in the gastrointestinal microflora of children with persistent diarrhea although the bacterial genus has been reported to cause dangerous diseases in humans with immunodeficiency.

Exploring The Protease Diversity of Psychrophilic Yeast, Glaciozyma antarctica Through Genome Mining Analysis

Proteases are one of the most significant classes of enzymes, holding immense physiological relevance and extensive industrial applications. The genome of Glaciozyma antarctica was fully sequenced, showing 7,857 open reading frames that offer an intriguing opportunity to investigate its proteolytic repertoire. This study aims to unveil the protease landscape of G. antarctica, a psychrophilic yeast that produces cold-active enzymes that offer remarkable benefits, particularly in the food and pharmaceutical industries. In this work, we performed a comprehensive analysis to identify the diverse families of proteases encoded within the G. antarctica genome and compare them with proteases from other mesophilic and thermophilic fungi in the MEROPS database. The sequence similarity searches resulted in the identification of 195 open reading frames predicted to encode for proteases in G. antarctica with a high number of intracellular proteases. These findings suggest an evolved system for protein quality control and turnover, essential for cell viability and adaptation to environmental stressors. The MEROPS classification analysis showed an abundance of metalloproteases, constituting 38% of the total protease genes, a proportion surpassing that found in other yeast and fungal genomes studied. This reflects the vital role of metalloproteases in the cold adaptation of microbes in the Antarctic region. This unique profile not only sheds light on the adaptive mechanisms of psychrophilic organisms but also presents a rich reservoir of potential cold-active proteases for various applications. The findings of this study provide a foundation for targeted enzyme discovery and engineering, unlocking new frontiers in industrial biotechnology and extremophile biology.

Testing the Capability of Embedding-Based Alignments on the GST Superfamily Classification: The Role of Protein Length.

In order to shed light on the usage of protein language model-based alignment procedures, we attempted the classification of Glutathione S-transferases (GST; EC 2.5.1.18) and compared our results with the ARBA/UNI rule-based annotation in UniProt. GST is a protein superfamily involved in cellular detoxification from harmful xenobiotics and endobiotics, widely distributed in prokaryotes and eukaryotes. What is particularly interesting is that the superfamily is characterized by different classes, comprising proteins from different taxa that can act in different cell locations (cytosolic, mitochondrial and microsomal compartments) with different folds and different levels of sequence identity with remote homologs. For this reason, GST functional annotation in a specific class is problematic: unless a structure is released, the protein can be classified only on the basis of sequence similarity, which excludes the annotation of remote homologs. Here, we adopt an embedding-based alignment to classify 15,061 GST proteins automatically annotated by the UniProt-ARBA/UNI rules. Embedding is based on the Meta ESM2-15b protein language. The embedding-based alignment reaches more than a 99% rate of perfect matching with the UniProt automatic procedure. Data analysis indicates that 46% of the UniProt automatically classified proteins do not conserve the typical length of canonical GSTs, whose structure is known. Therefore, 46% of the classified proteins do not conserve the template/s structure required for their family classification. Our approach finds that 41% of 64,207 GST UniProt proteins not yet assigned to any class can be classified consistently with the structural template length.

Lelliottia wanjuensis sp. nov. Isolated from Korean Lettuce in Wanju, South Korea

Ten Gram stain-negative, oxidase-negative, catalase-positive, rod-shaped strains were isolated from lettuce in the city Wanju in South Korea. Comparative 16S rRNA gene analysis and multilocus sequence analysis indicated that the strains grouped closely together with all other Lelliottia (L.)-type strains. The average nucleotide identity (ANI) comparisons of the isolates showed a high relationship between the strains, as the ANI values of all strains ranged from 91.01 to 91.31% when compared to the L. jeotgali-type strain PFL01T. All isolates showed the highest genomic DNA sequence similarity to the L. jeotgali PFL01T strain at 43.3% when compared with digital DNA–DNA hybridization (dDDH). Strain V104_15T of the proposed novel Lelliottia species showed 91.2% and 43.3% similarity with the most closely related L. jeotgali PFL01T-type strain in the ANI and dDDH comparisons, respectively. Strain V104_15T could not grow at 45 °C and 7% NaCl, while L. jeotgali PFL01T strain could grow at both these conditions. Strain V104_15T showed ß-glucosidase activity but not α-glucosidase activity, while the L. jeotgali PFL01T strain was α-glucosidase positive but ß-glucosidase negative. The major cellular fatty acids of strain V104_15T were C16:0 and cyclo-C17:0 including summed features. The mol % G + C content of the genomic DNA of strain V104_15T was 55.74%. Phenotypic and biochemical characteristics, as well as the phylogenomic analysis indicated that the strain V104_15T represents a novel species of the genus Lelliottia, for which the name Lelliottia wanjuensis sp. nov. is proposed. The type strain is V104_15T (= LMG 32996 T = DSM 115585 T).

Structure-Function Relationship of a Novel MTX-like Peptide (MTX1) Isolated and Characterized from the Venom of the Scorpion Maurus palmatus.

Maurotoxin (MTX) is a 34-residue peptide from Scorpio maurus venom. It is reticulated by four disulfide bridges with a unique arrangement compared to other scorpion toxins that target potassium (K+) channels. Structure-activity relationship studies have not been well performed for this toxin family. The screening of Scorpio maurus venom was performed by different steps of fractionation, followed by the ELISA test, using MTX antibodies, to isolate an MTX-like peptide. In vitro, in vivo and computational studies were performed to study the structure-activity relationship of the new isolated peptide. We isolated a new peptide designated MTX1, structurally related to MTX. It demonstrated toxicity on mice eight times more effectively than MTX. MTX1 blocks the Kv1.2 and Kv1.3 channels, expressed in Xenopus oocytes, with IC50 values of 0.26 and 180 nM, respectively. Moreover, MTX1 competitively interacts with both 125I-apamin (IC50 = 1.7 nM) and 125I-charybdotoxin (IC50 = 5 nM) for binding to rat brain synaptosomes. Despite its high sequence similarity (85%) to MTX, MTX1 exhibits a higher binding affinity towards the Kv1.2 and SKCa channels. Computational analysis highlights the significance of specific residues in the β-sheet region, particularly the R27, in enhancing the binding affinity of MTX1 towards the Kv1.2 and SKCa channels.

Enzymatic biodegradation of a mannan and galactoglucomannan extracted from African rose wood and Agba wood by hemicellulase from Bacillus trypoxylicola

Biodegradability varies from polymer to polymer due to the difference in chemical composition. The purpose of this study is to provide a proper understanding on the biodegradability of two previously extracted and characterized hemicellulose biopolymers; ARW (a linear mannan) and AW (a galactoglucomannan). In the current study, previously extracted and characterized hemicellulose from African rose wood (ARW) and Agba wood (AW) were subjected to hydrolysis by hemicellulase from a freshly isolated soil bacterium identified as Bacillus trypoxylicola with 99% sequence similarity. The hemicellulose from ARW and AW were soluble in water. The specific activity of hemicellulase from B. trypoxylicola on hemicellulose extracted from ARW from day 2 to 7 (694.44 ± 1.61 to 734.19 ± 14.12 U/mg) was significantly higher than that of AW (434.09 ± 3.76 to 37.36 ± 25.65 U/mg) with P-values ≤ 0.05. The concentration of reducing sugars released from AW between day 2 and day 6 (3.46 ± 0.04 to 3.00 ± 0.04 mM) exceeded that of ARW (2.53 ± 0.01 to 2.40 ± 0.02 mM), p-values ≤ 0.05, except for day 7 which was 2.51 ± 1.15 and 2.18 ± 0.03 U/mg for AW and ARW, respectively, P-value = 0.185. Hemicellulose from ARW showed some degree of resistance to microbial/enzymatic degradation with maximum reducing sugar release of 2.92 ± 0.08 mM on D4 when compared to that of AW, 3.56 ± 0.07 mM on D3.

The identification of Finegoldia dalianensis sp. nov., isolated from the pus of the patient with skin abscess and genomic analysis of the strains belonging to Finegoldia genus

ObjectivesTo comprehensively characterize a new species, named Finegoldia dalianensis sp. nov., isolated from the pus of a skin abscess from a patient and genomic analysis of the strains belonging to Finegoldia genus. MethodsStrain LY240594T was definitively characterized through phylogenetic, genomic, and biochemical approach. Extensive genomic comparisons, involving the genome of LY240594T and those of 82 Finegoldia strains from GenBank, were instrumental in revealing genetic relationships within the Finegoldia genus. ResultsStrain LY240594 was initially identified as F. magna based on MALDI-TOF MS analysis, showing 99.7% 16S rRNA gene sequence similarity with the type strain of F. magna CCUG 17636T. However, there were 68.5% similarity with dDDH method and 90.9% similarity by ANI analysis respectively, between LY240594T and the selected type strain, F. magna DSM 20470T.Biochemical differences were also found between two strains. The ANI and genomic analysis of 82 Finegoldia sp. strains and Strain LY240594 revealed that those strains could be categorized into at least three groups using a 95% ANI threshold. ConclusionComprehensive characterization supported the proposal of a new species within the genus Finegoldia, named Finegoldia dalianensis sp. nov. The type strain, LY240594T (=GDMCC 1.4375T =KCTC 25838T), features 1,938 genes and a G+C content of 31.8 mol%. Genomic comparisons and ANI studies elucidated substantial heterogeneity within the Finegoldia genus.

Flagellimonas algarum sp. nov., isolated from dense mats of filamentous algae.

A novel Gram-stain-negative, strictly aerobic, rod-shaped, light-yellow-pigmented, and chemo-organoheterotrophic bacterium, designated DF-77T, was isolated from dense mats of filamentous algae collected in March 2004 at Okinawa in Japan. The microorganism grew at 0-2.0% NaCl concentrations (w/v), pH 6.0-9.0, and 20-30°C. The 16S rRNA gene sequence-based phylogenetic tree demonstrated that the strain DF-77T is a novel member of the family Flavobacteriaceae and was greatly related to Flagellimonas nanhaiensis SM1704T with sequence similarity of 95.5%. The main fatty acids were iso-C15:1 G, iso-C15:0, and iso-C17:0 3-OH, and the only isoprenoid quinone was menaquinone-6. The dominant polar lipids were phosphatidylethanolamine, two unidentified aminolipids, an unidentified phosphoaminolipid, and four unidentified lipids. The genome size of strain DF-77T was 3.60 Mbp with a DNA G + C content of 47.5%. The average nucleotide identity (ANI) value between the genomes of strain DF-77T and its closely related species was 69.8-70.7%. The digital DNA - DNA hybridization (dDDH) value of strain DF-77T with the strain of F. nanhaiensis SM1704T was 16.8%. The genome of the strain DF-77T revealed that it encoded several genes involved in bio-macromolecule degradation, indicating a high potential for producing industrially useful enzymes. Consequently, the strain is described as a new species in the genus Flagellimonas, for which the name Flagellimonasalgarum sp. nov., is proposed with the type strain DF-77T (= KCTC 72791T = NBRC 114251T).

Identification of Potent, Broad-Spectrum Coronavirus Main Protease Inhibitors for Pandemic Preparedness.

The COVID-19 pandemic highlights the ongoing risk of zoonotic transmission of coronaviruses to global health. To prepare for future pandemics, it is essential to develop effective antivirals targeting a broad range of coronaviruses. Targeting the essential and clinically validated coronavirus main protease (Mpro), we constructed a structurally diverse Mpro panel by clustering all known coronavirus sequences by Mpro active site sequence similarity. Through screening, we identified a potent covalent inhibitor that engaged the catalytic cysteine of SARS-CoV-2 Mpro and used structure-based medicinal chemistry to develop compounds in the pyrazolopyrimidine sulfone series that exhibit submicromolar activity against multiple Mpro homologues. Additionally, we solved the first X-ray cocrystal structure of Mpro from the human-infecting OC43 coronavirus, providing insights into potency differences among compound-target pairs. Overall, the chemical compounds described in this study serve as starting points for the development of antivirals with broad-spectrum activity, enhancing our preparedness for emerging human-infecting coronaviruses.

Taxometer: Improving taxonomic classification of metagenomics contigs

For taxonomy based classification of metagenomics assembled contigs, current methods use sequence similarity to identify their most likely taxonomy. However, in the related field of metagenomic binning, contigs are routinely clustered using information from both the contig sequences and their abundance. We introduce Taxometer, a neural network based method that improves the annotations and estimates the quality of any taxonomic classifier using contig abundance profiles and tetra-nucleotide frequencies. We apply Taxometer to five short-read CAMI2 datasets and find that it increases the average share of correct species-level contig annotations of the MMSeqs2 tool from 66.6% to 86.2%. Additionally, it reduce the share of wrong species-level annotations in the CAMI2 Rhizosphere dataset by an average of two-fold for Metabuli, Centrifuge, and Kraken2. Futhermore, we use Taxometer for benchmarking taxonomic classifiers on two complex long-read metagenomics data sets where ground truth is not known. Taxometer is available as open-source software and can enhance any taxonomic annotation of metagenomic contigs.

Cloning and Expression of Pigeon-Derived Escherichia coli Type 1 Pilus Clusters and Analysis of Amino Acid Sequence Characteristics of Functional Proteins.

Type 1 pili, as an important virulence factor of E. coli, has certain homology between APEC and UPEC, but the homology degree is not clear enough. This study aims to compare the homology between them. The recombinant bacteria were constructed by homologous recombination. The pili were observed by TEM, and the hemagglutination characteristics were determined by MHSA. The complete gene sequence was determined by sequencing, and the amino acid sequences of the functional proteins of type 1 pili of APEC and UPEC were compared. TEM showed that they could express pili, which were slender, straight, and dense. Stable-pUC-fimBH has MHSA but stable-pUC-fimBG does not. The amino acid sequence similarity of FimB of NJ05 and UPEC was 98.8%, FimE was 99.4%, and the similarity between them was 51.5%. Compared with UPEC's type 1 pili FimC and FimD sequences, the similarity was 99.52% and 87.8%, respectively. The amino acid sequence of FimA of NJ05 was 89-96%, similar to UPEC, and the N-terminal and C-terminal amino acid sequences were exactly the same. The gene sequence and amino acid sequence similarity of FimH between them were both above 99%. The similarity of the pilus binding domain of FimH was 52.8%, but only 27.6% in the receptor binding domain. A few of the same amino acid residues were found in the corresponding regions of FimA, FimF, FimG, and FimH. The type 1 pili of APEC and UPEC come from the same origin, which is helpful to further reveal the pathogenic mechanism of E. coli infection in the poultry respiratory tract.

Acidisoma cladoniae sp. nov., an acidotolerant bacterium isolated from an Antarctic lichen.

Gram-staining-negative, aerobic, white-cream-pearly colony, coccobacilli, and non-motile bacterial strain, PAMC 29798T was isolated from an Antarctic lichen. The strain was acidotolerant and psychrotolerant growing at pH 4.0-7.5 (optimally at pH 4.0-6.5) and 0-25°C (optimally at 10-20°C). The major fatty acids are Summed Feature 8, C18:1 2OH, and C19:0 cyclo ω8c. The major respiratory quinone was Q-10. Phylogenetic and phylogenomic analyses indicated that strain PAMC 29798T belonged to the genus Acidisoma and 16S rRNA gene sequences of PAMC 29798T were closely related to Acidisoma silvae (97.7% sequence similarity), Acidisoma cellulosilyticum (96.5%), Acidisoma tundrae (96.5%), and Acidisoma sibiricum (96.3%). Genomic relatedness analyses showed that strain PAMC 29798T was clearly distinguished from type strains of the genus Acidisoma based on values of average nucleotide identity (< 75%) and the digital DNA-DNA hybridization (< 19.6%). Genome analysis revealed that the genome size of PAMC 29798T is approximately 5.0 Mb with a G+C content of 63.4%. The complete genome comprises 5 contigs containing 4636 protein-coding genes, 46 tRNA genes, and 2 rRNA operons. The genome possesses genes for light-harvesting complexes, type-II photosynthetic reaction center, and C-P lyase to solubilize organic phosphates, while genes encoding nitrogenase iron protein involved in the nitrogen fixation were not present. Based on the results of phylogenetic, genome-based relatedness, and physiological and genomic analyses, strain PAMC 29798T is proposed to represent a novel species of the genus Acidisoma, with the name Acidisoma cladoniae. The type strain is PAMC 29798T (= KCTC 82159T = JCM 35634T).

Overexpression of Auxin/Indole-3-Acetic Acid Gene TrIAA27 Enhances Biomass, Drought, and Salt Tolerance in Arabidopsis thaliana

White clover (Trifolium repens L.) is an important forage and aesthetic plant species, but it is susceptible to drought and heat stress. The phytohormone auxin regulates several aspects of plant development and alleviates the effects of drought stress in plants, including white clover, by involving auxin/indole acetic acid (Aux/IAA) family genes. However, Aux/IAA genes and the underlying mechanism of auxin-mediated drought response remain elusive in white clover. To extend our understanding of the multiple functions of Aux/IAAs, the current study described the characterization of a member of the Aux/IAA family TrIAA27 of white clover. TrIAA27 protein had conserved the Aux/IAA family domain and shared high sequence similarity with the IAA27 gene of a closely related species and Arabidopsis. Expression of TrIAA27 was upregulated in response to heavy metal, drought, salt, NO, Ca2+, H2O2, Spm, ABA, and IAA treatments, while downregulated under cold stress in the roots and leaves of white clover. TrIAA27 protein was localized in the nucleus. Constitutive overexpression of TrIAA27 in Arabidopsis thaliana led to enhanced hypocotyl length, root length, plant height, leaf length and width, and fresh and dry weights under optimal and stress conditions. There was Improved photosynthesis activity, chlorophyll content, survival rate, relative water content, endogenous catalase (CAT), and peroxidase (POD) concentration with a significantly lower electrolyte leakage percentage, malondialdehyde (MDA) content, and hydrogen peroxide (H2O2) concentration in overexpression lines compared to wild-type Arabidopsis under drought and salt stress conditions. Exposure to stress conditions resulted in relatively weaker roots and above-ground plant growth inhibition, enhanced endogenous levels of major antioxidant enzymes, which correlated well with lower lipid peroxidation, lower levels of reactive oxygen species, and reduced cell death in overexpression lines. The data of the current study demonstrated that TrIAA27 is involved in positively regulating plant growth and development and could be considered a potential target gene for further use, including the breeding of white clover for higher biomass with improved root architecture and tolerance to abiotic stress.

Lacticaseibacillus jixiensis sp. nov., Isolated from Traditional Chinese Pickle.

A novel lactic acid bacterial strain (designated N163-3-2T), isolated from traditional Chinese pickle ('Suan cai'), was characterized using a polyphasic approach. Strain N163-3-2T was most closely related to the type strains of Lacticaseibacillus baoqingensis, Lacticaseibacillus manihotivorans, and Lacticaseibacillus porcinae, having 97.9-98.4% 16S rRNA gene, 82.0-85.1% pheS, 87.5-87.8% rpoA, and 85.8-86.7% concatenated pheS and rpoA sequence similarities. Strain N163-3-2T had 74.4-81.7% ANI, 22.6-23.9% dDDH, and 74.0-75.1% AAI values with L. baoqingensis 47-3T, L. manihotivorans DSM 13343T and L. porcinae JCM 19617T, less than the threshold for species demarcation (95-96%, 70% and 95-96%, respectively), indicating that strain N163-3-2T represented a novel species of the genus Lacticaseibacillus. Based upon the data obtained in the present study, a novel species, Lacticaseibacillus jixiensis sp. nov., is proposed, and the type strain is N163-3-2T (= CCTCC AB 2024125T = JCM 36999T).

Paracraurococcus lichenis sp. nov., isolated from lichen in Thailand.

A novel bacterium, designated as strain LOR1-02T and isolated from a lichen sample collected from Kham Riang Subdistrict, Kantharawichai District, Maha Sarakham Province, Thailand, underwent thorough investigation utilizing a polyphasic taxonomic approach. Strain LOR1-02T demonstrated growth within a temperature range of 20-42°C (optimal at 30°C), pH range of 5.0-7.5 (optimal at pH 7.0), and tolerance to 4.0% (w/v) NaCl. Phylogenetic analysis revealed its close relation to Paracraurococcus ruber JCM 9931T, with a 16S rRNA gene sequence similarity of 97.16%, placing it within the genus Paracraurococcus. The approximate genome size of strain LOR1-02T was determined to be 8.6Mb, with a G + C content of 70.9mol%. Additionally, ANIb, ANIm, and AAI values between the whole genomes of strain LOR1-02T and type strains were calculated as 82.6-83.4%, 86.1-86.8%, and 81.4-82.2%, respectively, while the dDDH value was determined to be 26.3-28.5% (C.I. 24.0-31.0%). The predominant fatty acids detected were C18:1ω7c and/or C18:1ω6c, C16:0, and C18:12OH. The major ubiquinone identified was Q-10, and the polar lipids included phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, along with unidentified phosphoaminolipid, lipids, and an amino lipid. Based on comprehensive phenotypic, chemotaxonomic, and genotypic characterization, it is concluded that strain LOR1-02T represents a novel species within the genus Paracraurococcus, for which the name Paracraurococcus lichenis sp. nov. is proposed. The type strain designation is LOR1-02T (= JCM 33121T =NBRC 112776T = TISTR 2503T).

Dongia sedimenti sp. nov., isolated from river sediment.

A Gram-stain-negative, non-spore-forming and strictly aerobic bacterial strain, designated R-7T, was isolated from river sediment in Wuxi, Jiangsu, PR China. Cells (1.6-3.8 µm long and 0.6-0.8 µm wide) were slightly curved to straight rods and motile by means of a polar flagellum. The strain grew optimally on Reasoner's 2A medium at 30 °C, pH 7.0 and with 1.0% (w/v) NaCl. Strain R-7T exhibited closest 16S rRNA gene sequence similarities to Dongia mobilis CGMCC 1.7660T (95.4%), D. rigui 04SU4-PT (94.6%) and D. soli D78T (93.8%). The phylogenetic trees based on genomic and 16S rRNA gene sequences showed that strain R-7T was clustered in the genus Dongia. The obtained average nucleotide identity and digital DNA-DNA hybridization values between R-7T and the three type strains of the genus Dongia were 73.4, 72.8 and 72.4% and 19.5, 19.0 and 18.7%, respectively. The major respiratory quinone was Q-10. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids, two unidentified aminophospholipids and nine unidentified polar lipids. The major cellular fatty acids (>5% of the total) were cyclo-C19 : 0 ω8c, C16 : 0 and C16 : 0 2-OH. The DNA G+C content was 65.5 mol%. On the basis of the evidence presented in this study, strain R-7T represents a novel species of the genus Dongia, for which the name Dongia sedimenti sp. nov. is proposed, with strain R-7T (=KCTC 8082T=MCCC 1K08805T) as the type strain.

Prevalence and Characteristics of Plasmid-Mediated Fosfomycin Resistance Gene fosA3 among Salmonella Enteritidis Isolates from Retail Chickens and Children with Gastroenteritis in China.

A total of 265 Salmonella Enteritidis isolates collected from retail markets and children's hospitals in Shanghai were used to investigate the prevalence and molecular epidemiology of plasmid-mediated fosfomycin resistance genes. Nine of the isolates-7 from the 146 (4.79%) retail chicken-related samples and 2 from the 119 (1.68%) samples from clinical children-were fosfomycin-resistant (FosR). The fosA3 gene was detected in all of the nine FosR isolates, which were located on Inc F-type (8/9, 88.9%) and unknown-type (1/9, 11.1%) transferable plasmids. In total, five plasmid types, namely Inc HI2 (1/9, 11.1%), Inc I1 (3/9, 33.3%), Inc X (8/9, 88.9%), Inc FIIs (9/9, 100%), and Inc FIB (9/9, 100%), were detected in these FosR isolates, which possessed five S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) profiles. The extended-spectrum β-lactamase determinant blaCTX-M-14 subtype was identified in one FosRS. Enteritidis isolate, which was located in a transferable unknown-type plasmid co-carrying fosA3 and tetR genes. Sequence homology analysis showed that this plasmid possessed high sequence similarity to previously reported blaCTX-M-14- and fosA3-positive plasmids from E. coli strains, implying that plasmids carrying the fosA3 gene might be disseminated among Enterobacterales. These findings highlight further challenges in the prevention and treatment of Enterobacteriaceae infections caused by plasmids containing fosA3.