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Comparative Genome Analysis of Polar Mesorhizobium sp. PAMC28654 to Gain Insight into Tolerance to Salinity and Trace Element Stress

Mon, 01 Jan 2024 00:00:00 GMT

Title: Comparative Genome Analysis of Polar Mesorhizobium sp. PAMC28654 to Gain Insight into Tolerance to Salinity and Trace Element Stress Authors: Khanal Anamika; Han So-Ra; Lee, Jun Hyuck; Oh Tae-Jin Abstract: In this study, Mesorhizobium sp. PAMC28654 was isolated from a soil sample collected from the polar region of Uganda. Whole-genome sequencing and comparative genomics were performed to better understand the genomic features necessary for Mesorhizobium sp. PAMC28654 to survive and thrive in extreme conditions and stresses. Additionally, diverse sequence analysis tools were employed for genomic investigation. The results of the analysis were then validated using wet-lab experiments. Genome analysis showed trace elements' resistant proteins (CopC, CopD, CzcD, and Acr3), exopolysaccharide (EPS)-producing proteins (ExoF and ExoQ), and nitrogen metabolic proteins (NarG, NarH, and NarI). The strain was positive for nitrate reduction. It was tolerant to 100 mM NaCl at 15 degrees C and 25 degrees C temperatures and resistant to multiple trace elements (up to 1 mM CuSO45H(2)O, 2 mM CoCl26H(2)O, 1 mM ZnSO47H(2)O, 0.05 mM Cd(NO3)(2)4H(2)O, and 100 mM Na2HAsO47H(2)O at 15 degrees C and 0.25 mM CuSO45H(2)O, 2 mM CoCl26H(2)O, 0.5 mM ZnSO47H(2)O, 0.01 mM Cd(NO3)(2)4H(2)O, and 100 mM Na2HAsO47H(2)O at 25 degrees C). This research contributes to our understanding of bacteria's ability to survive abiotic stresses. The isolated strain can be a potential candidate for implementation for environmental and agricultural purposes.

Elucidation of bacterial trehalose-degrading trehalase and trehalose phosphorylase: physiological significance and its potential applications

Mon, 01 Jan 2024 00:00:00 GMT

Title: Elucidation of bacterial trehalose-degrading trehalase and trehalose phosphorylase: physiological significance and its potential applications Authors: Prasansah Shrestha; Jayram Karmacharya; So-RaHan; Lee, Jun Hyuck; Tae-Jin Oh Abstract: Bacteria possess diverse metabolic and genetic processes, resulting in the inability of certain bacteria to degrade trehalose. However, some bacteria do have the capability to degrade trehalose, utilizing it as a carbon source, and for defense against environmental stress. Trehalose, a disaccharide, serves as a carbon source for many bacteria, including some that are vital for pathogens. The degradation of trehalose is carried out by enzymes like trehalase (EC 3.2.1.28) and trehalose phosphorylase (EC 2.4.1.64/2.4.1.231), which are classified under the glycoside hydrolase families GH37, GH15, and GH65. Numerous studies and reports have explored the physiological functions, recombinant expression, enzymatic characteristics, and potential applications of these enzymes. However, further research is still being conducted to understand their roles in bacteria. This review aims to provide a comprehensive summary of the current understanding of trehalose degradation pathways in various bacteria, focusing on three key areas: (i) identifying different trehalose-degrading enzymes in Gram-positive and Gram-negative bacteria, (ii) elucidating the mechanisms employed by trehalose-degrading enzymes belonging to the glycoside hydrolases GH37, GH15, and GH65, and (iii) discussing the potential applications of these enzymes in different sectors. Notably, this review emphasizes the bacterial trehalose-degrading enzymes, specifically trehalases (GH37, GH15, and GH65) and trehalose phosphorylases (GH65), in both Gram-positive and Gram-negative bacteria, an aspect that has not been highlighted before.

An Antarctic lichen isolate (Cladonia borealis) genome reveals potential adaptation to extreme environments

Mon, 01 Jan 2024 00:00:00 GMT

Title: An Antarctic lichen isolate (Cladonia borealis) genome reveals potential adaptation to extreme environments Authors: Cho Minjoo; Lee Seung Jae; Choi Eunkyung; Kim Jinmu; Choi Soyun; Lee, Jun Hyuck; Park Hyun Abstract: Cladonia borealis is a lichen that inhabits Antarctica's harsh environment. We sequenced the whole genome of a C. borealis culture isolated from a specimen collected in Antarctica using long-read sequencing technology to identify specific genetic elements related to its potential environmental adaptation. The final genome assembly produced 48 scaffolds, the longest being 2.2 Mbp, a 1.6 Mbp N50 contig length, and a 36 Mbp total length. A total of 10,749 protein-coding genes were annotated, containing 33 biosynthetic gene clusters and 102 carbohydrate-active enzymes. A comparative genomics analysis was conducted on six Cladonia species, and the genome of C. borealis exhibited 45 expanded and 50 contracted gene families. We identified that C. borealis has more Copia transposable elements and expanded transporters (ABC transporters and magnesium transporters) compared to other Cladonia species. Our results suggest that these differences contribute to C. borealis' remarkable adaptability in the Antarctic environment. This study also provides a useful resource for the genomic analysis of lichens and genetic insights into the survival of species isolated from Antarctica.

Editorial: Structural immunology of molecular innate immunity

Sun, 01 Jan 2023 00:00:00 GMT

Title: Editorial: Structural immunology of molecular innate immunity Authors: Lee, Jun Hyuck; Yin Qian; Park Hyun Ho Abstract: The Research Topic “Structural Immunology of Molecular Innate Immunity” highlights 13 recent studies that delve into the process of innate immunity at the molecular level, with a specific focus on toll-like receptor (TLR)-mediated immune responses, cGAS-STINGmediated innate immunity, GTPase-mediated antiviral processes, the structural biology of the complement system, and Janus kinase as a drug for inflammatory diseases.