Members of the TrmB family act as global transcriptional regulators for the activation or repression of sugar ABC transporters and central sugar metabolic pathways, including glycolytic, gluconeogenic, and other metabolic pathways, and also as chromosomal stabilizers in archaea. As a relatively newly classified transcriptional regulator family, there is limited experimental evidence for their role in Thermococcales, halophilic archaeon Halobacterium salinarum NRC1, and crenarchaea Sulfolobus strains, despite being one of the extending protein families in archaea. Recently, the protein structures of Pyrococcus furiosus TrmB and TrmBL2 were solved, and the transcriptomic data uncovered by microarray and ChIP-Seq were published. In the present review, recent evidence of the functional roles of TrmB family members in archaea is explained and extended to bacteria.

Minwook Kim, Yoojeong Park, You Sun Kim, Sungjin Ko. Gut and Liver -0001;0:. https://doi.org/10.5009/gnl240005

Strain CBA3207T, a novel Gram-staining negative, aerobic, and rod-shaped bacterium was isolated from the seashore sand of Jeju island in South Korea. Strain CBA3207T grew optimally at 25-30°C and pH 7.0-7.5 with 3.0-4.0% (w/v) NaCl. It was catalase-positive, oxidase-negative, and hydrolysed starch, gelatin, and Tweens 20, 40, and 80. The 16S rRNA gene sequence of strain CBA3207T showed 96.0, 95.6, 95.6, 95.5, and 95.5% similarity to that of Aquimarina mytili PSC33T, A. agarivorans HQM9T, A. latercula DSM 2041T, A. intermedia KMM 6258T, and A. amphilecti 92VT, respectively. The major fatty acids were iso-C15:0, iso-C17:0 3-OH, iso-C15:1 G, and summed feature 9 (10-methyl C16:0 and/or iso-C17:1 ω9c). The major respiratory quinone was MK-6, and major polar lipids were phosphatidylethanolamine, an unidentified aminolipid, and six unidentified lipids. The G+C content of the genomic DNA was 38.8 mol%. Based on the phenotypic, genotypic, and phylogenetic analyses, strain CBA3207T represents a novel species in the genus Aquimarina, for which the name Aquimarina versatilis sp. nov. is proposed. The type strain is CBA3207T (=KACC 17666T = JCM 19528T).

A cystine-dependent anti-oxidative stress response is characterized in Deinococcus geothermalis for the first time. Nevertheless, the same transcriptional directed Δdgeo_1985F mutant strain was revealed to have an identical phenotype to the wild-type strain, while the reverse transcriptional directed Δdgeo_1985R mutant strain was more resistant to oxidative stress at a certain concentration of H₂O₂ than the wild-type strain. The wild-type and mutant strains expressed equal levels of superoxide dismutase and catalase under H₂O₂-induced stress. Although the expression levels of the general DNA-damage response-related genes recA, pprA, ddrA, and ddrB were up-regulated by more than five-fold in the wild-type strain relative to the Δdgeo_1985R mutant strain, the mutant strain had a higher survival rate than the wild-type under H₂O₂ stress. The Δdgeo_1985R mutant strain highly expressed a cystine-transporter gene (dgeo_1986), at levels 150-fold higher than the wild-type strain, leading to the conclusion that this cystine transporter might be involved in the defensive response to H₂O₂ stress. In this study, the cystine transporter was identified and characterized through membrane protein expression analysis, a cystine-binding assay, and assays of intracellular H₂O₂, cysteine, and thiol levels. The genedisrupted mutant strain of the cystine importer revealed high sensitivity to H₂O₂ and less absorbed cystine, resulting in low concentrations of total thiol. Thus, the absorbed cystine via this cystine-specific importer may be converted into cysteine, which acts as a primitive defense substrate that non-enzymatically scavenges oxidative stress agents in D. geothermalis.

A Gram-stain-negative, gliding, non-endospore-forming and slightly halophilic bacterial strain, CBA3204T, was isolated from seawater and characterized by polyphasic taxonomic analysis. Phylogenetic analysis based on 16S rRNA sequences revealed that strain CBA3204T formed a distinct lineage within the family Flavobacteriaceae . The 16S rRNA sequences of strain CBA3204T had a sequence similarity level of 96.96 % to Maribacter arcticus KOPRI 20941T as the nearest phylogenetic neighbour. The strain grew optimally at 25–30 °C and in the presence of 2–4 % (w/v) NaCl. The dominant menaquinone was MK-6 and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The DNA G+C content was 35.1 mol%. There were some differences in phenotypic properties among strain CBA3204T and other Maribacter species. On the basis of polyphasic analysis containing phenotypic, phylogenetic and chemotaxonomic data, strain CBA3204T (=KACC 17671T=JCM 19533T) is proposed as a novel species Maribacter pelagius sp. nov.

Combined hepatocellular carcinoma–cholangiocarcinoma (cHCC-CCA) is a challenging primary liver cancer subtype with limited treatment options and a devastating prognosis. Recent studies have underscored the context-dependent roles of SOX9 in liver cancer formation in a preventive manner. Here, we revealed that liver-specific developmental Sox9 elimination using Alb-Cre;Sox9^(flox/flox) (LKO) and CRISPR/Cas9-based tumor-specific acute Sox9 elimination (CKO) in SB-HDTVI-based Akt-YAP1 (AY) and Akt-NRAS (AN) cHCC-CCA models showed contrasting responses. LKO abrogates the AY CCA region while stimulating poorly differentiated HCC proliferation, whereas CKO prevents AY and AN cHCC-CCA development irrespective of tumor cell fate. Additionally, AN, but not AY, tumor formation partially depends on the Sox9-Dnmt1 cascade. SOX9 is dispensable for AY-mediated, HC-derived, LPC-like immature CCA formation but is required for their maintenance and transformation into mature CCA. Therapeutic Sox9 elimination using the OPN-CreERT2 strain combined with inducible Sox9 iKO specifically reduces AY but not AN cHCC-CCA tumors. This necessitates the careful consideration of genetic liver cancer studies using developmental Cre and somatic mutants, particularly for genes involved in liver development. Our findings suggest that SOX9 elimination may hold promise as a therapeutic approach for a subset of cHCC-CCA and highlight the need for further investigation to translate these preclinical insights into personalized clinical applications.