YF-2

Flavobacterium shanxiense sp. nov., isolated from soil

Strain YF-2(T), a Gram-staining-negative, non-motile, non-spore-forming, light-yellow-pigmented bacterium, was isolated from soil samples collected in the city of Yuncheng, Shanxi province of China. Strain YF-2(T) grew over a temperature range of 25-37 °C, at pH 5.0-8.0 and with 0-5 % (w/v) NaCl. Phylogenetic analysis based on sequence of the 16S rRNA gene showed that strain YF-2(T) was closely related to strains Flavobacterium akiainvivens CIP 110358(T) and Flavobacterium hauense KCTC 32147(T) with 95.99 and 95.92 % sequence similarity, respectively. The dominant fatty acids of strain YF-2(T) were Summed Feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c) (21.97 %), iso-C15:0 (18.65 %), iso-C17:0 3OH (11.41 %), C16:0 (9.92 %), and anteiso-C15:0 (6.21 %). It contained phosphatidylethanolamine and menaquinone MK-6 as major polar lipid and respiratory quinone, respectively. Strain YF-2(T) differs from other Flavobacterium species in many characteristics and represents a novel species, for which the name Flavobacterium shanxiense sp. nov. is proposed. The type strain is strain YF-2(T) (=CCTCC AB 2014079(T) = JCM 30153(T)).

Transcriptome Analysis Reveals Key Genes and Pathways Associated with the Petal Color Formation in Cabbage ( Brassica oleracea L. var. capitata)

Petal color is an important agronomic trait in cabbage (Brassica oleracea L. var. capitata). Although the key gene BoCCD4 has been functionally characterized, the underlying molecular regulatory mechanism of petal color formation in cabbage is still unclear. In this study, we applied the transcriptome analysis of yellow petals from the cabbage inbred line YL-1 and white petals from the Chinese kale inbred line A192-1 and the BoCCD4-overexpressing transgenic line YF-2 (YL-1 background), which revealed 1928 DEGs common to both the A192-1 vs. YL-1 and the YL-1 vs. YF-2 comparison groups. One key enzyme-encoding gene, BoAAO3, and two key TF-encoding genes, Bo2g151880 (WRKY) and Bo3g024180 (SBP), related to carotenoid biosynthesis were significantly up-regulated in both the A192-1 and YF-2 petals, which was consistent with the expression pattern of BoCCD4. We speculate that these key genes may interact with BoCCD4 to jointly regulate carotenoid biosynthesis in cabbage petals. This study provides new insights into the molecular regulatory mechanism underlying petal color formation in cabbage.

Increasing Genome Editing Efficiency of Cas9 Nucleases by the Simultaneous Use of Transcriptional Activators and Histone Acetyltransferase Activator

The CRISPR-Cas9 system shows diverse levels of genome editing activities on eukaryotic chromatin, and high-efficiency sgRNA targets are usually desired in application. In this study, we show that chromatin open status is a pivotal determinant of the Cas9 editing activity in mammalian cells, and increasing chromatin accessibility can efficiently improve Cas9 genome editing. However, the strategy that increases chromatin openness by fusing the VP64 transcriptional activation domain at the C-terminus of Cas9 can only promote genome editing activity slightly at most tested CRISPR-Cas9 targets in Lenti-X 293T cells. Under the enlightenment that histone acetylation increases eukaryotic chromatin accessibility, we developed a composite strategy to further improve genome editing by activating histone acetylation. We demonstrate that promoting histone acetylation using the histone acetyltransferase activator YF-2 can improve the genome editing by Cas9 and, more robustly, by the Cas9 transcriptional activator (Cas9-AD). This strategy holds great potential to enhance CRISPR-Cas9 genome editing and to enable broader CRISPR gRNA target choices for experiments in eukaryotes.

Ternary Complexes Stabilized by Chalcogen and Alkaline-Earth Bonds: Crucial Role of Cooperativity and Secondary Noncovalent Interactions

High-level G4 calculations show that the strength of chalcogen interactions is enhanced dramatically if chalcogen compounds simultaneously form alkaline-earth bonds. This phenomenon is studied by exploring binary YX₂ ???N-Base complexes and two types of ternary MCl₂ ???YX₂ ???N-Base, YX₂ ???N-Base???MCl₂ complexes, in which YX₂ is a chalcogen compound (Y=S, Se; X=F, Cl), the N-Bases are sp, sp² , and sp³ bases (NCH, HN=CH₂ , NH₃ ), and MCl₂ are alkaline-earth BeCl₂ or MgCl₂ derivatives. Starting from the chalcogen-bonded complexes YX₂ ???NH₃ and YX₂ ???HN=CH₂ , the binding site of a new incoming alkaline-earth bond is found, surprisingly, to depend on the nature of the halogen atom attached to the chalcogen. For the YF₂ binary complexes the association site is the F atom of the YF₂ subunit, whereas for YCl₂ it is the N atom of the nitrogen base. Regarding YX₂ ???NCH complexes, N is the most favorable site for an alkaline-earth interaction in ternary complexes, regardless of which YX₂ derivative is used. The explanation relies on the interplay of all the noncovalent interactions involved: the strong cooperativity between chalcogen and alkaline-earth bonds, and the appearance of secondary noncovalent interactions in the form of hydrogen bonds.

Preparation of GM1 ganglioside with sialidase-producing marine bacteria as a microbial biocatalyst

This paper describes the preparation of monosialoganglioside GM1 with sialidase-producing marine bacteria as a microbial biocatalyst. A new sialidase-producing bacterium, identified tentatively as Pseudomonas sp. strain YF-2, was isolated from seawater by enrichment culture with ganglioside as the sole source of carbon. When YF-2 was cultured in a synthetic medium containing crude bovine brain gangliosides at 25 degrees C for 3 days, 80 to 90% of the gangliosides were converted to GM1. GM1 was then purified from the supernatant of YF-2 culture by C18 reverse-phased chromatography, followed by DEAE-Sephadex A25 anion-exchange chromatography. In a typical experiment, 178 mg of highly purified GM1 was obtained from 500 mg of the crude ganglioside fraction. The GM1 induced neurite outgrowth of neuroblastoma Neuro2a cells at a concentration of 33 to 100 microM in the presence of fetal calf serum. Sialidase was purified 33-fold with 13.3% recovery from the culture supernatant of YF-2. The purified enzyme hydrolyzed polysialogangliosides to produce GM1 but did not act on GM1. It was therefore concluded that polysialogangliosides in the culture of strain YF-2 were converted to GM1 by this sialidase.