Development of an efficient Agrobacterium-mediated transformation system and production of herbicide-resistant transgenic plants in garlic (Allium sativum L.)

The genetic improvement of garlic plants (Allium sativum L.) with agronomical beneficial traits is rarely achieved due to the lack of an applicable transformation system. Here, we developed an efficient Agrobacterium-mediated transformation procedure with Danyang, an elite Korean garlic cultivar. Examination of sGFP (synthetic green fluorescence protein) expression revealed that treatment with 2-(N-morpholino) ethanesulfonic acid (MES), L-cysteine and/or dithiothreitol (DTT) gives the highest efficiency in transient gene transfer during Agrobacterium co-cultivation with calli derived from the roots of in vitro plantlets. To increase stable transformation efficiency, a two-step selection was employed on the basis of hygromycin resistance and sGFP expression. Of the hygromycin-resistant calli initially produced, only sGFP-expressing calli were subcultured for selection of transgenic calli. Transgenic plantlets produced from these calli were grown to maturity. The transformation efficiency increased up to 10.6% via our optimized procedure. DNA and RNA gel-blot analysis indicated that transgenic garlic plants stably integrated and expressed the phosphinothricin acetyltransferase (PAT) gene. A herbicide spraying assay demonstrated that transgenic plants of garlic conferred herbicide resistance, whilst nontransgenic plants and weeds died. These results indicate that our transformation system can be efficiently utilized to produce transgenic garlic plants with agronomic benefits.     

Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels

Since the completion of the bovine sequencing projects, a substantial number of genetic variations such as single nucleotide polymorphisms have become available across the cattle genome. Recently, cataloguing such genetic variations has been accelerated using massively parallel sequencing technology. However, most of the recent studies have been concentrated on European Bos taurus cattle breeds, resulting in a severe lack of knowledge for valuable native cattle genetic resources worldwide. Here, we present the first whole-genome sequencing results for an endangered Korean native cattle breed, Chikso, using the Illumina HiSeq 2,000 sequencing platform. The genome of a Chikso bull was sequenced to approximately 25.3-fold coverage with 98.8% of the bovine reference genome sequence (UMD 3.1) covered. In total, 5,874,026 single nucleotide polymorphisms and 551,363 insertion/deletions were identified across all 29 autosomes and the X-chromosome, of which 45% and 75% were previously unknown, respectively. Most of the variations (92.7% of single nucleotide polymorphisms and 92.9% of insertion/deletions) were located in intergenic and intron regions. A total of 16,273 single nucleotide polymorphisms causing missense mutations were detected in 7,111 genes throughout the genome, which could potentially contribute to variation in economically important traits in Chikso. This study provides a valuable resource for further investigations of the genetic mechanisms underlying traits of interest in cattle, and for the development of improved genomics-based breeding tools.     

Thermostabilization of Candida antarctica lipase B by double immobilization: Adsorption on a macroporous polyacrylate carrier and R1 silaffin-mediated biosilicification

A large improvement in the thermostability of Candida antarctica lipase B (CALB) was achieved through double immobilization, i.e., physical adsorption and R1 silaffin-mediated biosilicification. The C-terminus of CALB was fused with the R1 silaffin peptide for biosilicification. The CALB-R1 fusion protein was adsorbed onto a macroporous polyacrylate carrier and then subsequently biosilicified with tetramethyl orthosilicate (TMOS). After R1 silaffin-mediated biosilicification, the double-immobilized CALB-R1 exhibited remarkable thermostability. The T₅₀⁶⁰ of the double-immobilized CALB-R1 increased dramatically from 45 to 72 °C and that was 27, 13.8, 9.8 and 9.9 °C higher than the T₅₀⁶⁰ values of free CALB-R1, CALB-R1 adsorbed onto a resin, commercial Novozym 435, and Novozym 435 treated with TMOS, respectively. In addition, the time required for the residual activity to be reduced to half (t_1/2) of the double immobilized CALB-R1 elevated from 12.2 to 385 min, which is over 30 times longer life time compared free CALB-R1. The optimum pH for biosilicification was determined to be 5.0, and the double-immobilized enzyme showed much better reusability than the physically adsorbed enzyme even after 6 repeated reuses. This R1-mediated biosilicification approach for CALB thermostabilization is a good basis for the thermostabilization of industrial enzymes that are only minimally stabilized by protein engineering.     

A Low-Copy-Number Plasmid for Retrieval of Toxic Genes from BACs and Generation of Conditional Targeting Constructs

Bacterial Artificial Chromosome (BAC) clones are widely used for retrieving genomic DNA sequences for gene targeting. In this study, low-copy-number plasmids pBAC-FB, pBAC-FC, and pBAC-DE, which carry the F plasmid replicon, were generated from pBACe3.6. pBAC-FB was successfully used to retrieve a sequence of a BAC that was resistant to retrieval by a high-copy-number plasmid via λ Red-mediated recombineering (gap-repair cloning). This plasmid was also used to retrieve two other genes from BAC, indicating its general usability retrieving genes from BAC. The retrieved genes were manipulated in generating targeting vectors for gene knockouts by recombineering. The functionality of the targeting vector was further validated in a targeting experiment with C57BL/6 embryonic stem cells. The low-copy-number plasmid pBAC-FB is a plasmid of choice to retrieve toxic DNA sequences from BACs and to manipulate them to generate gene-targeting constructs by recombineering.     

Human HOXA5 homeodomain enhances protein transduction and its application to vascular inflammation

Cellular protein delivery is an emerging technique by which exogenous recombinant proteins are delivered into mammalian cells across the membrane. We have developed an Escherichia coli expression vector including human specific gene sequences for protein cellular delivery. The plasmid was generated by ligation the nucleotides 770–817 of the homeobox A5 mRNA sequence which was matched with protein transduction domain (PTD) of homeodomain protein A5 (HOXA5) into pET expression vector. The cellular uptake of HOXA5-PTD-EGFP was detected in 1 min and its transduction reached a maximum at 1 h within cell lysates. The cellular uptake of HOXA5-EGFP at 37 °C was greater than in 4 °C. For study for the functional role of human HOXA5-PTD, we purified HOXA5-APE1/Ref-1 and applied it on monocyte adhesion. Pretreatment with HOXA5-APE1/Ref-1 (100 nM) inhibited TNF-α-induced monocyte adhesion to endothelial cells, compared with HOXA5-EGFP. Taken together, our data suggested that human HOXA5-PTD vector provides a powerful research tools for uncovering cellular functions of proteins or for the generation of human PTD-containing proteins.     

Geraniol inhibits prostate cancer growth by targeting cell cycle and apoptosis pathways

Elongation factor-2 kinase (eEF-2 kinase, also known as calmodulin-dependent protein kinase III), is a unique calcium/calmodulin-dependent enzyme that inhibits protein synthesis by phosphorylating and inactivating elongation factor-2 (eEF-2). We previously reported that expression/activity of eEF-2 kinase was up-regulated in several types of malignancies including Gliomas, and was associated with response of tumor cells to certain therapeutic stress. In the current study, we sought to determine whether eEF-2 kinase expression affected sensitivity of glioma cells to treatment with tumor the necrosis factor-related apoptosis-inducing ligand (TRAIL), a targeted therapy able to induce apoptosis in cancer cells but causes no toxicity in most normal cells. We found that inhibition of eEF-2 kinase by RNA interference (RNAi) or by a pharmacological inhibitor (NH125) enhanced TRAIL-induced apoptosis in the human glioma cells, as evidenced by an increase in apoptosis in the tumor cells treated with eEF-2 kinase siRNA or the eEF-2 kinase inhibitor. We further demonstrated that sensitization of tumor cells to TRAIL was accompanied by a down-regulation of the anti-apoptotic protein, Bcl-xL, and that overexpression of Bcl-xL could abrogate the sensitizing effect of inhibiting eEF-2 kinase on TRAIL. The results of this study may help devise a new therapeutic strategy for enhancing the efficacy of TRAIL against malignant glioma by targeting eEF-2 kinase.     

Complete genome sequence of the polycyclic aromatic hydrocarbon-degrading bacterium Alteromonas sp. strain SN2

Alteromonas sp. strain SN2, able to metabolize polycyclic aromatic hydrocarbons, was isolated from a crude oil-contaminated sea-tidal flat. Here we report the complete 4.97-Mb genome sequence and annotation of strain SN2. These will advance the understanding of strain SN2's adaptation to the sea-tidal flat ecosystem and its pollutant metabolic versatility.     

Complete genome sequence of Leuconostoc kimchii strain C2, isolated from Kimchi

Leuconostoc kimchii strain C2 was isolated from fermented kimchi in Korea. Here we announce the complete genome sequence of Leuconostoc kimchii strain C2, consisting of a 1,877,174-bp chromosome with a G+C content of 37.9% and no plasmid and describe major findings from its annotation.