Complete mitochondrial genome of the Walking goby Scartelaos histophorus (Perceformes, Gobiidae)

The Walking goby Scartelaos histophorus (Perciformes, Gobiidae) is an amphibious gobioid fish. In this paper, the complete mitochondrial genome of S. histophorus was first determined. The genome is 16,496 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 1 control region. The overall base composition of S. histophorus is 27.5% for T, 28.0% for C, 28.3% for A, and 16.1% for G, with a slight A+T bias of 55.8%. It has the typical vertebrate mitochondrial gene arrangement.     

Complete mitochondrial genome of the mudskipper Boleophthalmus pectinirostris (Perciformes, Gobiidae): repetitive sequences in the control region

The mudskipper, Boleophthalmus pectinirostris (Perciformes, Gobiidae), is an amphibious gobioid fish. In this paper, the complete mitochondrial genome of B. pectinirostris was firstly determined. The mitogenome (17,111 bp) comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 putative control region. 130-bp tandem repeat was identified in the control region, which was almost identical among the 10 individuals examined, and three different frequencies of the repeat unit (five, six or seven) were found among these individuals.     

Phylogeny and molecular evolution of the DMC1 gene within the StH genome species in Triticeae (Poaceae)

To estimate the phylogeny and molecular evolution of a single-copy nuclear disrupted meiotic cDNA (DMC1) gene within the StH genome species, two DMC1 homoeologous sequences were isolated from nearly all the sampled StH genome species and were analyzed with those from seven diploid taxa representing the St and H genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1) there is a close relationship among North American StH genome species; (2) the DMC1 gene sequences of the StH genome species from North America and Eurasia are evolutionarily distinct; (3) the StH genome polyploids have higher levels of sequence diversity in the St genome homoeolog than the H genome homoeolog; (4) the DMC1 sequence may evolve faster in the polyploid species than in the diploids; (5) high dN and dN/dS values in the St genome within polyploid species could be caused by low selective constraints or AT-biased mutation pressure. Our result provides some insight on evolutionary dynamics of duplicate DMC1 gene, the polyploidization events and phylogeny of the StH genome species.     

Effective approach to greatly enhancing selective secretion and expression of three cytoplasmic enzymes in Escherichia coli through synergistic effect of EDTA and lysozyme

An effective approach to greatly enhancing the selective secretion and expression of recombinant cytoplasmic enzymes in Escherichia coli was successfully developed through the synergistic effect of ethylenediaminetetraacetate (EDTA) and lysozyme. The method was applied to two endoglucanases (EGs) and an amylase. The optimal culture conditions of temperature and concentration of isopropyl-β-D: -1-thiogalactopyranoside (IPTG) were 23-30?°C and 0.2?mM, respectively, under which the three enzymes could be expressed in active form. Among all the chemicals tested, EDTA was found to be most suitable for enhancing the secretion of EG-I-1A into the medium. Addition of lysozyme alone had little influence on the secretion and expression. In contrast, on the basis of the addition of 5?g?EDTA/L at the induction time of 12?h, the simultaneous addition of 0.15?g?lysozyme/L further significantly increased the secretion and expression of the three enzymes, demonstrating the synergistic effect of EDTA and lysozyme. The production of EG-I-1A in the culture medium by adding 5?g?EDTA/L and 0.15?g?lysozyme/L under the optimal culture conditions of 23?°C and 0.2?mM IPTG was over 260-fold higher than that without EDTA and lysozyme under the standard conditions of 37?°C and 1?mM IPTG. In summary, the advantage of this novel cultivation approach for secretion was that not only did it selectively enhance the secretion of the proteins of interest, but also greatly increased the expression of the three enzymes by over 80?%.     

Enzymatic transformation of the major ginsenoside Rb2 to minor compound Y and compound K by a ginsenoside-hydrolyzing β-glycosidase from Microbacterium esteraromaticum

The ginsenoside-hydrolyzing β-glycosidase (Bgp3) derived from Microbacterium esteraromaticum transformed the major ginsenoside Rb2 to more pharmacologically active minor ginsenosides including compounds Y and K. The bgp3 gene consists of 2,271?bp encoding 756 amino acids which have homology to the glycosyl hydrolase family 3 protein domain. Bgp3 is capable of hydrolyzing beta-glucose links and arabinose links. HPLC analysis of the time course of ginsenoside Rb2 hydrolysis by Bgp3 (0.1?mg?enzyme?ml(-1) in 20?mM sodium phosphate buffer at 40?°C and pH 7.0) showed that the glycosidase first hydrolyzed the inner glucose moiety attached to the C-3 position and then the arabinopyranose moiety attached to the C-20 position. Thus, Bgp3 hydrolyzed the ginsenoside Rb2 via the following pathway: Rb2?→?compound Y?→?compound K.     

Reduction of N-terminal methionylation while increasing titer by lowering metabolic and protein production rates in E. coli auto-induced fed-batch fermentation

A standard fed-batch fermentation process using 1 mM isopropyl-β-D: -thiogalactopyranoside (IPTG) induction at 37 °C in complex batch and feed media had been developed for manufacturing of a therapeutic protein (TP) expressed in inclusion bodies (IBs) by E. coli BL21 (DE3) driven by T7 promoter. Six unauthentic TP N-terminal variants were identified, of which methionylated TP (Met-TP) ratio was predominant. We hypothesized that lowering metabolic and protein production rates would reduce the Met-TP ratio while improving TP titer. The standard process was surprisingly auto-induced without added IPTG due to galactose in the complex media. Without changing either the clone or the batch medium, a new process was developed using lower feed rates and auto-induction at 29 °C after glucose depletion while increasing induction duration. In comparison to the standard process, the new process reduced the unauthentic Met-TP ratio from 23.6 to 9.6 %, increased the TP titer by 85 %, and the specific production yield from 210 to 330 mg TP per gram of dry cell weight. Furthermore, the TP recovery yield in the purified IBs was improved by ~20 %. Adding together, ~105 % more TP recovered in the purified IBs from per liter of fermentation broth for the new process than the standard process. The basic principles of lowering metabolic and production rates should be applicable to other recombinant protein production in IBs by fed-batch fermentations.