Pla2g12b and Hpn Are Genes Identified by Mouse ENU Mutagenesis That Affect HDL Cholesterol

Despite considerable progress understanding genes that affect the HDL particle, its function, and cholesterol content, genes identified to date explain only a small percentage of the genetic variation. We used N-ethyl-N-nitrosourea mutagenesis in mice to discover novel genes that affect HDL cholesterol levels. Two mutant lines (Hlb218 and Hlb320) with low HDL cholesterol levels were established. Causal mutations in these lines were mapped using linkage analysis: for line Hlb218 within a 12 Mbp region on Chr 10; and for line Hlb320 within a 21 Mbp region on Chr 7. High-throughput sequencing of Hlb218 liver RNA identified a mutation in Pla2g12b. The transition of G to A leads to a cysteine to tyrosine change and most likely causes a loss of a disulfide bridge. Microarray analysis of Hlb320 liver RNA showed a 7-fold downregulation of Hpn; sequencing identified a mutation in the 3' splice site of exon 8. Northern blot confirmed lower mRNA expression level in Hlb320 and did not show a difference in splicing, suggesting that the mutation only affects the splicing rate. In addition to affecting HDL cholesterol, the mutated genes also lead to reduction in serum non-HDL cholesterol and triglyceride levels. Despite low HDL cholesterol levels, the mice from both mutant lines show similar atherosclerotic lesion sizes compared to control mice. These new mutant mouse models are valuable tools to further study the role of these genes, their affect on HDL cholesterol levels, and metabolism.     

Regulation of SOBIR1 accumulation and activation of defense responses in bir1–1 by specific components of ER quality control

Receptor‐like kinases play diverse roles in plant biology. Arabidopsis BAK1‐INTERACTING RECEPTOR‐LIKE KINASE 1 (BIR1) functions as a negative regulator of plant immunity. bir1‐1 mutant plants display spontaneous cell death and constitutive defense responses that are dependent on SUPPRESSOR OF BIR1,1 (SOBIR1) and PHYTOALEXIN DEFICIENT4 (PAD4). Here we report that mutations in three components of ER quality control, CALRETICULIN3 (CRT3), ER‐LOCALIZED DnaJ‐LIKE PROTEIN 3b (ERdj3b) and STROMAL‐DERIVED FACTOR‐2 (SDF2), also suppress the spontaneous cell death and constitutive defense responses in bir1‐1. Further analysis revealed that accumulation of the SOBIR1 protein is reduced in crt3‐1 and erdj3b‐1 mutant plants. These data suggest that ER quality control plays important roles in the biogenesis of SOBIR1, and is required for cell death and defense responses in bir1‐1.     

Strategy for Identification of Novel Fungal and Bacterial Glycosyl Hydrolase Hybrid Mixtures that can Efficiently Saccharify Pretreated Lignocellulosic Biomass

A rational four-step strategy to identify novel bacterial glycosyl hydrolases (GH), in combination with various fungal enzymes, was applied in order to develop tailored enzyme cocktails to efficiently hydrolyze pretreated lignocellulosic biomass. The fungal cellulases include cellobiohydrolase I (CBH I; GH family 7A), cellobiohydrolase II (CBH II; GH family 6A), endoglucanase I (EG I; GH family 7B), and β-glucosidase (βG; GH family 3). Bacterial endocellulases (LC1 and LC2; GH family 5), β-glucosidase (LβG; GH family 1), endoxylanases (LX1 and LX2; GH family 10), and β-xylosidase (LβX; GH family 52) from multiple sources were cloned, expressed, and purified. Enzymatic hydrolysis for varying enzyme combinations was carried out on ammonia fiber expansion (AFEX)-treated corn stover at three total protein loadings (i.e., 33, 16.5, and 11 mg enzyme/g glucan). The optimal mass ratio of enzymes necessary to maximize both glucan and xylan yields was determined using a suitable design of experiments. The optimal hybrid enzyme mixtures contained fungal cellulases (78% of total protein loading), which included CBH I (loading ranging between 9-51% of total enzyme), CBH II (9-51%), EG I (10-50%), and bacterial hemicellulases (22% of total protein loading) comprising of LX1 (13%) and LβX (9%). The hybrid mixture was effective at 50°C, pH 4.5 to maximize saccharification of AFEX-treated corn stover resulting in 95% glucan and 65% xylan conversion. This strategy of screening novel enzyme mixtures on pretreated lignocellulose would ultimately lead to the development of tailored enzyme cocktails that can hydrolyze plant cell walls efficiently and economically to produce cellulosic ethanol.     

N‐glycosylation proteomic characterization and cross‐species comparison of milk whey proteins from dairy animals

Glycosylated proteins in milk have been implicated in multiple biological roles. However, the N‐glycoprotein components and their complexity in milk whey from dairy animals are not well characterized. Here, a modified proteomics approach consisting of N‐glycopeptide enrichment and identification was used to map the N‐glycoproteome profile of milk whey from Holstein and Jersey cows, buffaloes, yaks, goats, camels, and horses. A total of 233 N‐glycosylation sites, corresponding to 147 N‐glycoproteins, were detected in the studied animals. Most of the identified N‐glycosylation sites were not characterized in the database and were considered as unknown. Functional analysis of the identified glycoproteins demonstrated that response to stimulus was the most abundant GO category shared in the studied animals according to their annotation. Lysosome, glycosaminoglycan degradation, and extracellular matrix‐receptor interaction pathways were shared between Holstein and Jersey cows, and yaks. N‐glycoprotein components of milk whey from Holstein and Jersey cows, buffaloes, yaks, and goats were more similar to each other than to those of camels and horses. These results significantly extend the number of known N‐glycosylation sites and reveal in‐depth composition and potential functions of N‐glycoproteins in milk whey, which in turn provides insights to further explore N‐glycoprotein biosynthesis in the studied animals.     

Catalysis with CuII(bpy) improves alkaline hydrogen peroxide pretreatment

Copper(II) 2,2′‐bipyridine (Cu^II(bpy))‐catalyzed alkaline hydrogen peroxide (AHP) pretreatment was performed on three biomass feedstocks including alkali pre‐extracted switchgrass, silver birch, and a hybrid poplar cultivar. This catalytic approach was found to improve the subsequent enzymatic hydrolysis of plant cell wall polysaccharides to monosaccharides for all biomass types at alkaline pH relative to uncatalyzed pretreatment. The hybrid poplar exhibited the most significant improvement in enzymatic hydrolysis with monomeric sugar release and conversions more than doubling from 30% to 61% glucan conversion, while lignin solubilization was increased from 36.6% to 50.2% and hemicellulose solubilization was increased from 14.9% to 32.7%. It was found that Cu^II(bpy)‐catalyzed AHP pretreatment of cellulose resulted in significantly more depolymerization than uncatalyzed AHP pretreatment (78.4% vs. 49.4% decrease in estimated degree of polymerization) and that carboxyl content the cellulose was significantly increased as well (fivefold increase vs. twofold increase). Together, these results indicate that Cu^II(bpy)‐catalyzed AHP pretreatment represents a promising route to biomass deconstruction for bioenergy applications. Biotechnol. Bioeng. 2013; 110: 1078–1086. © 2012 Wiley Periodicals, Inc.     

N‐glycosylation proteomic characterization and cross‐species comparison of milk fat globule membrane proteins from mammals

Glycosylation of proteins has been implicated in various biological functions and has received much attention; however, glycoprotein components and inter‐species complexity have not yet been elucidated fully in milk proteins. N‐linked glycosylation sites and glycoproteins in milk fat globule membrane (MFGM) fractions were investigated by combining N‐glycosylated peptides enrichment and high‐accuracy Q Exactive identification, to map the N‐glycoproteome profiles in Holstein and Jersey cows, buffaloes, yaks, goats, camels, horses, and humans. A total of 399 N‐glycoproteins with 677 glycosylation sites were identified in the MFGM fractions of the studied mammals. Most glycosylation sites in humans were classified as known and those in the other studied mammals as unknown, according to Swiss‐Prot annotations. Functionally, most of the identified glycoproteins were associated with the ‘response to stimulus’ GO category. N‐glycosylated protein components of MFGM fractions from Holstein and Jersey cows, buffaloes, yaks, and goats were more similar to each other compared with those of camels, horses and human. The findings increased the number of known N‐glycosylation sites in the milk from dairy animal species, revealed the complexity of the MFGM glycoproteome, and provided useful information to further explore the mechanism of MFGM glycoproteins biosynthesis among the studied mammals.     

Matrix metalloproteinase 2 promotes cell growth and invasion in colorectal cancer

Colorectal cancer (CRC) is the third leading cause of cancer-related death in the western world. In this study, we evaluated the expression of matrix metalloproteinase 2 gene (MMP2) in CRC and analyzed its correlation with clinicopathological features. We found that the expression of MMP2 was significantly higher in CRC tissues than in the colorectal tissues. In addition, high levels of MMP2 protein were positively correlated with the status of tumor size, lymph node metastasis, distant metastasis, Dukes' stage, and tumor invasion. Moreover, patients with higher MMP2 levels had markedly shorter overall survivals than those with low MMP2 levels. Multivariate analysis results suggested that the level of MMP2 expression is an independent prognostic indicator for the survival of patients with CRC. Silencing MMP2 expression in CRC cell lines with lentiviral-mediated shRNA markedly suppressed cell proliferation, colony formation, and invasion. Furthermore, we observed that vascular endothelial growth factor (VEGF) and membrane type 1 (MT1)-MMP protein levels were decreased in MMP2-down-regulated colorectal cells. Therefore, our study demonstrated that MMP2 is an important factor related to carcinogenesis and metastasis of CRC, and MMP2 promotes CRC cell growth and invasion by up-regulating VEGF and MT1-MMP expression, which makes this pathway a potential target for cancer treatment.