Genetic and molecular characterization of determinant of six-rowed spike of barley carrying vrs1.a4.

KEY MESSAGE: Decisive role of reduced vrs1 transcript abundance in six-rowed spike of barley carrying vrs1.a4 was genetically proved and its potential causes were preliminarily analyzed. Six-rowed spike 1 (vrs1) is the major determinant of the six-rowed spike phenotype of barley (Hordeum vulgare L.). Alleles of Vrs1 have been extensively investigated. Allele vrs1.a4 in six-rowed barley is unique in that it has the same coding sequence as Vrs1.b4 in two-rowed barley. The determinant of row-type in vrs1.a4 carriers has not been experimentally identified. Here, we identified Vrs1.b4 in two-rowed accessions and vrs1.a4 in six-rowed accessions from the Qinghai-Tibet Plateau at high frequency. Genetic analyses revealed a single nuclear gene accounting for row-type alteration in these accessions. Physical mapping identified a 0.08-cM (~ 554-kb) target interval on chromosome 2H, wherein Vrs1 was the most likely candidate gene. Further analysis of Vrs1 expression in offspring of the mapping populations or different Vrs1.b4 and vrs1.a4 lines confirmed that downregulated expression of vrs1.a4 causes six-rowed spike. Regulatory sequence analysis found a single 'TA' dinucleotide deletion in vrs1.a4 carriers within a 'TA' tandem-repeat-enriched region ~ 1 kb upstream of the coding region. DNA methylation levels did not correspond to the expression difference and therefore did not affect Vrs1 expression. More evidence is needed to verify the causal link between the 'TA' deletion and the downregulated Vrs1 expression and hence the six-rowed spike phenotype.

Polymorphisms in the vitamin D receptor gene and risk of primary biliary cirrhosis: a meta-analysis.

BACKGROUND AND AIM: Primary biliary cirrhosis (PBC) is a chronic and progressive cholestatic autoimmune liver disease. Although many studies have evaluated the association between many functional polymorphisms in the vitamin D receptor (VDR) gene and PBC risk, debates still exist. Our aim is to evaluate the association between VDR gene polymorphisms, including TaqI (rs731236), BsmI (rs1544410), and ApaI (rs7975232), and the risk of PBC by a systematic review. METHODS: We searched literatures in PubMed, SCOPUS, and EMBASE until July 2013. We calculated pooled odds ratios (OR) and 95% confidence intervals (CIs) using a fixed effects model or a random effects model for the risk to PBC associated with different VDR gene polymorphisms. And the heterogeneity assumption decided the effect model. RESULTS: A total of six relevant studies, with 1322 PBC cases and 2264 controls, were included in this meta-analysis. The results indicated that TaqI (rs731236) polymorphism was significantly associated with PBC risk (for T vs t OR = 0.75, 95% CI 0.63, 0.89, Pz = 0.001; TT + Tt vs tt OR = 0.62, 95% CI 0.44, 0.86, Pz = 0.005; OR = 0.74, 95% CI 0.58, 0.94, Pz = 0.016 for recessive model), while ApaI (rs7975232) or BsmI (rs1544410) polymorphism did not. CONCLUSION: Based on current evidences from published studies, the cumulative effect of TaqI polymorphism in VDR was significantly associated with PBC. Larger studies with mixed ethnicity subjects and stratified by clinical and sub clinical characteristics are needed to validate our findings.

Starch granule-associated proteins of hull-less barley (Hordeum vulgare L.) from the Qinghai-Tibet Plateau in China.

BACKGROUND: The starch granule-associated proteins (SGAPs) are the minor components of the starch granules and a majority of them are believed to be starch biosynthetic enzymes. The Qinghai-Tibet Plateau in China, one of the centres of origin of cultivated barley, is abundant in hull-less barley resources which exhibit high polymorphism in SGAPs. RESULTS: The SGAPs of hull-less barley from Qinghai-Tibet Plateau were analysed by one-dimensional (1-D) SDS-PAGE, 2-D PAGE and ESI-Q-TOF MS/MS. In the 1-D SDS-PAGE gel, four proteins including a 80 kDa starch synthase, actin, actin 4 and ATP synthase ß-subunit were identified as novel SGAPs. A total of six different bands were identified as starch granule-bound starch synthase I (GBSSI) and the segregation of the novel GBSSI bands in F(1) and F(2) seeds derived from yf127 × yf70 was in accordance with Mendel's law. In the 2-D PAGE gel, 92 spots were identified as 42 protein species which could be classified into 15 functional groups. Thirteen protein species were identified as SGAPs for the first time and multiple spots were identified as GBSSI. CONCLUSION: This study revealed novel SGAPs in hull-less barley from the Qinghai-Tibet Plateau in China and these will be significant in further studies of starch biosynthesis in barley.

Cloning and characterization of four B-hordein genes from Tibetan hull-less barley (Hordeum vulgare subsp. vulgare).

Four B-hordein genes, designated BH1-BH4, were cloned using PCR amplification from two hull-less barley cultivars, ZQ7239 and ZQ148, collected from Tibet. The results of sequencing indicated that BH1-BH4 contained complete open reading frames (ORFs). Comparison of their predicted polypeptide sequences with the published sequences suggested that they all share the same basic protein structure. Phylogenetic analysis indicated that the deduced amino-acid sequences of BH1-BH4 genes were more closely related to B-hordeins from cultivated barley (Hordeum vulgare L.) than to any other prolamins from wild barley and Aegilops tauschii. Comparison of the coding regions of BH1-BH4 genes showed that BH1 had a lower sequence identity to other previously published B-hordeins than the other three B-hordeins obtained in this study. BH1 was then cloned in a bacterial expression vector based on bacteriophage T7 RNA polymerase. The resulting plasmid produced a 28.15 kDa protein in Escherichia coli. The potential value of B-hordein genes in grain quality improvement of hull-less barley has been discussed.

The complete mitochondrial genome of Tibetan hulless barley.

Hulless barley (Hordeum vulgar L. var. nudum) is one of the staple foods for Tibetans and an important livestock feed in the Tibetan Plateau. We report the complete mitochondrial genome of Tibetan hulless barely. The complete mitochondrial genome size is 416,675 bp. Hulless barely mitochondrial genome encode 34 protein-coding genes, 19 tRNA genes and three rRNA genes. The mitochondrial genome has 50 forward and palindrome repeats totally. Nucleotide sequence of coding region takes over 13.60%, GC content is 44.33%. The maximum-likelihood (ML) phylogenetic tree based on 11 protein-coding genes common to seven plant mitochondrial genomes using Arabidopsis thaliana as out-group support that hulless barely is close to Triticum species.

Syntaxin 1A promotes the endocytic sorting of EAAC1 leading to inhibition of glutamate transport.

The neuronal glutamate transporter, excitatory amino-acid carrier 1 (EAAC1), plays an important role in the modulation of neurotransmission and contributes to synthesis of the inhibitory neurotransmitter gamma-aminobutyric acid (GABA) and to epileptogenesis. However, the mechanisms that regulate EAAC1 endocytic sorting and function remain largely unknown. Here, we first demonstrate that EAAC1 undergoes internalization through the clathrin-mediated pathway and further show that syntaxin 1A, a key molecule in synaptic exocytosis, potentiates EAAC1 internalization, thus leading to the functional inhibition of EAAC1. In the presence of the transmembrane domain of syntaxin 1A, its H3 coiled-coil domain of syntaxin 1A is necessary and sufficient for the inhibition of EAAC1. Furthermore, specific suppression of endogenous syntaxin 1A significantly blocked EAAC1 endocytic sorting and lysosomal degradation promoted by kainic acid, a drug for kindling the animal model of human temporal lobe epilepsy in rat, indicating a potential role of syntaxin 1A in epileptogenesis. These findings provide new evidence that syntaxin 1A serves as an intrinsic enhancer to EAAC1 endocytic sorting and further suggest that syntaxin 1A is conversant with both ;ins' and ;outs' of synaptic neurotransmission.