Genomic location and expression analysis of expansin gene family reveals the evolutionary and functional significance in <Emphasis Type="Italic">Triticum aestivum</Emphasis>

The plant-specific expansin proteins constitute an ancient and major gene family known to have roles in regulating diverse biological processes in plants. Although the functions of many expansin genes have been identified in wheat and other species, little is known about the evolution and genomic locations of the expansin genes in wheat (Triticum aestivum). In this study, a total of 87 expansin genes were identified in the wheat genome, including 52 EXPAs, 42 EXPBs and 4 EXLAs. The EXLB gene was not found in the wheat genome. Phylogenetic tree and comparative analysis revealed amplification of the EXPBs in rice, maize and wheat. The predicted wheat expansins were distributed across 14 of 21 chromosomes with different densities, 3 tightly co-located clusters and 15 paralogous pairs, indicating that tandem duplication and segmental duplication events also played roles in the evolution of expansins in wheat. In addition, the gene structures and conserved protein domains of wheat expansins suggest high levels of conservation within the phylogenetic subgroups. Analysis of a published microarray database showed that most wheat expansin genes exhibit different expression levels in different tissues and developmental stages. To our knowledge, this is the first report of a genome-wide analysis of the wheat expansin gene family, which should provide valuable information for further elucidating the classification and putative functions of the entire gene family.     

Oxygen isotope temperature calibrations for modern Tridacna shells in western Pacific

Coral Reefs - The oxygen isotope ratio of carbonate in Tridacna shell (δ18Oshell) is assumed to be precipitated in isotopic equilibrium with surrounding seawater and thus reflects a...     

Identification and characterization of CBL and CIPK gene families in canola (Brassica napus L.)

Background

Canola (Brassica napus L.) is one of the most important oil-producing crops in China and worldwide. The yield and quality of canola is frequently threatened by environmental stresses including drought, cold and high salinity. Calcium is a ubiquitous intracellular secondary messenger in plants. Calcineurin B-like proteins (CBLs) are Ca²⁺ sensors and regulate a group of Ser/Thr protein kinases called CBL-interacting protein kinases (CIPKs). Although the CBL-CIPK network has been demonstrated to play crucial roles in plant development and responses to various environmental stresses in Arabidopsis, little is known about their function in canola.

Results

In the present study, we identified seven CBL and 23 CIPK genes from canola by database mining and cloning of cDNA sequences of six CBLs and 17 CIPKs. Phylogenetic analysis of CBL and CIPK gene families across a variety of species suggested genome duplication and diversification. The subcellular localization of three BnaCBLs and two BnaCIPKs were determined using green fluorescence protein (GFP) as the reporter. We also demonstrated interactions between six BnaCBLs and 17 BnaCIPKs using yeast two-hybrid assay, and a subset of interactions were further confirmed by bimolecular fluorescence complementation (BiFC). Furthermore, the expression levels of six selected BnaCBL and 12 BnaCIPK genes in response to salt, drought, cold, heat, ABA, methyl viologen (MV) and low potassium were examined by quantitative RT-PCR and these CBL or CIPK genes were found to respond to multiple stimuli, suggesting that the canola CBL-CIPK network may be a point of convergence for several different signaling pathways. We also performed a comparison of interaction patterns and expression profiles of CBL and CIPK in Arabidospsis, canola and rice, to examine the differences between orthologs, highlighting the importance of studying CBL-CIPK in canola as a prerequisite for improvement of this crop.

Conclusions

Our findings indicate that CBL and CIPK family members may form a dynamic complex to respond to different abiotic or hormone signaling. Our comparative analyses of the CBL-CIPK network between canola, Arabidopsis and rice highlight functional differences and the necessity to study CBL-CIPK gene functions in canola. Our data constitute a valuable resource for CBL and CPK genomics.     

Fine Mapping of <Emphasis Type="Italic">qHD4-1</Emphasis>, a QTL Controlling the Heading Date,to a 20.7-kb DNA Fragment in Rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

A library consisting of 1,123 single-segment substitution lines (SSSLs) in the same genetic background of an elite rice variety Huajingxian74 (HJX74) was evaluated for heading date. From this library, the SSSL W05-1-11-5-16-2-5 with the substituted interval of PSM103—RM348-OSR15-PSM382-RM131-RM127—RM280 was found having a gene, which stably performed extreme late heading date which performed stable and late heading in the different environments of Shandong, Guangdong, and Hainan. To map the gene governing heading date, the SSSL W05-1-11-5-16-2-5 was crossed with the recipient HJX74 to develop an F₂ segregating population. The distribution of late and early heading plants in this population fitted a segregation ratio of 3:1, indicating the late heading was controlled by a dominant gene. The gene locus for heading date was tentatively designated as qHD4-1. Using a random sample of 460 individuals from the F₂ segregation population, the qHD4-1 locus was mapped between two SSR markers RM3335 and RM17572, with genetic distances of 0.1 and 0.2 cM, respectively. For fine mapping of qHD4-1, a large F_2:3 segregating population of 3,000 individuals were developed from F₂ plants heterozygous in the RM3335-RM17572 region. Recombinants analyses further mapped qHD4-1 to an interval of 20.7-kb-bounded WB05 and the WB06. Sequence analysis of this 20.7-kb region revealed that it contains three open reading frames (ORFs), encoding wall-associated receptor kinase-like 5, putative F-box domain containing protein, and putative arogenate/prephenate dehydratase. Of them, ORF1, predicting to encode serine/threonine kinase, is considered the most likely as the candidate gene. The genetic and physical map of the qHD4-1 locus will be very useful in molecular cloning of the qHD4-1gene.     

The Akt signaling pathway contributes to postconditioning's protection against stroke; the protection is associated with the MAPK and PKC pathways

We previously reported that ischemic postconditioning with a series of mechanical interruptions of reperfusion reduced infarct volume 2 days after focal ischemia in rats. Here, we extend this data by examining long-term protection and exploring underlying mechanisms involving the Akt, mitogen-activated protein kinase (MAPK) and protein kinase C (PKC) signaling pathways. Post-conditioning reduced infarct and improved behavioral function assessed 30 days after stroke. Additionally, postconditioning increased levels of phosphorylated Akt (Ser473) as measured by western blot and Akt activity as measured by an in vitro kinase assay. Inhibiting Akt activity by a phosphoinositide 3-kinase inhibitor, LY294002, enlarged infarct in postconditioned rats. Postconditioning did not affect protein levels of phosphorylated-phosphatase and tensin homologue deleted on chromosome 10 or -phosphoinositide-dependent protein kinase-1 (molecules upstream of Akt) but did inhibit an increase in phosphorylated-glycogen synthase kinase 3β, an Akt effector. In addition, postconditioning blocked β-catenin phosphorylation subsequent to glycogen synthase kinase, but had no effect on total or non-phosphorylated active β-catenin protein levels. Furthermore, postconditioning inhibited increases in the amount of phosphorylated-c- Jun N-terminal kinase and extracellular signal-regulated kinase 1/2 in the MAPK pathway. Finally, postconditioning blocked death-promoting δPKC cleavage and attenuated reduction in phosphorylation of survival-promoting εPKC. In conclusion, our data suggest that postconditioning provides long-term protection against stroke in rats. Additionally, we found that Akt activity contributes to postconditioning's protection; furthermore, increases in εPKC activity, a survival-promoting pathway, and reductions in MAPK and δPKC activity; two putative death-promoting pathways correlate with postconditioning's protection.     

Inhibition of PFKFB3 suppresses osteoclastogenesis and prevents ovariectomy‐induced bone loss

Osteoclasts are multinucleated cells derived from the monocyte/macrophage cell lineage under the regulation of receptor activator of nuclear factor‐κB ligand (RANKL). In previous studies, stimulation by RANKL during osteoclastogenesis was shown to induce a metabolic switch to enhanced glycolytic metabolism. Thus, we hypothesized that blockage of glycolysis might serve as a novel strategy to treat osteoclast‐related diseases. In the present study, 6‐phosphofructo‐2‐kinase/fructose‐2,6‐bisphosphatase 3 (PFKFB3), an essential regulator of glycolysis, was up‐regulated during osteoclast differentiation. Genetic and pharmacological inhibition of PFKFB3 in bone marrow‐derived macrophages suppressed the differentiation and function of osteoclasts. Moreover, intraperitoneal administration of the PFKFB3 inhibitor PFK15 prevented ovariectomy‐induced bone loss. In addition, glycolytic activity characterized by lactate accumulation and glucose consumption in growth medium was reduced by PFKFB3 inhibition. Further investigation indicated that the administration of L‐lactate partially reversed the repression of osteoclastogenesis caused by PFKFB3 inhibition and abrogated the inhibitory effect of PFK15 on the activation of NF‐κB and MAPK pathways. In conclusion, the results of this study suggest that blockage of glycolysis by targeting PFKFB3 represents a potential therapeutic strategy for osteoclast‐related disorders.     

出芽短梗霉菌株PA-2全基因组测序及分析

【背景】出芽短梗霉菌株PA-2是一株分离自青海省海东市平安区患病杨树叶片上的真菌,前期研究表明该菌株具有除草和抑菌能力,说明其在生物农药方面具有潜在的应用前景。【目的】了解菌株PA-2的基因组序列信息,挖掘其生防相关功能基因簇,为进一步研究解析该菌株生防机理及生防功能改造提供遗传背景信息。【方法】利用IlluminaHiSeq高通量测序平台对生防菌株PA-2进行全基因组测序,用生物信息学的方法对测序数据进行基因组组装、基因预测及功能注释、碳水化合物活性酶预测、次级代谢产物合成基因簇预测,利用刚果红染色等方法对水解酶活性进行衡量。【结果】菌株PA-2基因组序列全长28 932 793 bp,平均GC含量为50%,共编码10 839个基因,预测到该菌株具有4个已知的次级代谢产物合成基因簇,编码Melanin、Burnettramic Acid A、ACR-Toxin I、Abscisic Acid,该菌株能水解纤维素和果胶。【结论】有助于在基因组层面上解析菌株PA-2生防机制的内在原因,为深入了解出芽短梗霉菌次级代谢物合成途径提供参考,对菌株PA-2的下一步相关研究具有重要意义。     

Fine Mapping of <Emphasis Type="Italic">qHD8-1</Emphasis>, a QTL Controlling the Heading Date,to a 26-kb DNA Fragment in Rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Heading date is one of the importance agronomic traits. A library consisting of 1,123 single segment substitution lines (SSSLs) in the same genetic background of an elite rice variety Huajingxian 74 (HJX74) was evaluated for heading date (HD). From this library, the SSSL W06-26-35-1-5-2 with the substituted interval of PSM152–PSM154–PSM155–RM25–RM547–RM72–RM404 was found having a gene, which performed stable and late heading in the different environments of Shandong and Hainan provinces. To map the gene governing heading date, the SSSL W06-26-35-1-5-2 was crossed with the recipient HJX74 to develop an F₂ segregating population. The distribution of late and early heading plants in this population fitted a segregation ratio of 3:1, indicating the late heading was controlled by a dominant gene. The gene locus for heading date was tentatively designated as qHD8-1. Using a random sample of 460 individuals from the F₂ population, the qHD8-1 was narrowed down to a region flanking by two SSR markers PSM155 and RM547. For fine mapping of qHD8-1, a large F_2:3 segregating population of 3,000 individuals were developed from F₂ plants heterozygous in the PSM155–RM547 region. Recombinants analysis further mapped qHD8-1 to an interval of region 26 kb with markers RM22492 and P23 bounded on the left and right sides, respectively. Sequence analysis of this 26-kb fragment revealed that it contains five putative open reading frames, which were regarded as candidates of qHD8-1. These results will be useful in cloning of the qHD8-1 gene.