Lipolysis - a highly regulated multi-enzyme complex mediates the catabolism of cellular fat stores

Lipolysis is the biochemical pathway responsible for the catabolism of triacylglycerol (TAG) stored in cellular lipid droplets. The hydrolytic cleavage of TAG generates non-esterified fatty acids, which are subsequently used as energy substrates, essential precursors for lipid and membrane synthesis, or mediators in cell signaling processes. Consistent with its central importance in lipid and energy homeostasis, lipolysis occurs in essentially all tissues and cell types, it is most abundant, however, in white and brown adipose tissue. Over the last 5years, important enzymes and regulatory protein factors involved in lipolysis have been identified. These include an essential TAG hydrolase named adipose triglyceride lipase (ATGL) [annotated as patatin-like phospholipase domain-containing protein A2], the ATGL activator comparative gene identification-58 [annotated as α/β hydrolase containing protein 5], and the ATGL inhibitor G0/G1 switch gene 2. Together with the established hormone-sensitive lipase [annotated as lipase E] and monoglyceride lipase, these proteins constitute the basic "lipolytic machinery". Additionally, a large number of hormonal signaling pathways and lipid droplet-associated protein factors regulate substrate access and the activity of the "lipolysome". This review summarizes the current knowledge concerning the enzymes and regulatory processes governing lipolysis of fat stores in adipose and non-adipose tissues. Special emphasis will be given to ATGL, its regulation, and physiological function.     

Genome-wide identification of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families and their expression analyses in response to viral infection and abiotic stresses in Solanum lycopersicum

Dicer, Argonaute and RNA-dependent RNA polymerase form the core components to trigger RNA silencing. Although tomato (Solanum lycopersicum) is a dicotyledon model plant, no systematic analysis and expression profiling of these genes in tomato has been undertaken previously. In this study, seven Dicer-like (SlDCLs), 15 Argonaute (SlAGOs) and six RNA-dependent RNA polymerase (SlRDRs) genes were identified in tomato. These genes were categorized into four subgroups based on phylogenetic analyses. Comprehensive analyses of gene structure, genomic localization and similarity among these genes were performed. Their expression patterns were investigated by means of expression models in different tissues and organs using online data and semi-quantitative RT-PCR. Many of the candidate genes were up-regulated in response to Tomato yellow leaf curl virus infection and abiotic stresses. The expression models of tandem gene duplications among SlDCL2s indicated the DCL2 family plays an important role in the evolution of tomato.     

Sequencing and analysis of four BAC clones containing innate immune genes from the Zhikong scallop (Chlamys farreri)

The sequencing of BAC clones (~100 kb) can reveal some characteristics of a genome that are challenging to obtain based on short sequences. Additionally, although the immune genes of the Zhikong scallop (Chlamys farreri) have been studied widely, few analyses have been conducted at the DNA level. In this study, four C. farreri BAC clones containing innate immune genes, including hsp70, l gbp (lipopolysaccharide and beta-1,3-glucan binding protein), serine protease and a gene with an immunoglobulin-like domain, were sequenced and analyzed both to explore the genomic characteristics of C. farreri based on long DNA sequences and to promote the study of C. farreri immune genes at the DNA level. The total length of the four BACs was 389.98 kb. A total of 34 genes were predicted in these sequences, and several features of protein-coding regions in the C. farreri genome were inferred based on this information. Two LGBP genes were located close together in a 22-kb region in one BAC clone, indicating the physical linkage of some immune genes in C. farreri. A cluster of membrane transport genes was also observed; these genes might play important roles in eliminating toxins in C. farreri, which lives as a filter feeder. Further analysis showed 15.43% of the BAC sequence was repetitive. Tandem repeats were the most abundant repeat type, followed by transposable elements. A total of 31 SSRs were predicted in the four BACs. An IS10 family transposon was identified, and a suspected regulatory non-coding RNA gene for this transposon (RNA-OUT) was observed to overlap with it complementarily. This work will promote future studies on the genomics, immune system and non-coding regions of C. farreri.     

原核生物基因组的CDS与ORF序列的几点分析

基因组的开放阅读框（ORF）是基因识别与基因组分析的基础,有多种软件包给出了它们的生成算法,但结果与指标并不统一.本文给出了po-MORF的定义与它的生成算法,证明了由基因组所确定的po-MORF集合的存在与唯一性,并由该生成算法可以得到全部po-MORF序列.我们还比较了若干原核生物基因组中所有CDS与po-MORF序列的相互关系,并讨论了关于基因识别中的有关问题.     

Abundance of microRNA target motifs in the 3'-UTRs of 20527 human genes

A mechanism, selective avoidance, proposes that microRNA (miRNA) target sites are selectively depleted in the 3'-UTRs of genes expressed at the same time and place as a miRNA. If this mechanism is ubiquitous, the target motif occurrences in the 3'-UTRs would be decreased. To test this hypothesis, we examined miRNA target motif occurrences in the 3'- and 5'-UTRs of 20527 human protein-coding genes. The results revealed that miRNA target motifs appeared more frequently than non-target motifs and were enriched in the 3'-UTRs. This enrichment was relatively reduced in a set of 2525 genes coexpressed with miR-124a in the prefrontal cortex, but still remained at a high level, suggesting that miRNA target motifs are fostered by some other factors that surpass the influence of selective avoidance.     

Human oncogene tissue-specific expression level significantly correlates with sequence compositional features

To explore whether there exist correlations between human gene expressions and corresponding sequence features, the expression levels for 81 oncogenes in 24 human tissues were collected and correlated with 159 sequence features. It was found that there do exist significant correlations between them, some of which are of significance to understanding translational selection on sequence features of human genes and some have important implications for diagnosing cancers.