Unraveling complexity of interconnected regulatory circuits in lipid metabolism

In this issue of Journal of Biomedical Research,3review articles are published that cover a broad range of topics addressing current understanding on regulation of nutrient metabolism through protein phosphatases,homeostatic regulation of cellular lipid droplets by small GTPases,and mechanisms by which hepatic assembly and secretion of triglyceride-rich lipoproteins are regulated.

Nonchaoticity of Ordinary Differential Equations Describing Autonomous Transcriptional Regulatory Circuits

Gene transcriptional regulation （TR） processes are often described by coupled nonlinear ordinary differential equations （ODEs）. When the dimension of TR circuits is high （e.g. n≥3） the motions of the corresponding ODEs may, very probably, show self-sustained oscillations and chaos. On the other hand, chaoticity may be harmful for the normal biological functions of TR processes. In this letter we numerically study the dynamics of 3-gene TR ODEs in great detail, and investigate many 4-, 5-, and lO-gene TR systems by randomly choosing figures and parameters in the conventionally accepted ranges. And we find that oscillations are very seldom and no chaotic motion is observed, even if the dimension of systems is sufficiently high （n≥3）. It is argued that the observation of nonchaoticity of these ODEs agrees with normal functions of actual TR processes.

Differential Expression of Rice Valine-Qlutamine Gene Family in Response to Nitric Oxide and Regulatory Circuit of OsVQ7 and OsWRKY24

The functional diversity of plant valine-qlutamine(VQ) proteins is closely associated with their partners WRKY transcription factors, and also with a complex network of signaling pathways that mediated by hormone molecules. We reported genome-wide expression profiles of differentially expressed rice VQ genes under nitric oxide(NO) treatment based on a microarray analysis. Cluster analysis of expression patterns revealed that some VQ genes and WRKY genes shared similar expression trends. Prediction of cis-elements showed that W-box or W-box-like sequences were overrepresented within the promoters of most of NO-responsive VQ genes. In particular, the similarly expressed Os VQ7 and Os WRKY24 showed great induction upon NO triggering. Transient expression assay and chromatin immunoprecipitation analysis demonstrated that OsWRKY24 was specifically bound to the promoter regions of Os VQ7 and Os WRKY24 itself, which contain multiple copies of W-box or W-box-like cis-elements. Yeast-two-hybrid assay indicated that OsWRKY24 can interact physically with OsVQ7 through the C-terminal of WRKY domain. The results suggested that OsVQ7 and OsWRKY24 may form an auto-and cross-regulation circuit that is required for tight regulation and fine-tuning of physiological processes they are involved in. These findings provided a solid foundation for exploring the specific functions of the VQ protein family in NO signaling pathway.

A widespread response of Gram-negative bacterial acyl-homoserine lactone receptors to Gram-positive Streptomyces γ-butyrolactone signaling molecules

Cell-cell communication is critical for bacterial survival in natural habitats,in which miscellaneous regulatory networks are encompassed.However,elucidating the interaction networks of a microbial community has been hindered by the population complexity.This study reveals thatγ-butyrolactone(GBL)molecules from Streptomyces species,the major antibiotic producers,can directly bind to the acyl-homoserine lactone(AHL)receptor of Chromobacterium violaceum and influence violacein production controlled by the quorum sensing(QS)system.Subsequently,the widespread responses of more Gram-negative bacterial AHL receptors to Gram-positive Streptomyces signaling molecules are unveiled.Based on the cross-talk between GBL and AHL signaling systems,combinatorial regulatory circuits(CRC)are designed and proved to be workable in Escherichia coli(E.coli).It is significant that the QS systems of Gram-positive and Gram-negative bacteria can be bridged via native Streptomyces signaling molecules.These findings pave a new path for unlocking the comprehensive cell-cell communications in microbial communities and facilitate the exploitation of innovative regulatory elements for synthetic biology.