Hubs in the protein-protein interaction network have been classified as "party" hubs, which are highly correlated in their mRNA expression with their partners while "date" hubs show lesser correlation. In this study, we explored the role of intrinsic disorder in date and party hub interactions. The data reveals that intrinsic disorder is significantly enriched in date hub proteins when compared with party hub proteins. Intrinsic disorder has been largely implicated in transient binding interactions. The disorder to order transition, which occurs during binding interactions in disordered regions, renders the interaction highly reversible while maintaining the high specificity. The enrichment of intrinsic disorder in date hubs may facilitate transient interactions, which might be required for date hubs to interact with different partners at different times.

The study of unfolded protein regions has gained importance because of their prevalence and important roles in various cellular functions. These regions have characteristically high net charge and low hydrophobicity. The amino acid sequence determines the intrinsic unstructuredness of a region and, therefore, efforts are ongoing to delineate the sequence motifs, which might contribute to protein disorder. We find that PEST motifs are enriched in the characterized disordered regions as compared with globular ones. Analysis of representative PDB chains revealed very few structures containing PEST sequences and the majority of them lacked regular secondary structure. A proteome-wide study in completely sequenced eukaryotes with predicted unfolded and folded proteins shows that PEST proteins make up a large fraction of unfolded dataset as compared with the folded proteins. Our data also reveal the prevalence of PEST proteins in eukaryotic proteomes (approximately 25%). Functional classification of the PEST-containing proteins shows an over- and under-representation in proteins involved in regulation and metabolism, respectively. Furthermore, our analysis shows that predicted PEST regions do not exhibit any preference to be localized in the C terminals of proteins, as reported earlier.

No abstract

Intrinsic disorder has been shown to be important in mediating protein-protein and protein-DNA interactions. Proteins involved in regulatory functions are particularly enriched in intrinsic disorder. In this study we explored the role of intrinsic disorder in transcriptional regulatory network of yeast. Using disorder prediction programs we show that transcription factors (TFs) regulating large number of targets (transcriptional hubs) have significantly increased intrinsic disorder, though targets regulated by multiple TFs did not show increased intrinsic disorder. Intrinsic disorder may allow these transcriptional hubs to bind to diverse promoter regions of their targets in different contexts, and may also allow complex regulatory control of transcriptional hubs that are involved in coordinating different cellular processes.

b Salmonella enterica serovar Typhimurium (S. Typhimurium) is one of the leading causative agents of food-borne bacterial gastroenteritis. Swift invasion through the intestinal tract and successful establishment in systemic organs are associated with the adaptability of S. Typhimurium to different stress environments. Low-pH stress serves as one of the first lines of defense in mammalian hosts, which S. Typhimurium must efficiently overcome to establish an infection. Therefore, a better understanding of the molecular mechanisms underlying the adaptability of S. Typhimurium to acid stress is highly relevant. In this study, we have performed a transcriptome analysis of S. Typhimurium under the acid tolerance response (ATR) and found a large number of genes (ϳ47%) to be differentially expressed (more than 1.5-fold or less than ؊1.5-fold; P < 0.01). Functional annotation revealed differentially expressed genes to be associated with regulation, metabolism, transport and binding, pathogenesis, and motility. Additionally, our knockout analysis of a subset of differentially regulated genes facilitated the identification of proteins that contribute to S. Typhimurium ATR and virulence. Mutants lacking genes encoding the K ؉ binding and transport protein KdpA, hypothetical protein YciG, the flagellar hook cap protein FlgD, and the nitrate reductase subunit NarZ were significantly deficient in their ATRs and displayed varied in vitro virulence characteristics. This study offers greater insight into the transcriptome changes of S. Typhimurium under the ATR and provides a framework for further research on the subject. Salmonella enterica serovar Typhimurium is a neutralophilic, Gram-negative food-and waterborne pathogen that causes diseases ranging from gastroenteritis to systemic infection in humans. The intestinal tract of wild and domestic animals serves as a vehicle by which salmonellae find their way into humans through contaminated food and water. It has been estimated that globally this species accounts for about 80.3 million cases of food-borne gastroenteritis with about 1.5 million deaths (1). A large number of outbreaks have been linked to contaminated fruits and vegetables, including apples, mangoes, lettuce, tomatoes, celery, and unpasteurized juice (2). During host-pathogen interaction, Salmonella constantly encounters various stress conditions, such as changing pH, high osmotic pressure, low oxygen availability, and the presence of bile salts and antimicrobial peptides, that constantly test the adaptability of this pathogen. One such stress condition is low pH, and Salmonella confronts this on transit through the stomach, as well as during survival within the Salmonellacontaining vacuole (SCV) of phagocytic and nonphagocytic cells. Hence, the ability of Salmonella to perceive low-pH environments and respond to such stress is crucial for its survival and pathogenicity.The mechanism by which S. Typhimurium senses acidic environments and adapts to survive under low pH is termed the acid tolerance response (ATR) (3-...

Secreted proteins of

SUMMARYTo explore the role of the 10-kDa Mycobacterium tuberculosis -specific secreted antigen (MTSA-10 or CFP-10) in modulation of macrophage function, J774 macrophages were transfected stably with DNA encoding MTSA-10. Compared to normal or mock-transfected controls, MTSA-10-expressing macrophages had markedly lower levels of co-stimulatory molecule B7·1 on their surface, while the expression of B7·2 and ICAM-1 was not affected. MTSA-transfected cells also produced significantly less microbicidal free radical nitric oxide (NO) upon stimulation with interferon (IFN)-g , lipopolysaccharide or M. tuberculosis cell lysate. Western blot analysis revealed the absence of tyrosine-phosphorylated protein slightly larger than 112 kDa in MTSA-transfected macrophages. Moreover, the treatment of control J774 cells with protein tyrosine kinase inhibitor genistein completely mimicked the effects of transfection with MTSA-10, selectively down-regulating NO and B7·1, but not B7·2 or ICAM-1 expression. The observed MTSA-10-mediated block of B7·1 expression and NO release might contribute to the suppression of antimycobacterial response in tuberculosis.

Mutations in Plasmodium falciparum gene kelch13 (pfkelch13) are strongly and causally associated with resistance to anti-malarial drug artemisinin, but their effects on PfKelch13 structure and function remain unclear. Utilizing the publicly available three-dimensional structure of PfKech13 (PDB ID: 4yy8), we find that most of the mutations in its propeller domain occur in two spatial clusters. Of these, one cluster is enriched in surface exposed residues which may drive PfKelch13-centered protein interactions, and the second cluster mostly contains residues which are buried and whose mutations may destabilize PfKelch13 structure. The most prevalent resistant mutations C580Y and Y493H are distal from the above two clusters. The C580Y mutation creates sterically unfavourable contacts while Y493H possibly alters the hydrophobic core of the propeller domain. These analyses will facilitate further experimental studies aimed at understanding how mutations in pfkelch13 lead to artemisinin resistance.