The CbbQO-type rubisco activases encoded in carboxysome gene clusters can activate carboxysomal form IA rubiscos

The CO₂-fixing enzyme rubisco is responsible for almost all carbon fixation. This process frequently requires rubisco activase (Rca) machinery, which couples ATP hydrolysis to the removal of inhibitory sugar phosphates, including the rubisco substrate ribulose 1,5-bisphosphate (RuBP). Rubisco is sometimes compartmentalized in carboxysomes, bacterial microcompartments that enable a carbon dioxide concentrating mechanism (CCM). Characterized carboxysomal rubiscos, however, are not prone to inhibition, and often no activase machinery is associated with these enzymes. Here, we characterize two carboxysomal rubiscos of the form IA^C clade that are associated with CbbQO-type Rcas. These enzymes release RuBP at a much lower rate than the canonical carboxysomal rubisco from Synechococcus PCC6301. We found that CbbQO-type Rcas encoded in carboxysome gene clusters can remove RuBP and the tight-binding transition state analog carboxy-arabinitol 1,5-bisphosphate from cognate rubiscos. The Acidithiobacillus ferrooxidans genome encodes two form IA rubiscos associated with two sets of cbbQ and cbbO genes. We show that the two CbbQO activase systems display specificity for the rubisco enzyme encoded in the same gene cluster, and this property can be switched by substituting the C-terminal three residues of the large subunit. Our findings indicate that the kinetic and inhibitory properties of proteobacterial form IA rubiscos are diverse and predict that Rcas may be necessary for some α-carboxysomal CCMs. These findings will have implications for efforts aiming to introduce biophysical CCMs into plants and other hosts for improvement of carbon fixation of crops.     

A novel human striated muscle RING zinc finger protein, SMRZ, interacts with SMT3b via its RING domain

The RING domain is a conserved zinc finger motif, which serves as a protein-protein interaction interface. Searches of a human heart expressed sequence tag data base for genes encoding the RING domain identified a novel cDNA, named striated muscle RING zinc finger protein (SMRZ). The SMRZ cDNA is 1.9 kilobase pairs in length and encodes a polypeptide of 288 amino acid residues; analysis of the peptide sequence demonstrated an N-terminal RING domain. Fluorescence in situ hybridization localized SMRZ to chromosome 1p33-34. Northern blots demonstrated that SMRZ is expressed exclusively in striated muscle. In the cardiovascular system, SMRZ is more highly expressed in the fetal heart than in the adult heart (slightly higher expression in the ventricle than in the atrium), suggesting that SMRZ is developmentally regulated. SMRZ was found to interact with SMT3b, a ubiquitin-like protein, through the SMRZ-RING domain. This interaction was abolished by mutagenesis of conserved RING domain residues. Transient transfection of SMRZ into C2C12 myoblasts showed localization of SMRZ to the nucleus. These data suggest that SMRZ may play an important role in striated muscle cell embryonic development and perhaps in cell cycle regulation.     

A novel pathway regulating lipopolysaccharide-induced shock by ST2/T1 via inhibition of Toll-like receptor 4 expression

ST2/ST2L, a member of the IL-1R gene family, is expressed by fibroblasts, mast cells, and Th2, but not Th1, cells. It exists in both membrane-bound (ST2L) and soluble forms (ST2). Although ST2L has immunoregulatory properties, its ligand, cellular targets, and mode of action remain unclear. Using a soluble ST2-human IgG fusion protein, we demonstrated that ST2 bound to primary bone marrow-derived macrophages (BMM) and that this binding was enhanced by treatment with LPS. The sST2 treatment of BMMs inhibited production of the LPS-induced proinflammatory cytokines IL-6, IL-12, and TNF-alpha but did not alter IL-10 or NO production. Treatment of BMMs with sST2 down-regulated expression of Toll-like receptors-4 and -1 but induced nuclear translocation of NF-kappaB. Administration of sST2 in vivo after LPS challenge significantly reduced LPS-mediated mortality and serum levels of IL-6, IL-12, and TNF-alpha. Conversely, blockade of endogenous ST2 through administration of anti-ST2 Ab exacerbated the toxic effects of LPS. Thus, ST2 has anti-inflammatory properties that act directly on macrophages. We demonstrate here a novel regulatory pathway for LPS-induced shock via the ST2-Toll-like receptor 4 route. This may be of considerable therapeutic potential for reducing the severity and pathology of inflammatory diseases.     

Cloning and characterization of a cDNA encoding a novel fibroblast growth factor preferentially expressed in human heart

A novel human fibroblast growth factor (hFGF), which shows 75% sequence homology with fibroblast growth factor-9, was isolated in random sequencing of a human heart cDNA library. The full-length sequence is 928 bp, the encoded protein is composed of 168 amino acid residues, and its pI value and molecular weight were estimated to be 8.13 and 19.1 kDa, respectively. RT-PCR using Marathon human heart cDNA shows that the coding region is approximately 507 bp. Southern hybridization showed a single band which indicates that this is a single copy gene. Northern hybridization done on a human multiple tissues blot showed that the gene is preferentially expressed in human heart, very weakly detectable in human brain and not detectable in 18 other different human tissues.     

Purification of filamentous bacteriophage M13 by expanded bed anion exchange chromatography

In this paper, we investigated the development of a simplified and rapid primary capture step for the recovery of M13 bacteriophage from particulate-containing feedstock. M13 bacteriophage, carrying an insert, was propagated and subsequently purified by the application of both conventional multiple steps and expanded bed anion exchange chromatography. In the conventional method, precipitation was conducted with PEG/NaCl, and centrifugation was also performed. In the single step expanded bed anion exchange adsorption, UpFront FastLine 20 (20 mm i.d.) from UpFront Chromatography was used as the contactor, while 54 ml (Ho = 15 cm) of STREAMLINE DEAE (rho = 1.2 g/cm3) from Amersham Pharmacia Biotechnology was used as the anion exchanger. The performance of the two methods were evaluated, analysed, and compared. It was demonstrated that the purification of the M13 bacteriophage, using expanded bed anion exchange adsorption, yielded the higher recovery percentage, at 82.86%. The conventional multiple step method yielded the lower recovery percentage, 36.07%. The generic application of this integrated technique has also been assessed.     

Cellware--a multi-algorithmic software for computational systems biology

The intracellular environment of a cell hosts a wide variety of enzymatic reactions, diffusion events, molecular binding, polymerization and metabolic channeling. To transform these biological events into a computational framework, distinct modeling strategies are required. While currently no tool is capable of capturing all these events, progress is being made to create an integrated environment for the modeling community. To address this niche requirement, Cellware has been developed to offer a multi-algorithmic environment for modeling and simulating both deterministic and stochastic events in the cell. AVAILABILITY: The software is available for free and can be downloaded from http://www.bii.a-star.edu.sg/sbg/cellware     

CD4+CD25+ regulatory T cells suppress differentiation and functions of Th1 and Th2 cells,Leishmania major infection,and colitis in mice

Regulatory T cells play a major role in modulating the immune response. However, most information on these cells centers on autoimmunity, and there is also considerable controversy on the functional characteristics of these cells. Here we provide direct in vitro and in vivo evidence that CD4+CD25+ regulatory T cells inhibit the differentiation and functions of both Th1 and Th2 cells. Importantly, CD4+CD25+ T cells suppressed the disease development of Leishmania major infection in SCID mice reconstituted with naive CD4+CD25- T cells. Furthermore, CD4+CD25+ T cells inhibited the development of colitis induced by both Th1 and Th2 cells in SCID mice. Our results therefore document that CD4+CD25+ regulatory T cells suppress both Th1 and Th2 cells and that these regulatory T cells have a profound therapeutic potential against diseases induced by both Th1 and Th2 cells in vivo.     

Dyrithiopsis lakefuxianensis gen. et sp. nov. from Fuxian Lake, Yunnan, China, and notes on the taxonomic confusion surrounding Dyrithium

A new taxon with Dyrithium-like characteristics was collected from Lake Fuxian in China. The taxon is typical of the Amphisphaeriaceae in that it has relatively large, ostiolate, immersed ascomata, unitunicate asci with a J+ subapical ring, and brown ascospores. It is similar to Dyrithium in that it has muriform ascospores, but considerable confusion surrounds this genus. In Dyrithium asci are bitunicate and lack a J+ subapical ring, while this was not true of our species. A new genus, Dyrithiopsis, therefore is established to accommodate this new taxon. Details of its anamorph also are provided, based on cultural studies. Parsimony analyses of part of the large-subunit rDNA provide further evidence to support the familial placement of this new genus in the Amphisphaeriaceae. The taxonomic position of Dyrithium also is discussed.     

Preparation of orthogonally protected chitosan oligosaccharides: observation of an anomalous remote substituent effect

Orthogonally protected chitosan tetrasaccharides were synthesized in a convergent fashion by trichloroacetimidate activation. The anomeric substituent at the reducing end of the disaccharide acceptor has a remarkably strong influence on glycosidic coupling; a thiophenyl-substituted disaccharide was observed to be an unusually poor glycosyl acceptor in comparison with the corresponding allyloxy-substituted disaccharide.     

Characterization and taxonomic placement of Rhizoctonia-like endophytes from orchid roots

Twenty-one Rhizoctonia-like fungal strains were isolated from the roots of four terrestrial orchid species from various locations in Hong Kong. The cultural morphology, nuclear number of the hyphal cell, pore ultrastructure, and RAPD and CAPS analyses of rDNA fragments revealed that most of these isolates were associated with the genera Ceratorhiza and Epulorhiza. RAPD analysis showed the presence of genetic diversity between the isolates from different hosts and locations. The compatibility between a selection of these Ceratorhiza and Epulorhiza isolates and 14 orchid species was determined using a symbiotic germination method. The germination and development of three orchid species, Arundina chinensis, Spathoglottis pubescens, and Spiranthes hongkongensis, were strongly stimulated by the Epulorhiza isolates. Habenaria dentata was found to form symbionts successfully with a Ceratorhiza isolate.