Investigating Models of Protein Function and Allostery With a Widespread Mutational Analysis of a Light-Activated Protein

To investigate the relationship between a protein’s sequence and its biophysical properties, we studied the effects of more than 100 mutations in Avena sativa light-oxygen-voltage domain 2, a model protein of the Per-Arnt-Sim family. The A. sativa light–oxygen–voltage domain 2 undergoes a photocycle with a conformational change involving the unfolding of the terminal helices. Whereas selection studies typically search for winners in a large population and fail to characterize many sites, we characterized the biophysical consequences of mutations throughout the protein using NMR, circular dichroism, and ultraviolet/visible spectroscopy. Despite our intention to introduce highly disruptive substitutions, most had modest or no effect on function, and many could even be considered to be more photoactive. Substitutions at evolutionarily conserved sites can have minimal effect, whereas those at nonconserved positions can have large effects, contrary to the view that the effects of mutations, especially at conserved positions, are predictable. Using predictive models, we found that the effects of mutations on biophysical function and allostery reflect a complex mixture of multiple characteristics including location, character, electrostatics, and chemistry.     

Thymic stromal cell clone with nursing activity supports the growth and differentiation of murine CD4+8+ thymocytes in vitro

Thymic stromal cell clone, TNC-R3.1 cell, was established from spontaneous AKR/J mouse thymoma. TNC-R3.1 cell, which has the similar properties to thymic nurse cells, formed a unique complex with normal thymocyte subpopulations. Flow cytometry analysis demonstrated that CD4+8+ and CD4-8- immature thymocytes preferentially interacted with TNC-R3.1 stromal cell clone. CD4+8+ thymocytes, which interacted with TNC-R3.1 stromal cell clone, contained a higher proportion of large size and cycling T cells than did noninteracting CD4+8+ thymocytes. As is generally accepted, CD4+8+ thymocytes did not respond to any stimulation such as IL-2, anti-CD3 mAb (2C11), or IL-2 plus 2C11. However, culture of isolated CD4+8+ thymocytes on TNC-R3.1 stromal cell monolayer in the presence of suboptimal dose of IL-2 induced a significant cell growth. Moreover, the addition of 2C11 and IL-2 into this coculture system resulted in a dramatic increase of the proliferative response of thymocytes. Flow cytometry analysis showed the proliferating cells on TNC-R3.1, which originated from CD4+8+ thymocytes, were mostly TCR-alpha beta+ CD3+CD4-8+ T cells. These results provide in vitro evidence that CD4+8+ thymocytes are at an intermediate stage of T cell maturation and TNC-R3.1 stromal cell clone induces the growth and differentiation of CD4+8+ thymocytes into CD4-8+ T cells.     

A seed-specific Brassica napus oleosin promoter interacts with a G-box-specific protein and may be bi-directional

Corrigendum

Upstream regulatory sequences from two -conglycinin genes     

Studies on the generation of B lymphocytes in fetal liver and bone marrow.

With the use of immunofluorescence techniques, cells containing cytoplasmic IgM (cIgM+), but lacking detectable surface IgM (sIgM+), have been identified in mouse fetal liver and adult bone marrow as a distinct cell population to sIgM+ B lymphocytes. We have shown that there is a considerable difference in the rate of entry of cIgM+ and sIgM+ cells into DNA synthesis in these locations. Moreover, within the cIgM+ population, the largest cells are the main group entering DNA synthesis. Our results are compatible with the notion that a pool of rapidly proliferating, large cIgM+ cells is present in fetal liver and adult bone marrow and that these cells give rise to populations of smaller cIgM+ cells, which move out of cell cycle, and convert to sIgM+ B lymphocytes. However, we recognize that this interpretation is speculative. Finally, we have shown that fetal bone marrow is a site of generation of sIgM+ B lymphocytes, but the question as to whether these cells are derived from Ig- precursors within marrow itself remains open.     

T cells in a suppressor circuit and non-T: non-B cells bear different 1-J determinants

T cells involved in the generation of suppressor activity bear an I-J-subregion controlled determinant (e. g., J₁) which is distinct from that (e. g., J₁) found on non-T: non-13 accessory cells. T-cell subsets examined include Ly-1 inducer and Ly-1,2 acceptor cells which collaborate to generate suppressor activity in the in vitro sheep red blood cell antibody system. Non-T:non-B accessory cells examined include accessory cells involved in concanavalin-A induced, T-cell proliferative responses and in in vitro antibody responses to sheep red blood cells. These results provide evidence for serologic and genetic complexity of the I-J subregion of the murine H-2 gene complex.     

A non-T: Non-B cell bears I-A,I-E,I-J,and Tla (Qa-1?) determinants

A non-T:non-B accessory cell in peritoneal washout or spleen-cell suspensions facilitates T-cell proliferative responses to the mitogen, concanavalin A. Utilizing monoclonal antibody, we show that this accessory cell bears the same I-A- and I-E-subregion controlled determinants as found on B cells. In addition, the same accessory cell bears a Tla (Qa-1?)-region and an I-J-subregion controlled determinant. This I-J determinant is also present on splenic accessory cells involved in in vitro antibody responses to sheep red blood cells. Data in a companion paper show that not all anti-I-J sera contain antibody reactive with the accessory cell, and suggest that T cells involved in the generation of suppressor activity and accessory cells bear different I-J-subregion controlled determinants.     

Structure and regulated expression of Kunitz chymotrypsin inhibitor genes in winged bean [Psophocarpus tetragonolobus (L.) DC.]

We analyzed the structure and the expression of Kunitz chymotrypsin inhibitor (WCI) genes in winged bean. WCI was encoded by a multigene family which comprised at least seven members. From their primary structures, four genes (WCI-2, WCI-3a, WCI-3b, and WCI-x) were expected to be functional ones and the other three (WCI-P1, WCI-P2, and WCI-P3) to be pseudogenes. The nucleotide sequences of the WCI-3a and WCI-3b genes were nearly identical, and they encoded the WCI-3 protein, the major chymotrypsin inhibitor in seeds. The WCI-2 gene also encoded the chymotrypsin inhibitor found in seeds and the WCI-x gene was expected to encode an unidentified chymotrypsin inhibitor. WCI messenger RNA and protein accumulated mainly in developing seeds and tuberous roots, small amounts of WCI mRNA being present in stems and pericarps. In seeds, transient accumulation of WCI mRNA was observed during the seed maturation period. These results suggest that the expression of WCI genes is regulated organ-specifically and developmentally in winged bean.     

Generation propagation, and targeting of human CD4+ helper/killer T cells induced by anti-CD3 monoclonal antibody plus recombinant IL-2. An efficient strategy for adoptive tumor immunotherapy.

We developed a culture system for the rapid generation of CD4+ T cells that have both helper and killer functions. CD4+ T cells isolated from human PBL did not proliferate or develop significant cytotoxicity when treated with rIL-2 because of the lack of p75 IL-2R expression. However, culture of isolated CD4+ T cells with immobilized anti-CD3 mAb plus rIL-2 resulted in a marked proliferation (500-fold increase in 14 days) of CD4+ T cells. The proliferating CD4+ T cells produced IL-2 (92 U/ml) and showed strong cytotoxicity against OKT3 hybridoma cells and Daudi, K562, and U937 tumor cells in an anti-CD3 mAb-dependent manner. The CD4+ T cells contained significant amounts of cytolytic granule-related proteins such as serine esterase and perforin. Activated CD4+ helper/killer cells can be generated from both healthy donors and tumor patients and can be propagated in vitro for 14 to 35 days by biweekly restimulation with immobilized anti-CD3 mAb plus rIL-2. This culture yielded about 20,000-fold increase in cell number after a 21-day culture. Bispecific antibody containing anti-CD3 and anti-glioma Fab components enhanced the cytotoxicity of activated CD4+ helper/killer cells against IMR32 glioma cells. Moreover, the activated CD4+ helper/killer cells showed both helper and antitumor activity in vivo and prevented growth of anti-CD3 hybridoma cells in nude mice whether or not IL-2 was administered. These results indicate that anti-CD3 mAb plus IL-2-activated CD4+ helper/killer cells may provide an effective strategy for adoptive tumor immunotherapy of cancer.     

Receptors for Dolichos biflorus agglutinin: New cell surface markers on a spontaneous leukemia

$\text{Dolichos biflorus}$ agglutinin (DBA), which is specific for terminal α-N-acetylgalactosamine, bound to a spontaneous leukemia cell of $\text{GRS}\text{A}$ mice, but not to lymphoid cells of the host. The DBA receptors were isolated from the leukemia cell labeled with [³H]-galactose after detergent solubilization and affinity chromatography on DBA-agarose. The major component of the receptors migrated as a glycoprotein of apparent molecular weight 100,000 upon SDS gel electrophoresis. Alkaline treatment degraded the glycoproteins, releasing oligosaccharides of molecular weight around 1,000.     

Competitive interactions between entomopathogenic nematodes and parasitoid venom

Entomopathogenic nematodes and parasitoid larvae of some wasps play important roles in the natural control of the pest insects. However, it has not been excluded that competition between nematodes and wasps may in some cases reduce their efficacy in the pest control. Using caterpillars of Spodoptera littoralis, we examined interactions between the nematode Steinernema carpocapsae and the venom of the parasitoid Habrobracon hebetor. The survival of S. littoralis caterpillars was reduced in a dose-dependent manner when 5 to 500 nematodes or 0.005–0.1 venom units were applied to single caterpillars. High doses of either nematodes or the venom caused death within 1–3 days in all treated hosts. The low doses of nematodes killed caterpillars within a week, in some cases when they attempted to pupate. Caterpillars receiving low venom doses were characterized by extended survival time terminated with death due to starvation. Combined treatment of nematodes and the venom were mutually synergistic and elicited severe lethal effects. The nematodes were fully resistant to the venom and can feed and grow on the symbiotic bacteria in vitro. The venom impairs food processing and causes death of caterpillars due to starvation. Disruption of the hormonal regulation of metamorphosis by ecdysteroids and juvenile hormone could be responsible for defective moults block at different stages of the moulting process, regionally restricted moulting, moults to “intermediates” combining regions of newly secreted larval and pupal cuticles.