Testing biochemistry revisited: how in vivo metabolism can be understood from in vitro enzyme kinetics

A decade ago, a team of biochemists including two of us, modeled yeast glycolysis and showed that one of the most studied biochemical pathways could not be quite understood in terms of the kinetic properties of the constituent enzymes as measured in cell extract. Moreover, when the same model was later applied to different experimental steady-state conditions, it often exhibited unrestrained metabolite accumulation.Here we resolve this issue by showing that the results of such ab initio modeling are improved substantially by (i) including appropriate allosteric regulation and (ii) measuring the enzyme kinetic parameters under conditions that resemble the intracellular environment. The following modifications proved crucial: (i) implementation of allosteric regulation of hexokinase and pyruvate kinase, (ii) implementation of V(max) values measured under conditions that resembled the yeast cytosol, and (iii) redetermination of the kinetic parameters of glyceraldehyde-3-phosphate dehydrogenase under physiological conditions.Model predictions and experiments were compared under five different conditions of yeast growth and starvation. When either the original model was used (which lacked important allosteric regulation), or the enzyme parameters were measured under conditions that were, as usual, optimal for high enzyme activity, fructose 1,6-bisphosphate and some other glycolytic intermediates tended to accumulate to unrealistically high concentrations. Combining all adjustments yielded an accurate correspondence between model and experiments for all five steady-state and dynamic conditions. This enhances our understanding of in vivo metabolism in terms of in vitro biochemistry.     

Tumor-associated myeloid cells can be activated in vitro and in vivo to mediate antitumor effects

Tumor growth is often accompanied by the accumulation of myeloid cells in the tumors and lymphoid organs. These cells can suppress T cell immunity, thereby posing an obstacle to T cell-targeted cancer immunotherapy. In this study, we tested the possibility of activating tumor-associated myeloid cells to mediate antitumor effects. Using the peritoneal model of B16 melanoma, we show that peritoneal cells (PEC) in tumor-bearing mice (TBM) had reduced ability to secrete nitric oxide (NO) following in vitro stimulation with interferon gamma and lipopolysaccharide, as compared to PEC from control mice. This reduced function of PEC was accompanied by the influx of CD11b(+) Gr-1(+) myeloid cells to the peritoneal cavity. Nonadherent PEC were responsible for most of the NO production in TBM, whereas in na?ve mice NO was mainly secreted by adherent CD11b(+) F4/80(+) macrophages. Sorted CD11b(+) Gr-1(-) monocytic and CD11b(+) Gr-1(+) granulocytic PEC from TBM had a reduced ability to secrete NO following in vitro stimulation (compared to na?ve PEC), but effectively suppressed proliferation of tumor cells in vitro. In vivo, treatment of mice bearing established peritoneal B16 tumors with anti-CD40 and CpG resulted in activation of tumor-associated PEC, reduction in local tumor burden and prolongation of mouse survival. Inhibition of NO did not abrogate the antitumor effects of stimulated myeloid cells. Taken together, the results indicate that in tumor-bearing hosts, tumor-associated myeloid cells can be activated to mediate antitumor effects.     

Tubulin Carboxypeptidase/Microtubules Association can be Detected in the Distal Region of Neural Processes

The association of tubulin carboxypeptidase with microtubules has been demonstrated in crude brain extracts and in living non-nervous cells. Here, we studied this phenomenon in cultured brain cells. To determine the association of the enzyme with neural microtubules we isolated the cytoskeletons (detergent-extraction under microtubule-stabilizing conditions) and measured the content of Tyr, Glu, and 2 tubulin as a function of the in vitro incubation time of the cytoskeletons. The carboxypeptidase was found associated with microtubules in 2 days-cultured cells but not in 7 days-cultured cells. Quantitative analysis of digitized images after immunofluorescent staining revealed that detyrosination during the incubation of the cytoskeletons occurred preferentially in the distal regions of the neural processes. Prolonged taxol-treatment of the cells promoted higher detyrosination but Tyr tubulin was not depleted suggesting the existence of a subset of microtubules that has not associated carboxypeptidase and therefore cannot be detyrosinated even after prolonged taxol-treatment. This hypothesis was supported, although not conclusively, by additional experiments.     

Thymus-repopulating capacity of cells that can be induced to differentiate to T cells in vitro.

It was established previously that committed precursors of T cells, which reside in bone marrow and spleen and lack T cell surface differentiation antigens, can be induced by thymopoietin and certain other agents to differentiate rapidly in vitro into T cells bearing typical surface antigens, including Thy-1 and TL (Komuro-Boyse assay). To relate this differentiative step observed in vitro to physiologic events in vivo, a system was devised to trace the migration of precursor cells to the thymus, and their maturation to T cells. Lethally irradiated mice of a TL- strain received spleen cells from TL+ hybrids i.v., and the TL+ population of the thymus was enumerated 13 to 20 days later. Donor TL+ cells first became detectable at 13 days and increased thereafter. Preliminary tests showed that cells capable of migrating to the thymus have a similar density to the cells that are inducible in the Komuro-Boyse assay, this being lower than that of mature of T cells. The thymus-repopulating properties of the donor spleen population were not affected by: 1) pre-treatment in vitro with thymus extract or thymopoietin, which initiates differentiation of T cells precursors, nor b) pre-treatment with anti Thy-1 serum plus complement, which eliminates differentiated T cells. But pre-treatment a) and b) applied in sequence markedly reduced the capacity of spleen cells to repopulate the thymus. These results can be interpreted as follows: induction of Thy-1-TL- precursor cells (pro-thymocyte) in vitro yields Thy-1+TL+ cells (early thymocytes) which have not yet lost their property of repopulating the thymus; therefore, thymus-repopulation was not depleted by treatment a) alone, which induced Thy-1 +TL+ cells, nor by treatment b) alone, which did not affect thymus-repopulation by Thy-1-TL- cells, although treatments a) plus b) did eliminate the newly induced Thy-1+TL+ cells and thus impaired repopulation of the thymus. We conclude that the cell which responds to thymopoietin in the Komuro-Boyse assay by expressing the T cell surface phenotype is the same cell (pro-thymocyte) that normally migrates in vivo from hemopoietic tissues to the thymus and is there induced by thymopoietin to express the phenotype of an early T cell.     

E-cadherin can be expressed by a small population of rat undifferentiated spermatogonia in vivo and in vitro

Spermatogonial stem cells (SSCs) maintain gamete production in the testes throughout adult life by balancing self-renewal and differentiation. In vitro culture of SSCs is a crucial technique for gene manipulation of SSCs to generate transgenic animals, for transplantation of SSCs to restore male fertility for infertile man, and for generation of pluripotent stem cells from SSCs to differentiate into various cell lineages. Isolation of highly purified SSCs is an all-important component for development of these techniques. However, definitive markers for SSCs, which purify SSCs (100% enrichment), are unknown. SSCs of many species can colonize the mouse testis; thus, we reasoned that same molecules of SSCs are conserved between species. In mouse, undifferentiated spermatogonia express the surface marker E-cadherin. The hypothesis tested in this work was that E-cadherin (also known as CDH1) can be expressed by undifferentiated spermatogonia of rat testes. In this paper, cross-section immunohistochemistry and whole-mount immunohistochemistry of rat seminiferous tubules were conducted to show that E-cadherin-positive cells were small in number and there are single, paired, and aligned spermatogonia attached along the basement membrane. During in vitro culture period, the undifferentiated rat spermatogonial colonies co-expressed E-cadherin and glial-derived neurotrophic factor family receptor alpha-1 or E-cadherin and promyelocytic leukemia zinc finger. Data collected during the study demonstrate that E-cadherin is expressed by a small population of rat undifferentiated spermatogonia both in vivo and during in vitro culture period.     

Separate cell types that express two different forms of somatostatin in anglerfish islets can be immunohistochemically differentiated

The somatostatin-related peptides somatostatin-14 (SS-14) and somatostatin-28 (aSS-28) are synthesized at the C-terminal end of two separate pre-pro-somatostatins in anglerfish pancreatic islets. The purpose of this study was to determine whether these peptides are expressed in the same or different cell types. Antisera R141 and R293, which recognize the central region of SS-14 and the C-terminal region of aSS-28 ([Tyr7,Gly10] SS-14), respectively, were used in an immunohistochemical examination of anglerfish islets. The R293 antiserum-labeled cells were distributed individually or in small clusters. These same cells, as well as a separate set of cells arranged in large clusters, were stained by the R141 antiserum. Pre-absorption of the R141 antiserum with [Tyr7,Gly10] SS-14 eliminated staining by R141 of only those cells also labeled by R293, whereas pre-absorption of R141 with SS-14 prevented all staining. Pre-absorption of R293 with [Tyr7,Gly10] SS-14 eliminated all staining, whereas pre-absorption with SS-14 had no effect on aSS-28-like immunoreactivity. These results suggest the existence of two separate cell types which express either SS-14 or aSS-28. The cells that contained the somatostatin-related peptides were found to be distinct from those cells that contained insulin, glucagon, or anglerfish peptide Y. However, the cells stained by the R293 antiserum were distributed in close association with glucagon-containing cells. The implications of the existence of separate cell types which express SS-14 or aSS-28 are discussed with regard to processing of the biosynthetic precursors to these peptides.     

2（4′噻唑）苯丙咪唑对猪脑微管蛋白体外聚合的影响

本研究利用猪脑中分离纯化的微管蛋白聚合和解聚反应,分析了具有争议的非整倍体诱发剂2（4′噻唑）苯丙咪唑（thiabendazole,TBZ）对微管蛋白聚合状态的影响。秋水仙素(colchicine)为本研究的阳性对照物。结果发现2（4′噻唑）苯丙咪唑能显著抑制体外微管蛋白的聚合,并呈明显的剂量效应关系。研究表明,TBZ可能通过抑制微管蛋白聚合来影响染色体正常分离,诱发非整倍体。     

Mammalian cells contain a DNA-recombining activity that can be dissociated from topoisomerase activity

The role of the topoisomerase enzyme in DNA recombination was investigated by extracting chromosomal deoxyribonucleoproteins from a variety of cultured mammalian ceils and assaying for the formation of recombinant DNA structures. Although each of the crude deoxyribonucleoprotein preparations contained topoisomerase activity, they did not all contain DNA-recombining activity. A distinct, perhaps novel, enzyme may therefore promote DNA recombination in these cell-free systems.     

Regulatory interactions between mitochondrial genes: Exon and intron phenotypes observed in vivo can be expressed in vitro

In Saccharomyces cerevisiae the mitochondrial gene responsible for the specification of apocytochrome b (cob-box) is believed to consist of both coding and intervening sequences. Mutations in the latter give rise to pleiotropic phenotypes in vivo, lacking not only cytochrome b but also subunit I of cytochrome oxidase, and producing sets of novel polypeptides. The experiments described here have examined 15 different mit^? mutants in this region and demonstrate that these results are faithfully reproduced by isolated mitochondria in vitro. This inference also applies to other types of mutational lesions in coding segments of the cob-box gene and of the gene oxi3, responsible for the specification of subunit I.     

The potency of acyclovir can be markedly different in different cell types

Acyclovir is an acyclic guanine analog with a considerable activity against herpes simplex viruses. We studied the antiherpetic activity of acyclovir in macrophages and fibroblast cell lines. Utilising a plaque reduction assay we found that acyclovir potently inhibited the HSV-1 replication in macrophages (EC50) = 0.0025 microM) compared to Vero (EC50 = 8.5 microM) and MRC-5 (EC50 = 3.3 microM) cells. The cytotoxicity of acyclovir was not detected at concentrations < or = 20 microM, thus the selective index in macrophages was >8000. This marked difference in antiherpetic activity between macrophages and fibroblasts was not observed with Foscarnet and PMEA. We suggest that this potent antiviral effect of acyclovir is mainly due to a proficient phosphorylation of the drug and/or a favourable dGTP/acyclovir triphosphate ratio in macrophage cells.     

Natural killing can be independent of interferon generated in vitro

PBL produce interferon in response to culture with the tumor cell line K562, but this production of interferon does not correlate with natural cytotoxicity. A basal level of natural killing is independent of interferon generated in vitro. We base this conclusion on the following findings: (i) natural killing and interferon level are not temporally correlated; (ii) preincubation of lymphocytes at 37 °C greatly reduces their ability to produce interferon but does not affect their lytic capacity against K562; and, (iii) addition of an anti-interferon antibody has no effect on NK. We conclude that NK against K562 is not dependent upon or correlated with the level of interferon generated during in vitro assay.     

Torsional tension in intracellular bacteriophage T4 DNA. Evidence that a linear DNA duplex can be supercoiled in vivo

Torsional tension in intracellular bacteriophage T4 DNA and host cell DNA was measured in infected Escherichia coli cells using the trimethylpsoralen photobinding assay. Early in infection superhelical tension in the host E. coli DNA was gradually reduced until at 8 min post-infection there was no detectable tension. Negative torsional tension in the T4 DNA appeared transiently, reaching a maximum 4 to 6 min post-infection (at 32 °C) and declined to undetectable levels by 10 min. The maximum level of tension averaged over all infecting T4 DNA molecules was equivalent to superhelical density of about σ = ?0.03.Sedimentation studies of the psoralen-associated T4 DNA isolated from infected cells at 5 min post-infection indicated that this DNA was primarily in an intact linear form. This is the first evidence indicating that a linear DNA molecule can acquire torsional tension in vivo: the finding suggests that intracellular T4 DNA can be topologically restrained probably by interaction with other structures in the cell. Effects of inhibitors of DNA gyrase and effects of mutations in T4 gene 39 indicated that the observed torsional tension was introduced by E. coli DNA gyrase, not by the T4 topoisomerase. Studies of the number of nicks required to relax the tension suggest that the entire T4 genome is organized into one topological domain of supercoiling.The possible role of the negative superhelical tension in the initiation of T4 DNA replication was examined. Initiation of DNA replication occurred shortly after the accumulation of tension in T4 DNA. However, replication occurred at near-normal levels under conditions where acquisition of tension was blocked in T4 DNA. Results suggest that although a topoisomerase activity is required for the initiation of DNA replication, the observed torsional tension is not a prerequisite.