Purification, crystallization and preliminary X-ray analysis of SGR6054, a Streptomyces homologue of the mycobacterial integration host factor mIHF.

The mycobacterial integration host factor (mIHF) is a small nonspecific DNA-binding protein that is essential for the growth of Mycobacterium smegmatis. mIHF homologues are widely distributed among Actinobacteria, and a Streptomyces homologue of mIHF is involved in control of sporulation and antibiotic production in S. coelicolor A3(2). Despite their important biological functions, a structure of mIHF or its homologues has not been elucidated to date. Here, the S. griseus mIHF homologue (SGR6054) was expressed and purified from Escherichia coli and crystallized in the presence of a 16-mer duplex DNA by the sitting-drop vapour-diffusion method. The plate-shaped crystal belonged to space group C2, with unit-cell parameters a = 88.53, b = 69.35, c = 77.71 Å, ß = 96.63°, and diffracted X-rays to 2.22 Å resolution.

Noninvasive chimeric DNA profiling identifies tumor-originated HBV integrants contributing to viral antigen expression in liver cancer.

BACKGROUND: Host genome integration of HBV sequence is considered to be significant in HBV antigen expression and the development of hepatocellular carcinoma (HCC). METHOD: We developed a probe-based capture strategy to enrich integrated HBV DNA for deep-sequencing analysis of integration sites in paired patient samples derived from tumor, liver tissue adjacent to tumor, saliva and plasma, as a platform for exploring the correlation, significance and utility of detecting integrations in these sample types. RESULTS: Most significantly, alpha fetoprotein levels significantly correlated to the amounts of integrations detected in tumor. Viral-host chimeric DNA fragments were successfully detected at high sequencing coverage in plasma rather than saliva samples from HCC patients, and each fragment of this type was only seen once in plasma from chronic hepatitis B patients. Almost all plasma chimeric fragments were derived from integrations in tumor rather than in adjacent liver tissues. Over 50% of them may produce viral-host chimeric transcripts according to deep RNA sequencing in paired tissue samples. Particularly, in patients with low HBV DNA level (< 250 UI/ml), the seemingly normal HBsAg titers may be explained by larger amounts of integrations detected. Meanwhile, we developed a strategy to predict integrants by pairing breakpoints for each integration event. Among four resolved viral patterns, the majority of Pattern I events (81.2%) retained the complete opening reading frame for HBV surface proteins. CONCLUSION: We achieve the efficient enrichment of plasma cell-free chimeric DNA from integration site, and demonstrate that chimeric DNA profiling in plasma is a promising noninvasive approach to monitor HBV integration in liver cancer development and to determine the ability of integrated sequences to express viral proteins that can be targeted, e.g. by immunotherapies.

Interaction of an IHF-like protein with the Rhizobium etli nifA promoter.

The nifA gene fulfills an essential role in the regulation of nitrogen fixation genes in Rhizobium etli. Transcription analysis of the nifA gene, assessed using promoter deletions, indicated an oxygen-independent expression, threefold higher during symbiosis as compared with free-living conditions. Electrophoretic mobility shift assays using those nifA promoter deletion fragments, which were actively transcribed, demonstrated the specific interaction with R. etli cellular protein(s) resulting in the formation of two DNA-protein complexes. An interacting protein was purified by liquid chromatography on Heparin Sepharose and Mono S columns. The purified 12 kDa R. etli protein cross-reacted with antibodies directed against Escherichia coli integration host factor (IHF). Furthermore, purified E. coli IHF was able to specifically bind to the R. etli nifA promoter region. These results point to an as yet undisclosed function of IHF in the regulation of R. etli nifA expression.

Identification of host translation inhibitory factor of Campoletis sonorensis ichnovirus on the tobacco budworm, Heliothis virescens.

Parasitization of a wasp, Campoletis sonorensis, against the larvae of Heliothis virescens depresses synthesis of specific host proteins related to growth and immunity. It has been suggested that the inhibition of host gene expression is targeted at a posttranscriptional level. This study aimed to verify the identity of host translation inhibitory factor (HTIF) derived from wasp parasitization. To identify HTIF, the proteins in the parasitized host were fractionated using different protein purification methods, and each fraction's HTIF activity was assessed. In the course of the protein purification steps, HTIF activity was highly correlated with the fractions containing VHv 1.4 protein, which has a conserved cysteine-motif and is encoded in C. sonorensis ichnovirus (CsIV). Purified VHv 1.4 protein using an immunoaffinity column exhibited a significant HTIF effect, while the heat-inactivated VHv 1.4 did not. Both recombinant VHv 1.4 and VHv 1.1 (another cys-motif protein encoded in CsIV) proteins were synthesized in Sf 9 cells through a baculovirus expression system. The purified recombinant VHv 1.4 and VHv 1.1 exhibited significant HTIF activities in a nanomolar range. However, VHv1.4 protein showed about four times higher HTIF activity than did VHv 1.1 protein. Both HTIFs acted directly on translation machinery because they inhibited a cell-free in vitro translation system using rabbit reticulocyte lysate. Both HTIFs are likely to discriminate specific target mRNAs because they inhibited translation of RNA extracts from the Tn 368 cell line, but not from Sf 9 cells. In addition, they inhibited translation of RNAs from fat body, hemocytes, and testis, but not from epidermis, gut, labial gland, and nerve tissues of H. virescens. These results indicate that both cys-motif proteins of VHv 1.4 and VHv 1.1 play a role as HTIF in C. sonorensis parasitization.