An Intelligent Search & Retrieval System (IRIS) and Clinical and Research Repository for Decision Support Based on Machine Learning and Joint Kernel-based Supervised Hashing

Large-scale, multi-site collaboration is becoming indispensable for a wide range of research and clinical activities in oncology. To facilitate the next generation of advances in cancer biology, precision oncology and the population sciences it will be necessary to develop and implement data management and analytic tools that empower investigators to reliably and objectively detect, characterize and chronicle the phenotypic and genomic changes that occur during the transformation from the benign to cancerous state and throughout the course of disease progression. To facilitate these efforts it is incumbent upon the informatics community to establish the workflows and architectures that automate the aggregation and organization of a growing range and number of clinical data types and modalities ranging from new molecular and laboratory tests to sophisticated diagnostic imaging studies. In an attempt to meet those challenges, leading health care centers across the country are making steep investments to establish enterprise-wide, data warehouses. A significant limitation of many data warehouses, however, is that they are designed to support only alphanumeric information. In contrast to those traditional designs, the system that we have developed supports automated collection and mining of multimodal data including genomics, digital pathology and radiology images. In this paper, our team describes the design, development and implementation of a multi-modal, Clinical & Research Data Warehouse (CRDW) that is tightly integrated with a suite of computational and machine-learning tools to provide actionable insight into the underlying characteristics of the tumor environment that would not be revealed using standard methods and tools. The System features a flexible Extract, Transform and Load (ETL) interface that enables it to adapt to aggregate data originating from different clinical and research sources depending on the specific EHR and other data sources utilized at a given deployment site.

Open and reusable deep learning for pathology with WSInfer and QuPath

Digital pathology has seen a proliferation of deep learning models in recent years, but many models are not readily reusable. To address this challenge, we developed WSInfer: an open-source software ecosystem designed to streamline the sharing and reuse of deep learning models for digital pathology. The increased access to trained models can augment research on the diagnostic, prognostic, and predictive capabilities of digital pathology.

Basics of advanced therapy medicinal product development in academic pharma and the role of a GMP simulation unit

Following successes of authorized chimeric antigen receptor T-cell products being commercially marketed in the United States and European Union, product development of T-cell-based cancer immunotherapy consisting of cell-based advanced therapy medicinal products (ATMPs) has gained further momentum. Due to their complex characteristics, pharmacological properties of living cell products are, in contrast to classical biological drugs such as small molecules, more difficult to define. Despite the availability of many new advanced technologies that facilitate ATMP manufacturing, translation from research-grade to clinical-grade manufacturing in accordance with Good Manufacturing Practices (cGMP) needs a thorough product development process in order to maintain the same product characteristics and activity of the therapeutic product after full-scale clinical GMP production as originally developed within a research setting. The same holds true for transferring a fully developed GMP-grade production process between different GMP facilities. Such product development from the research to GMP-grade manufacturing and technology transfer processes of established GMP-compliant procedures between facilities are challenging. In this review, we highlight some of the main obstacles related to the product development, manufacturing process, and product analysis, as well as how these hinder rapid access to ATMPs. We elaborate on the role of academia, also referred to as 'academic pharma', and the added value of GMP production and GMP simulation facilities to keep innovation moving by reducing the development time and to keep final production costs reasonable.

An Expandable Informatics Framework for Enhancing Central Cancer Registries with Digital Pathology Specimens, Computational Imaging Tools, and Advanced Mining Capabilities

BACKGROUND

Population-based state cancer registries are an authoritative source for cancer statistics in the United States. They routinely collect a variety of data, including patient demographics, primary tumor site, stage at diagnosis, first course of treatment, and survival, on every cancer case that is reported across all U.S. states and territories. The goal of our project is to enrich NCI's Surveillance, Epidemiology, and End Results (SEER) registry data with high-quality population-based biospecimen data in the form of digital pathology, machine-learning-based classifications, and quantitative histopathology imaging feature sets (referred to here as Pathomics features).

MATERIALS AND METHODS

As part of the project, the underlying informatics infrastructure was designed, tested, and implemented through close collaboration with several participating SEER registries to ensure consistency with registry processes, computational scalability, and ability to support creation of population cohorts that span multiple sites. Utilizing computational imaging algorithms and methods to both generate indices and search for matches makes it possible to reduce inter- and intra-observer inconsistencies and to improve the objectivity with which large image repositories are interrogated.

RESULTS

Our team has created and continues to expand a well-curated repository of high-quality digitized pathology images corresponding to subjects whose data are routinely collected by the collaborating registries. Our team has systematically deployed and tested key, visual analytic methods to facilitate automated creation of population cohorts for epidemiological studies and tools to support visualization of feature clusters and evaluation of whole-slide images. As part of these efforts, we are developing and optimizing advanced search and matching algorithms to facilitate automated, content-based retrieval of digitized specimens based on their underlying image features and staining characteristics.

CONCLUSION

To meet the challenges of this project, we established the analytic pipelines, methods, and workflows to support the expansion and management of a growing repository of high-quality digitized pathology and information-rich, population cohorts containing objective imaging and clinical attributes to facilitate studies that seek to discriminate among different subtypes of disease, stratify patient populations, and perform comparisons of tumor characteristics within and across patient cohorts. We have also successfully developed a suite of tools based on a deep-learning method to perform quantitative characterizations of tumor regions, assess infiltrating lymphocyte distributions, and generate objective nuclear feature measurements. As part of these efforts, our team has implemented reliable methods that enable investigators to systematically search through large repositories to automatically retrieve digitized pathology specimens and correlated clinical data based on their computational signatures.

PRISM: A Platform for Imaging in Precision Medicine

PURPOSE

Precision medicine requires an understanding of individual variability, which can only be acquired from large data collections such as those supported by the Cancer Imaging Archive (TCIA). We have undertaken a program to extend the types of data TCIA can support. This, in turn, will enable TCIA to play a key role in precision medicine research by collecting and disseminating high-quality, state-of-the-art, quantitative imaging data that meet the evolving needs of the cancer research community.

METHODS

A modular technology platform is presented that would allow existing data resources, such as TCIA, to evolve into a comprehensive data resource that meets the needs of users engaged in translational research for imaging-based precision medicine. This Platform for Imaging in Precision Medicine (PRISM) helps streamline the deployment and improve TCIA's efficiency and sustainability. More importantly, its inherent modular architecture facilitates a piecemeal adoption by other data repositories.

RESULTS

PRISM includes services for managing radiology and pathology images and features and associated clinical data. A semantic layer is being built to help users explore diverse collections and pool data sets to create specialized cohorts. PRISM includes tools for image curation and de-identification. It includes image visualization and feature exploration tools. The entire platform is distributed as a series of containerized microservices with representational state transfer interfaces.

CONCLUSION

PRISM is helping modernize, scale, and sustain the technology stack that powers TCIA. Repositories can take advantage of individual PRISM services such as de-identification and quality control. PRISM is helping scale image informatics for cancer research at a time when the size, complexity, and demands to integrate image data with other precision medicine data-intensive commons are mounting.

ImageBox 2 - Efficient and Rapid Access of Image Tiles from Whole-Slide Images Using Serverless HTTP Range Requests

BACKGROUND

Whole-slide images (WSI) are produced by a high-resolution scanning of pathology glass slides. There are a large number of whole-slide imaging scanners, and the resulting images are frequently larger than 100,000 × 100,000 pixels which typically image 100,000 to one million cells, ranging from several hundred megabytes to many gigabytes in size.

AIMS AND OBJECTIVES

Provide HTTP access over the web to Whole Slide Image tiles that do not have localized tiling servers but only basic HTTP access. Move all image decode and tiling functions to calling agent (ImageBox).

METHODS

Current software systems require tiling image servers to be installed on systems providing local disk access to these images. ImageBox2 breaks this requirement by accessing tiles from remote HTTP source via byte-level HTTP range requests. This method does not require changing the client software as the operation is relegated to the ImageBox2 server which is local (or remote) to the client and can access tiles from remote images that have no server of their own such as Amazon S3 hosted images. That is, it provides a data service [on a server that does not need to be managed], the definition of serverless execution model increasingly favored by cloud computing infrastructure.

CONCLUSIONS

The specific methodology described and assessed in this report preserves normal client connection semantics by enabling cloud-friendly tiling, promoting a web of http connected whole-slide images from a wide-ranging number of sources, and providing tiling where local tiling servers would have been otherwise unavailable.

Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor-Infiltrating Lymphocytes in Invasive Breast Cancer

Quantitative assessment of spatial relations between tumor and tumor-infiltrating lymphocytes (TIL) is increasingly important in both basic science and clinical aspects of breast cancer research. We have developed and evaluated convolutional neural network analysis pipelines to generate combined maps of cancer regions and TILs in routine diagnostic breast cancer whole slide tissue images. The combined maps provide insight about the structural patterns and spatial distribution of lymphocytic infiltrates and facilitate improved quantification of TILs. Both tumor and TIL analyses were evaluated by using three convolutional neural network networks (34-layer ResNet, 16-layer VGG, and Inception v4); the results compared favorably with those obtained by using the best published methods. We have produced open-source tools and a public data set consisting of tumor/TIL maps for 1090 invasive breast cancer images from The Cancer Genome Atlas. The maps can be downloaded for further downstream analyses.

A Containerized Software System for Generation, Management, and Exploration of Features from Whole Slide Tissue Images

Well-curated sets of pathology image features will be critical to clinical studies that aim to evaluate and predict treatment responses. Researchers require information synthesized across multiple biological scales, from the patient to the molecular scale, to more effectively study cancer. This article describes a suite of services and web applications that allow users to select regions of interest in whole slide tissue images, run a segmentation pipeline on the selected regions to extract nuclei and compute shape, size, intensity, and texture features, store and index images and analysis results, and visualize and explore images and computed features. All the services are deployed as containers and the user-facing interfaces as web-based applications. The set of containers and web applications presented in this article is used in cancer research studies of morphologic characteristics of tumor tissues. The software is free and open source. Cancer Res; 77(21); e79-82. ©2017 AACR.

Towards Generation, Management, and Exploration of Combined Radiomics and Pathomics Datasets for Cancer Research

Cancer is a complex multifactorial disease state and the ability to anticipate and steer treatment results will require information synthesis across multiple scales from the host to the molecular level. Radiomics and Pathomics, where image features are extracted from routine diagnostic Radiology and Pathology studies, are also evolving as valuable diagnostic and prognostic indicators in cancer. This information explosion provides new opportunities for integrated, multi-scale investigation of cancer, but also mandates a need to build systematic and integrated approaches to manage, query and mine combined Radiomics and Pathomics data. In this paper, we describe a suite of tools and web-based applications towards building a comprehensive framework to support the generation, management and interrogation of large volumes of Radiomics and Pathomics feature sets and the investigation of correlations between image features, molecular data, and clinical outcome.

Safe "cloudification" of large images through picker APIs

The "Box model" allows users with no particular training in informatics, or access to specialized infrastructure, operate generic cloud computing resources through a temporary URI dereferencing mechanism known as "drop-file-picker API" ("picker API" for sort). This application programming interface (API) was popularized in the web app development community by DropBox, and is now a consumer-facing feature of all major cloud computing platforms such as Box.com, Google Drive and Amazon S3. This reports describes a prototype web service application that uses picker APIs to expose a new, "cloudified", API tailored for image analysis, without compromising the private governance of the data exposed. In order to better understand this cross-platform cloud computing landscape, we first measured the time for both transfer and traversing of large image files generated by whole slide imaging (WSI) in Digital Pathology. The verification that there is extensive interconnectivity between cloud resources let to the development of a prototype software application that exposes an image-traversing REST API to image files stored in any of the consumer-facing "boxes". In summary, an image file can be upload/synchronized into a any cloud resource with a file picker API and the prototype service described here will expose an HTTP REST API that remains within the safety of the user's own governance. The open source prototype is publicly available at sbu-bmi.github.io/imagebox. Availability The accompanying prototype application is made publicly available, fully functional, with open source, at http://sbu-bmi.github.io/imagebox://sbu-bmi.github.io/imagebox. An illustrative webcasted use of this Web App is included with the project codebase at https://github.com/SBU-BMI/imageboxs://github.com/SBU-BMI/imagebox.

Antibody-Based Cancer Therapy: Successful Agents and Novel Approaches

Since their discovery, antibodies have been viewed as ideal candidates or "magic bullets" for use in targeted therapy in the fields of cancer, autoimmunity, and chronic inflammatory disorders. A wave of antibody-dedicated research followed, which resulted in the clinical approval of a first generation of monoclonal antibodies for cancer therapy such as rituximab (1997) and cetuximab (2004), and infliximab (2002) for the treatment of autoimmune diseases. More recently, the development of antibodies that prevent checkpoint-mediated inhibition of T cell responses invigorated the field of cancer immunotherapy. Such antibodies induced unprecedented long-term remissions in patients with advanced stage malignancies, most notably melanoma and lung cancer, that do not respond to conventional therapies. In this review, we will recapitulate the development of antibody-based therapy, and detail recent advances and new functions, particularly in the field of cancer immunotherapy. With the advent of recombinant DNA engineering, a number of rationally designed molecular formats of antibodies and antibody-derived agents have become available, and we will discuss various molecular formats including antibodies with improved effector functions, bispecific antibodies, antibody-drug conjugates, antibody-cytokine fusion proteins, and T cells genetically modified with chimeric antigen receptors. With these exciting advances, new antibody-based treatment options will likely enter clinical practice and pave the way toward more successful control of malignant diseases.

Influence of Organic Amendment and Compaction on Nutrient Dynamics in a Saturated Saline-Sodic Soil from the Riparian Zone

Cattle grazing in wet riparian pastures may influence nutrient dynamics due to nutrient deposition in feces and urine, soil compaction, and vegetation loss. We conducted a lab incubation study with a saline-sodic riparian soil to study nutrient (N, P, S, Fe, Mn, Cu, and Zn) dynamics in soil pore water using Plant Root Simulator (PRS) probes and release of nutrients into the overlying ponded water during flooding. The treatment factors were organic amendment (manure, roots, and unamended control), compaction (compacted, uncompacted), and burial time (3, 7, and 14 d). Amendment treatment had the greatest impact on nutrient dynamics, followed by burial time, whereas compaction had little impact. The findings generally supported our hypothesis that organic amendments should first increase nitrate loss, then increase Mn mobility, then Fe mobility and associated release of P, and finally increase sulfate loss. Declines in nitrate due to amendment addition were small because nitrate was at low levels in all treatments due to high denitrification potential instead of being released to soil pore water or overlying water. Addition of organic amendment strongly increased Mn and Fe concentrations in overlying water and of adsorbed Fe on PRS probes but only increased Mn on PRS probes on Day 3 due to subsequent displacement from ion exchange membranes. Transport of P to overlying water was increased by organic amendment addition but less so for manure than roots despite higher P on PRS probes. The findings showed that saline-sodic soils in riparian zones are generally a nutrient source for P and are a nutrient sink for N as measured using PRS probes after 3 to 7 d of flooding.

Elevated serum CXCL16 is an independent predictor of poor survival in ovarian cancer and may reflect pro-metastatic ADAM protease activity

BACKGROUND

In certain cancers, expression of CXCL16 and its receptor CXCR6 associate with lymphocyte infiltration, possibly aiding anti-tumour immune response. In other cancers, CXCL16 and CXCR6 associate with pro-metastatic activity. In the current study, we aimed to characterise the role of CXCL16, sCXCL16, and CXCR6 in ovarian cancer (OC).

METHODS

CXCL16/CXCR6 expression was analysed on tissue microarray containing 306 OC patient samples. Pre-treatment serum sCXCL16 was determined in 118 patients using ELISA. In vitro, (primary) OC cells were treated with an ADAM-10/ADAM-17 inhibitor (TAPI-2) and an ADAM-10-specific inhibitor (GI254023x), whereupon CXCL16 levels were evaluated on the cell membrane (immunofluorescent analysis, western blots) and in culture supernatants (ELISA). In addition, cell migration was assessed using scratch assays.

RESULTS

sCXCL16 independently predicted for poor survival (hazard ratio=2.28, 95% confidence interval=1.29-4.02, P=0.005), whereas neither CXCL16 nor CXCR6 expression correlated with survival. Further, CXCL16/CXCR6 expression and serum sCXCL16 levels did not associate with lymphocyte infiltration. In vitro inhibition of both ADAM-17 and ADAM-10, but especially the latter, decreased CXCL16 membrane shedding and strongly reduced cell migration of A2780 and cultured primary OC-derived malignant cells.

CONCLUSIONS

High serum sCXCL16 is a prognostic marker for poor survival of OC patients, possibly reflecting ADAM-10 and ADAM-17 pro-metastatic activity. Therefore, serum sCXCL16 levels may be a pseudomarker that identifies patients with highly metastatic tumours.

From EHRs to Linked Data: representing and mining encounter data for clinical expertise evaluation

Translational science, today, involves multidisciplinary teams of scientists rather than single scientists. Teams facilitate biologically meaningful and clinically consequential breakthroughs. There are a myriad of sources of data about investigators, physicians, research resources, clinical encounters, and expertise to promote team interaction; however, much of this information is not connected and is left siloed. Large amounts of data have been published as Linked Data (LD), but there still remains a significant gap in the representation and connection of research resources and clinical expertise data. The CTSAconnect project addresses the problem of fragmentation and incompatible coding of information by creating a Semantic Framework that facilitates the production and consumption of LD about biomedical research resources, clinical activities, as well as investigator and physician expertise.

Review: on TRAIL for malignant glioma therapy?

Glioblastoma (GBM) is a devastating cancer with a median survival of around 15 months. Significant advances in treatment have not been achieved yet, even with a host of new therapeutics under investigation. Therefore, the quest for a cure for GBM remains as intense as ever. Of particular interest for GBM therapy is the selective induction of apoptosis using the pro-apoptotic tumour necrosis factor-related apoptosis-inducing ligand (TRAIL). TRAIL signals apoptosis via its two agonistic receptors TRAIL-R1 and TRAIL-R2. TRAIL is normally present as homotrimeric transmembrane protein, but can also be processed into a soluble trimeric form (sTRAIL). Recombinant sTRAIL has strong tumouricidal activity towards GBM cells, with no or minimal toxicity towards normal human cells. Unfortunately, GBM is a very heterogeneous tumour, with multiple genetically aberrant clones within one tumour. Consequently, any single agent therapy is likely to be not effective enough. However, the anti-GBM activity of TRAIL can be synergistically enhanced by a variety of conventional and novel targeted therapies, making TRAIL an ideal candidate for combinatorial strategies. Here we will, after briefly detailing the biology of TRAIL/TRAIL receptor signalling, focus on the promises and pitfalls of recombinant TRAIL as a therapeutic agent alone and in combinatorial therapeutic approaches for GBM.

Evaluation of alternative planting strategies to reduce wheat stem sawfly (Hymenoptera: Cephidae) damage to spring wheat in the northern Great Plains

Wheat, Triticum aestivum L., producers are often reluctant to use solid-stemmed wheat cultivars resistant to wheat stem sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae), due to concerns regarding yield, efficacy or market opportunities. We evaluated the impact of several planting strategies on wheat yield and quality and wheat stem sawfly infestation at two locations over a three-year period. Experimental units consisted of large plots (50 by 200 m) located on commercial farms adjacent to wheat stem sawfly-infested fields. Compared with a monoculture of a hollow-stemmed cultivar ('AC Barrie'), planting a monoculture of a solid-stemmed cultivar ('AC Eatonia') increased yield by an average of 16% (0.4 mg ha(-1)) and increased the grade of wheat by one unit at the two most heavily infested site-years. Planting a 1:1 blend of AC Eatonia and AC Barrie increased yield by an average of 11%, whereas planting 20- or 40-m plot margins to AC Eatonia increased yield by an average of 8%. High wheat stem sawfly pressure limited the effectiveness of using resistant cultivars in field margins because plants were often infested beyond the plot margin, with uniform infestation down the length of the plots at the two most heavily infested site-years. The effectiveness of AC Eatonia to reduce wheat stem sawfly survivorship was modest in this study, probably due to weather-related factors influencing pith expression and to the high abundance of wheat stem sawfly. Greater benefits from planting field margins to resistant cultivars or planting a blend of resistant and susceptible cultivars might be achievable under lower wheat stem sawfly pressure.

Targeted cancer immunotherapy using ligands of the tumor necrosis factor super-family

Antibody-based therapeutic approaches are yielding more and more of the promise they have held since the conception of the 'magic bullet' theory by Paul Ehrlich. The beneficial effect of antibody-based therapies is directly related to antibody-dependent functions, such as neutralization and antibody-dependent cellular cytotoxicity, but in many cases also relies on the delivery of toxic compounds to cancerous cells. However, the clinical utility of toxic antibody conjugates can be significantly hampered by side effects. Ideal effector compounds are inactive 'en route', but gain full activity once the antibody conjugate has bound to cancerous cells. Of significant potential in this respect are the pro-apoptotic ligands Tumor Necrosis Factor (TNF), fibroblast-associated cell-surface ligand (FasL) and TNF-related apoptosis-inducing ligand (TRAIL). TNF ligands are normally present as homotrimeric transmembrane proteins, but can also be processed into a soluble trimeric form. Compared to their corresponding transmembrane counterpart, soluble TNF, FasL and TRAIL have a strongly reduced capacity to activate TNF receptor 2, Fas and TRAIL receptor 2. However, all sequence information required for full activation of these receptors is latently retained in these soluble ligands and can be unmasked by oligomerization or cell surface immobilization. The latter provides a clear rationale for the use of these ligands as effectors in antibody-based therapy. The antibody-targeted ligand will be in a relatively inactive soluble form while en route. However, once bound to the targeted cancer cell the soluble TNF ligand fusion proteins will be converted into fully active membrane ligand-like molecules. Here we will, after briefly detailing the biology of TNF, TRAIL and FasL, focus on the promises and pitfalls of targeted TNF ligand fusion proteins in achieving a 'magic bullet' with maximum cancer selective activity and minimal side effects.

Role of the progesterone receptor for paclitaxel resistance in primary breast cancer

Paclitaxel plays an important role in the treatment of primary breast cancer. However, a substantial proportion of patients treated with paclitaxel does not appear to derive any benefit from this therapy. We performed a prospective study using tumour cells isolated from 50 primary breast carcinomas. Sensitivity of primary tumour cells to paclitaxel was determined in a clinically relevant range of concentrations (0.85–27.2 μg ml⁻¹ paclitaxel) using an ATP assay. Chemosensitivity data were used to study a possible association with immunohistochemically determined oestrogen and progesterone receptor (ER and PR) status, as well as histopathological parameters. Progesterone receptor (PR) mRNA expression was also determined by quantitative RT–PCR. We observed a clear association of the PR status with chemosensitivity to paclitaxel. Higher levels of immunohistochemically detected PR expression correlated with decreased chemosensitivity (P=0.008). Similarly, high levels of PR mRNA expression were associated with decreased paclitaxel chemosensitivity (P=0.007). Cells from carcinomas with T-stages 3 and 4 were less sensitive compared to stages 1 and 2 (P=0.013). Multiple regression analysis identified PR receptor status and T-stage as independent predictors of paclitaxel chemosensitivity, whereas the ER, N-stage, grading and age were not influential. In conclusion, in vitro sensitivity to paclitaxel was higher for PR-negative compared with PR-positive breast carcinoma cells. Thus, PR status should be considered as a possible factor of influence when designing new trials and chemotherapy protocols.

The histone deacetylase inhibitor valproic acid potently augments gemtuzumab ozogamicin-induced apoptosis in acute myeloid leukemic cells

Gemtuzumab ozogamicin (GO) is a calicheamicin-conjugated antibody directed against CD33, an antigen highly expressed on acute myeloid leukemic (AML) cells. CD33-specific binding triggers internalization of GO and subsequent hydrolytic release of calicheamicin. Calicheamicin then translocates to the nucleus, intercalates in the DNA structure and subsequently induces double-strand DNA breaks. GO is part of clinical practice for AML, but is frequently associated with severe side effects. Therefore, combination of GO with other therapeutics is warranted to reduce toxicity, while maximizing therapeutic selectivity. We hypothesized that the histone deacetylase inhibitor valproic acid (VPA) sensitizes AML cells to GO. VPA-induced histone hyperacetylation opens the chromatin structure, whereby the DNA intercalation of calicheamicin should be augmented. We found that clinically relevant concentrations of VPA potently augmented the tumoricidal activity of GO towards AML cell lines and primary AML blasts. Moreover, VPA treatment indeed augmented the DNA intercalation of calicheamicin and enhanced DNA degradation. Importantly, synergy was restricted to CD33-positive AML cells and did not require caspase activation. In conclusion, the synergistic proapoptotic activity of cotreatment of AML cells with VPA and GO indicates the potential value of this strategy for AML.

Microtubule-associated protein tau and in vitro paclitaxel sensitivity in primary breast cancer

20088

Background: Paclitaxel has an important role in the adjuvant therapy of primary breast cancer. Recently, microtubule-associated protein tau was described as a marker of paclitaxel sensitivity. We attempted to validate these findings in vitro utilizing the ATP tumorchemosensitivity assay (ATP-TCA). Methods: The in vitro drug sensitivity to paclitaxel was evaluated in 48 fresh primary breast cancer specimens using the ATP-TCA. ATP-TCA results were analysed using the area under the curve (AUC) of growth inhibition. These results were correlated with the expression of tau mRNA measured by quantitative RT-PCR (Spearman’s correlation coefficient). Tau was also compared between progesterone receptor (PgR) positive and negative and estrogen receptor (ER) positive and negative tumors, respectively (Wilcoxon test). Results: The correlation of tau with the AUC for paclitaxel was weak (r = −0.20) and disappeared when considering PgR positive and negative tumors separately (r = −0.004 and r = −0.048, respectively). Tau was found to be differentially expressed between PgR positive and negative as well as between ER positive and negative tumors (p < 0.0005 in both tests). Conclusions: The expression of tau does not show independent predictive value for the in vitro paclitaxel sensitivity in primary breast cancer.

No significant financial relationships to disclose.

MiGenes: a searchable interspecies database of mitochondrial proteins curated using gene ontology annotation

MOTIVATION

There has been an explosion of interest in the role of mitochondria in programmed cell death and other fundamental pathological processes underlying the development of human diseases. Nevertheless, the inventory of mitochondrial proteins encoded in the nuclear genome remains incomplete, providing an impediment to mitochondrial research at the interface with systems biology. We created the MiGenes database to further define the scope of the mitochondrial proteome in humans and model organisms including mice, rats, flies and worms as well as budding and fission yeasts. MiGenes is intended to stimulate mitochondrial research using model organisms.

SUMMARY

MiGenes is a large-scale relational database that is automatically updated to keep pace with advances in mitochondrial proteomics and is curated to assure that the designation of proteins as mitochondrial reflects gene ontology (GO) annotations supported by high-quality evidence codes. A set of postulates is proposed to help define which proteins are authentic components of mitochondria. MiGenes incorporates >1160 new GO annotations to human, mouse and rat protein records, 370 of which represent the first GO annotation reflecting a mitochondrial localization. MiGenes employs a flexible search interface that permits batchwise accession number searches to support high-throughput proteomic studies. A web interface is provided to permit members of the mitochondrial research community to suggest modifications in protein annotations or mitochondrial status.

Osmosensing and osmoregulatory compatible solute accumulation by bacteria

Bacteria inhabit natural and artificial environments with diverse and fluctuating osmolalities, salinities and temperatures. Many maintain cytoplasmic hydration, growth and survival most effectively by accumulating kosmotropic organic solutes (compatible solutes) when medium osmolality is high or temperature is low (above freezing). They release these solutes into their environment when the medium osmolality drops. Solutes accumulate either by synthesis or by transport from the extracellular medium. Responses to growth in high osmolality medium, including biosynthetic accumulation of trehalose, also protect Salmonella typhimurium from heat shock. Osmotically regulated transporters and mechanosensitive channels modulate cytoplasmic solute levels in Bacillus subtilis, Corynebacterium glutamicum, Escherichia coli, Lactobacillus plantarum, Lactococcus lactis, Listeria monocytogenes and Salmonella typhimurium. Each organism harbours multiple osmoregulatory transporters with overlapping substrate specificities. Membrane proteins that can act as both osmosensors and osmoregulatory transporters have been identified (secondary transporters ProP of E. coli and BetP of C. glutamicum as well as ABC transporter OpuA of L. lactis). The molecular bases for the modulation of gene expression and transport activity by temperature and medium osmolality are under intensive investigation with emphasis on the role of the membrane as an antenna for osmo- and/or thermosensors.

Multiple genes for the last step of proline biosynthesis in Bacillus subtilis

The complete Bacillus subtilis genome contains four genes (proG, proH, proI, and comER) with the potential to encode Delta(1)-pyrroline-5-carboxylate reductase, a proline biosynthetic enzyme. Simultaneous defects in three of these genes (proG, proH, and proI) were required to confer proline auxotrophy, indicating that the products of these genes are mostly interchangeable with respect to the last step in proline biosynthesis.

Rhizobium population dynamics in the pea rhizosphere of rhizobial inoculant strain applied in different formulations

The effect of inoculant formulation on the population dynamics of rhizobia in the pea rhizosphere was investigated using a streptomycin-resistant mutant of Rhizobium leguminosarum bv. viceae NITRAGIN128C56G (128C56G strR). The isolate was formulated into liquid, peat powder, and granular peat carriers, and was tested on pea at field sites near Saskatoon, Saskatchewan, and Beaverlodge, Alberta, in 1996 and 1997. The liquid and peat powder formulations were applied to seed while the granular inoculant was applied to soil. In three out of four site years, population dynamics were similar among formulations: an initial decline or lag period lasting 2-5 days followed by an increase to approximately 10(5) colony-forming units (CFU)/seedling by 14-28 days after planting (DAP) and, where sampled, a continuing increase from 10(7) to 10(8) CFU/plant at 63 DAP. In these same site years, nodule number (not determined at Beaverlodge in 1997) and nodule occupancy at 60 days were not significantly different among formulations. In contrast, soil populations of 128C56G strR from the liquid formulation declined to near zero by 28 DAP at Beaverlodge in 1996, when soil moisture was excessive in spring because of high rainfall. Populations increased in this treatment after this time, but remained significantly lower than the populations of the other two formulations throughout the sampling period. Pea seed yields were not significantly different among treatments in either year at Beaverlodge, but were significantly higher with granular inoculant than the noninoculated control in Saskatoon. Within inoculated treatments at Saskatoon, there were no significant differences in grain yield.

Quantitative analysis of transgene protein, mRNA, and vector DNA following injection of an adenoviral vector harboring glial cell line-derived neurotrophic factor into the primate caudate nucleus

Gene therapy for neurodegenerative diseases relies on stable expression of a vector-mediated transgene in the human central nervous system (CNS). In nonhuman primate CNS, transgene expression has been primarily assessed using descriptive histological methods. Here, we quantified the expression of a human glial cell line-derived neurotrophic factor (hGDNF) transgene using an ELISA specific for hGDNF protein and real-time quantitative RT-PCR and PCR for hGDNF mRNA and vector DNA, respectively. Transgene expression was assessed 1 week after injection of an E1-, E3-deleted adenovirus harboring hGDNF into the caudate nucleus of St. Kitts green monkey. We found that 57-147 million and 116-771 million copies of hGDNF mRNA and vector DNA, respectively, were present per 10,000 copies of the beta-actin gene. In the same sites, 40-152 pg of hGDNF protein per milligram of tissue was measured. Comparisons of these measures among monkeys demonstrated variable vector DNA and protein levels, but consistent mRNA levels at one-third of the level of vector DNA. This suggests that local responses to the vector play a role in the level of transgene expression and that high levels of vector DNA do not necessarily predict a high level of transgene protein. However, the results of this study do show that neuroprotective levels of GDNF transgene expression can be achieved following injection of an adenoviral vector into nonhuman primate caudate. Moreover, these assays provide quantitative methods for evaluating and comparing viral vectors in primate CNS.

Two evolutionarily closely related ABC transporters mediate the uptake of choline for synthesis of the osmoprotectant glycine betaine in Bacillus subtilis

Biosynthesis of the compatible solute glycine betaine in Bacillus subtilis confers a considerable degree of osmotic tolerance and proceeds via a two-step oxidation process of choline, with glycine betaine aldehyde as the intermediate. We have exploited the sensitivity of B. subtilis strains defective in glycine betaine production against glycine betaine aldehyde to select for mutants resistant to this toxic intermediate. These strains were also defective in choline uptake, and genetic analysis proved that two mutations affecting different genetic loci (opuB and opuC) were required for these phenotypes. Molecular analysis allowed us to demonstrate that the opuB and opuC operons each encode a binding protein-dependent ABC transport system that consists of four components. The presumed binding proteins of both ABC transporters were shown to be lipoproteins. Kinetic analysis of [14C]-choline uptake via OpuB (K(m) = 1 microM; Vmax = 21 nmol min-1 mg-1 protein) and OpuC (K(m) = 38 microM; Vmax = 75 nmol min-1 mg-1 protein) revealed that each of these ABC transporters exhibits high affinity and substantial transport capacity. Western blotting experiments with a polyclonal antiserum cross-reacting with the presumed substrate-binding proteins from both the OpuB and OpuC transporter suggested that the expression of the opuB and opuC operons is regulated in response to increasing osmolality of the growth medium. Primer extension analysis confirmed the osmotic control of opuB and allowed the identification of the promoter of this operon. The opuB and opuC operons are located close to each other on the B. subtilis chromosome, and their high sequence identity strongly suggests that these systems have evolved from a duplication event of a primordial gene cluster. Despite the close relatedness of OpuB and OpuC, these systems exhibit a striking difference in substrate specificity for osmoprotectants that would not have been predicted readily for such closely related ABC transporters.

High-affinity transport of choline-O-sulfate and its use as a compatible solute in Bacillus subtilis

We report here that the naturally occurring choline ester choline-O-sulfate serves as an effective compatible solute for Bacillus subtilis, and we have identified a high-affinity ATP-binding cassette (ABC) transport system responsible for its uptake. The osmoprotective effect of this trimethylammonium compound closely matches that of the potent and widely employed osmoprotectant glycine betaine. Growth experiments with a set of B. subtilis strains carrying defined mutations in the glycine betaine uptake systems OpuA, OpuC, and OpuD and in the high-affinity choline transporter OpuB revealed that choline-O-sulfate was specifically acquired from the environment via OpuC. Competition experiments demonstrated that choline-O-sulfate functioned as an effective competitive inhibitor for OpuC-mediated glycine betaine uptake, with a Ki of approximately 4 microM. Uptake studies with [1, 2-dimethyl-14C]choline-O-sulfate showed that its transport was stimulated by high osmolality, and kinetic analysis revealed that OpuC has high affinity for choline-O-sulfate, with a Km value of 4 +/- 1 microM and a maximum rate of transport (Vmax) of 54 +/- 3 nmol/min. mg of protein in cells grown in minimal medium with 0.4 M NaCl. Growth studies utilizing a B. subtilis mutant defective in the choline to glycine betaine synthesis pathway and natural abundance 13C nuclear magnetic resonance spectroscopy of whole-cell extracts from the wild-type strain demonstrated that choline-O-sulfate was accumulated in the cytoplasm and was not hydrolyzed to choline by B. subtilis. In contrast, the osmoprotective effect of acetylcholine for B. subtilis is dependent on its biotransformation into glycine betaine. Choline-O-sulfate was not used as the sole carbon, nitrogen, or sulfur source, and our findings thus characterize this choline ester as an effective compatible solute and metabolically inert stress compound for B. subtilis. OpuC mediates the efficient transport not only of glycine betaine and choline-O-sulfate but also of carnitine, crotonobetaine, and gamma-butyrobetaine (R. Kappes and E. Bremer, Microbiology 144:83-90, 1998). Thus, our data underscore its crucial role in the acquisition of a variety of osmoprotectants from the environment by B. subtilis.

Uptake and synthesis of compatible solutes as microbial stress responses to high-osmolality environments

All microorganisms possess a positive turgor, and maintenance of this outward-directed pressure is essential since it is generally considered as the driving force for cell expansion. Exposure of microorganisms to high-osmolality environments triggers rapid fluxes of cell water along the osmotic gradient out of the cell, thus causing a reduction in turgor and dehydration of the cytoplasm. To counteract the outflow of water, microorganisms increase their intracellular solute pool by amassing large amounts of organic osmolytes, the so-called compatible solutes. These osmoprotectants are highly congruous with the physiology of the cell and comprise a limited number of substances including the disaccharide trehalose, the amino acid proline, and the trimethylammonium compound glycine betaine. The intracellular amassing of compatible solutes as an adaptive strategy to high-osmolality environments is evolutionarily well-conserved in Bacteria, Archaea, and Eukarya. Furthermore, the nature of the osmolytes that are accumulated during water stress is maintained across the kingdoms, reflecting fundamental constraints on the kind of solutes that are compatible with macromolecular and cellular functions. Generally, compatible solutes can be amassed by microorganisms through uptake and synthesis. Here we summarise the molecular mechanisms of compatible solute accumulation in Escherichia coli and Bacillus subtilis, model organisms for the gram-negative and gram-positive branches of bacteria.

Osmoregulation of the opuE proline transport gene from Bacillus subtilis: contributions of the sigma A- and sigma B-dependent stress-responsive promoters

The opuE gene from Bacillus subtilis encodes a transport system (OpuE) for osmoprotective proline uptake and is expressed from two osmoregulated promoters: opuE P-1 recognized by the vegetative sigma factor A (sigma A and opuE P-2 dependent on the stress-induced transcription factor sigma B (sigma B). The contributions of these two promoters to osmoregulation of opuE were analysed. Genetic studies using chromosomal opuE-treA operon fusions revealed that opuE transcription is rapidly induced after an osmotic upshock. The strength of opuE expression is proportionally linked to the osmolarity of the growth medium. Deletion analysis of the opuE regulatory region identified a 330 bp DNA segment carrying all sequences required in cis for full and osmoregulated transcription. The proper rotational orientation of the upstream region present within this fragment was essential for the function of both opuE promoters. Mutant opuE-treA fusions with defects in either the sigma A-or the sigma B-dependent promoters revealed different contributions of these sequences to the overall osmoregulation of opuE. opuE P-2 (sigma B) activity increased transiently after an osmotic upshock and did not significantly contribute to the level of opuE expression in cells subjected to long-term osmotic stress. In contrast, transcription initiating from opuE P-1 (sigma A) rose in proportion to the external osmolarity and was maintained at high levels. Moreover, both promoters exhibited a different response to the osmoprotectant glycine betaine in the medium. Our results suggest that at least two different signal transduction pathways operate in B. subtilis to communicate osmotic changes in the environment to the transcription apparatus of the cell.

Regulation of the Escherichia coli water channel gene aqpZ

Osmotic movement of water across bacterial cell membranes is postulated to be a homeostatic mechanism for maintaining cell turgor. The molecular water transporter remained elusive until discovery of the Escherichia coli water channel, AqpZ, however the regulation of the aqpZ gene expression and physiological function of the AqpZ protein are unknown. Northern analysis revealed a transcript of 0.7 kb, confirming the monocistronic nature of aqpZ. Regulatory studies performed with an aqpZ::lacZ low copy plasmid demonstrate enhanced expression during mid-logarithmic growth, and expression of the gene is dependent upon the extracellular osmolality, which increased in hypoosmotic environments but strongly reduced in hyperosmolar NaCl or KCl. While disruption of the chromosomal aqpZ is not lethal for E. coli, the colonies of the aqpZ knockout mutant are smaller than those of the parental wild-type strain. When cocultured with parental wild-type E. coli, the aqpZ knockout mutant exhibits markedly reduced colony formation when grown at 39 degrees C. Similarly, the aqpZ knockout mutant also exhibits greatly reduced colony formation when grown at low osmolality, but this phenotype is reversed by overexpression of AqpZ protein. These results implicate AqpZ as a participant in the adaptive response of E. coli to hypoosmotic environments and indicate a requirement for AqpZ by rapidly growing cells.

Glycine betaine aldehyde dehydrogenase from Bacillus subtilis: characterization of an enzyme required for the synthesis of the osmoprotectant glycine betaine

Production of the compatible solute glycine betaine from its precursors choline or glycine betaine aldehyde confers a considerable level of tolerance against high osmolarity stress to the soil bacterium Bacillus subtilis. The glycine betaine aldehyde dehydrogenase GbsA is an integral part of the osmoregulatory glycine betaine synthesis pathway. We strongly overproduced this enzyme in an Escherichia coli strain that expressed a plasmid-encoded gbsA gene under T7&phi;10 control. The recombinant GbsA protein was purified 23-fold to apparent homogeneity by fractionated ammonium sulfate precipitation, ion-exchange chromatography on Q-Sepharose, and subsequent hydrophobic interaction chromatography on phenyl-Sepharose. Molecular sieving through Superose 12 and sedimentation centrifugation through a glycerol gradient suggested that the native enzyme is a homodimer with 53.7-kDa subunits. The enzyme was specific for glycine betaine aldehyde and could use both NAD+ and NADP+ as cofactors, but NAD+ was strongly preferred. A kinetic analysis of the GbsA-mediated oxidation of glycine betaine aldehyde to glycine betaine revealed Km values of 125 microM and 143 microM for its substrates glycine betaine aldehyde and NAD+, respectively. Low concentrations of salts stimulated the GbsA activity, and the enzyme was highly tolerant of high ionic conditions. Even in the presence of 2.4 M KCl, 88% of the initial enzymatic activity was maintained. B. subtilis synthesizes high levels of proline when grown at high osmolarity, and the presence of this amino acid strongly stimulated the GbsA activity in vitro. The enzyme was stimulated by moderate concentrations of glycine betaine, and its activity was highly tolerant against molar concentrations of this osmolyte. The high salt tolerance and its resistance to its own reaction product are essential features of the GbsA enzyme and ensure that B. subtilis can produce high levels of the compatible solute glycine betaine under conditions of high osmolarity stress.

Lipoprotein from the osmoregulated ABC transport system OpuA of Bacillus subtilis: purification of the glycine betaine binding protein and characterization of a functional lipidless mutant

The OpuA transport system of Bacillus subtilis functions as a high-affinity uptake system for the osmoprotectant glycine betaine. It is a member of the ABC transporter superfamily and consists of an ATPase (OpuAA), an integral membrane protein (OpuAB), and a hydrophilic polypeptide (OpuAC) that shows the signature sequence of lipoproteins (B. Kempf and E. Bremer, J. Biol. Chem. 270:16701-16713, 1995). The OpuAC protein might thus serve as an extracellular substrate binding protein anchored in the cytoplasmic membrane via a lipid modification at an amino-terminal cysteine residue. A malE-opuAC hybrid gene was constructed and used to purify a lipidless OpuAC protein. The purified protein bound radiolabeled glycine betaine avidly and exhibited a KD of 6 microM for this ligand, demonstrating that OpuAC indeed functions as the substrate binding protein for the B. subtilis OpuA system. We have selectively expressed the opuAC gene under T7 phi10 control in Escherichia coli and have demonstrated through its metabolic labeling with [3H]palmitic acid that OpuAC is a lipoprotein. A mutant expressing an OpuAC protein in which the amino-terminal cysteine residue was changed to an alanine (OpuAC-3) was constructed by oligonucleotide site-directed mutagenesis. The OpuAC-3 protein was not acylated by [3H]palmitic acid, and part of it was secreted into the periplasmic space of E. coli, where it could be released from the cells by cold osmotic shock. The opuAC-3 mutation was recombined into an otherwise wild-type opuA operon in the chromosome of B. subtilis. Unexpectedly, this mutant OpuAC system still functioned efficiently for glycine betaine acquisition in vivo under high-osmolarity growth conditions. In addition, the mutant OpuA transporter exhibited kinetic parameters similar to that of the wild-type system. Our data suggest that the lipidless OpuAC-3 protein is held in the cytoplasmic membrane of B. subtilis via its uncleaved hydrophobic signal peptide.

The aquaporin-Z water channel gene of Escherichia coli: structure, organization and phylogeny

Aquaporin water channel proteins are found throughout the plant and animal kingdoms, but the first prokaryotic water channel gene, aqpZ, was only recently identified in wild type Escherichia coli (Calamita G et al (1995) J Biol Chem 270, 29063-29066). Here we define the organization of aqpZ in E coli, produce the AqpZ protein and compare the AqpZ phylogeny to that of some known bacterial homologs. Physical mapping and sequence analyses confirmed the location of aqpZ at minute 19.7 on the E coli chromosome where it is transcribed counterclockwise. The monocistronic nature of aqpZ was clearly indicated by the structural organization of its surrounding genes, ybjD and ybjE' and by the presence of a typical Rho-independent transcriptional terminator following the aqpZ stop codon. Computer sequence analysis indicated the -35/-10 region located 72 bases upstream of the aqpZ start codon as the most likely aqpZ promoter. A series of potential cis-regulatory elements were found in the 400 bp region preceding the aqpZ ORF. The AqpZ protein, produced under T7 phi 10 control, showed a size of about 20 kDa by SDS-PAGE. Striking similarities were found between the E coli aqpZ and a gene included in the genome of the cyanobacterium Synechocystis sp PCC6803, a species permanently living a fresh water. These results may represent a fundamental step to characterize the regulation and the physiological features of the AqpZ water channel in prokaryotes.

Osmostress response in Bacillus subtilis: characterization of a proline uptake system (OpuE) regulated by high osmolarity and the alternative transcription factor sigma B

Exogenously provided proline has been shown to serve as an osmoprotectant in Bacillus subtilis. Uptake of proline is under osmotic control and functions independently of the known transport systems for the osmoprotectant glycine betaine. We cloned the structural gene (opuE) for this proline transport system and constructed a chromosomal opuE mutant by marker replacement. The resulting B. subtilis strain was entirely deficient in osmoregulated proline transport activity and was no longer protected by exogenously provided proline, attesting to the central importance of OpuE for proline uptake in high-osmolarity environments. The transport characteristics and growth properties of the opuE mutant revealed the presence of a second proline transport activity in B. subtilis. DNA sequence analysis of the opuE region showed that the OpuE transporter (492 residues) consists of a single integral membrane protein. Database searches indicated that OpuE is a member of the sodium/solute symporter family, comprising proteins from both prokaryotes and eukaryotes that obligatorily couple substrate uptake to Na+ symport. The highest similarity was detected to the PutP proline permeases, which are used in Escherichia coli, Salmonella typhimurium and Staphylococcus aureus for the acquisition of proline as a carbon and nitrogen source, but not for osmoprotective purposes. An elevation of the osmolarity of the growth medium by either ionic or non-ionic osmolytes resulted in a strong increase in the OpuE-mediated proline uptake. This osmoregulated proline transport activity was entirely dependent on de novo protein synthesis, suggesting a transcriptional control mechanism. Primer extension analysis revealed the presence of two osmoregulated and tightly spaced opuE promoters. The activity of one of these promoters was dependent on sigma A and the second promoter was controlled by the general stress transcription factor sigma B.

Use of phoA and lacZ fusions to study the membrane topology of ProW, a component of the osmoregulated ProU transport system of Escherichia coli

The Escherichia coli ProU system is a member of the ATP-binding cassette (ABC) superfamily of transporters. ProU consists of three components (ProV, ProW, and ProX) and functions as a high-affinity, binding protein-dependent transport system for the osmoprotectants glycine betaine and proline betaine. The ProW protein is the integral inner membrane component of the ProU system. Its hydropathy profile predicts seven transmembrane spans and a hydrophilic amino terminus of approximately 100 residues, and it suggests the presence of an amphiphilic alpha-helix (L-61 to F-97) in close proximity to the first strongly hydrophobic segment of ProW. We have studied the membrane topology of the ProW protein by the phoA and lacZ gene fusion approach. A collection of 10 different proW-phoA fusions with alkaline phosphatase activity and 8 different proW-lacZ fusions with beta-galactosidase activity were isolated in vivo after TnphoAB and TnlacZ mutagenesis of a plasmid-encoded proW gene. The recovery of both enzymatically active ProW-PhoA and ProW-LacZ hybrid proteins indicates that segments of ProW are exposed on both sides of the cytoplasmic membrane. To compare the enzymatic activities of each of the indicator proteins joined at a particular site in ProW, we switched the phoA and lacZ reporter genes in vitro in each of the originally in vivo-isolated gene fusions. A mirror-like pattern in the enzyme activity of the resulting new ProW-PhoA and ProW-LacZ hybrid proteins emerged, thus providing positive signals for the location of both periplasmic and cytoplasmic domains in ProW. The protease kallikrein digests the amino-terminal tail of a ProW-LacZ hybrid protein in spheroplasts, suggesting that the amino terminus of ProW is located on the periplasmic side of the cytoplasmic membrane. From these data, a two-dimensional model for ProW was constructed; this model consists of seven transmembrane alpha-helices and an unusual amino-terminal tail of approximately 100 amino acid residues that protrudes into the periplasmic space.

Three transport systems for the osmoprotectant glycine betaine operate in Bacillus subtilis: characterization of OpuD

The accumulation of the osmoprotectant glycine betaine from exogenous sources provides a high degree of osmotic tolerance to Bacillus subtilis. We have identified, through functional complementation of an Escherichia coli mutant defective in glycine betaine uptake, a new glycine betaine transport system from B. subtilis. The DNA sequence of a 2,310-bp segment of the cloned region revealed a single gene (opuD) whose product (OpuD) was essential for glycine betaine uptake and osmoprotection in E. coli. The opuD gene encodes a hydrophobic 56.13-kDa protein (512 amino acid residues). OpuD shows a significant degree of sequence identity to the choline transporter BetT and the carnitine transporter CaiT from E. coli and a BetT-like protein from Haemophilus influenzae. These membrane proteins form a family of transporters involved in the uptake of trimethylammonium compounds. The OpuD-mediated glycine betaine transport activity in B. subtilis is controlled by the environmental osmolarity. High osmolarity stimulates de novo synthesis of OpuD and activates preexisting OpuD proteins to achieve maximal glycine betaine uptake activity. An opuD mutant was constructed by marker replacement, and the OpuD-mediated glycine betaine uptake activity was compared with that of the previously identified multicomponent OpuA and OpuC (ProU) glycine betaine uptake systems. In addition, a set of mutants was constructed, each of which synthesized only one of the three glycine betaine uptake systems. These mutants were used to determine the kinetic parameters for glycine betaine transport through OpuA, OpuC, and OpuD. Each of these uptake systems shows high substrate affinity, with Km values in the low micromolar range, which should allow B. subtilis to efficiently acquire the osmoprotectant from the environment. The systems differed in their contribution to the overall glycine betaine accumulation and osmoprotection. A triple opuA, opuC, and opuD mutant strain was isolated, and it showed no glycine betaine uptake activity, demonstrating that three transport systems for this osmoprotectant operate in B. subtilis.

Synthesis of the osmoprotectant glycine betaine in Bacillus subtilis: characterization of the gbsAB genes

Synthesis of the osmoprotectant glycine betaine from the exogenously provided precursor choline or glycine betaine aldehyde confers considerable osmotic stress tolerance to Bacillus subtilis in high-osmolarity media. Using an Escherichia coli mutant (betBA) defective in the glycine betaine synthesis enzymes, we cloned by functional complementation the genes that are required for the synthesis of the osmoprotectant glycine betaine in B. subtilis. The DNA sequence of a 4.1-kb segment from the cloned chromosomal B. subtilis DNA was established, and two genes (gbsA and gbsB) whose products were essential for glycine betaine biosynthesis and osmoprotection were identified. The gbsA and gbsB genes are transcribed in the same direction, are separated by a short intergenic region, and are likely to form an operon. The deduced gbsA gene product exhibits strong sequence identity with members of a superfamily of specialized and nonspecialized aldehyde dehydrogenases. This superfamily comprises glycine betaine aldehyde dehydrogenases from bacteria and plants with known involvement in the cellular adaptation to high-osmolarity stress and drought. The deduced gbsB gene product shows significant similarity to the family of type III alcohol dehydrogenases. B. subtilis mutants with defects in the chromosomal gbsAB genes were constructed by marker replacement, and the growth properties of these mutant strains in high-osmolarity medium were analyzed. Deletion of the gbsAB genes destroyed the choline-glycine betaine synthesis pathway and abolished the ability of B. subtilis to deal effectively with high-osmolarity stress in choline- or glycine betaine aldehyde-containing medium. Uptake of radiolabelled choline was unaltered in the gbsAB mutant strain. The continued intracellular accumulation of choline or glycine betaine aldehyde in a strain lacking the glycine betaine-biosynthetic enzymes strongly interfered with the growth of B. subtilis, even in medium of moderate osmolarity. A single transcription initiation site for gbsAB was detected by high-resolution primer extension analysis. gbsAB transcription was initiated from a promoter with close homology to sigma A-dependent promoters and was stimulated by the presence of choline in the growth medium.

A novel amidohydrolase gene from Bacillus subtilis cloning: DNA-sequence analysis and map position of amhX

The nucleotide sequence of a new Bacillus subtilis gene (amhX) was determined that encodes a protein (AmhX) with strong sequence identity to amidohydrolases from both plant and bacterial species and a carboxypeptidase from the archaeon Sulfolobus sulfataricus. The amhX gene encodes a hydrophilic polypeptide of 383 amino acids with a molecular mass of 41.5 kDa. The amhX gene was overexpressed in E. coli by using the T7 RNA polymerase/promoter system and the transcription initiation sites for the amhX mRNAs in B. subtilis were determined by primer extension analysis. Chromosomal amhX mutations were constructed by marker replacement and the amhX gene was positioned at 25 degrees on the genetic and physical map of the B. subtilis chromosome.

OpuA, an osmotically regulated binding protein-dependent transport system for the osmoprotectant glycine betaine in Bacillus subtilis

Exogenously provided glycine betaine can efficiently protect Bacillus subtilis from the detrimental effects of high osmolarity environments. Through functional complementation of an Escherichia coli mutant deficient in glycine betaine uptake with a gene library from B. subtilis, we have identified a multicomponent glycine betaine transport system, OpuA. Uptake of radiolabeled glycine betaine in B. subtilis was found to be osmotically stimulated and was strongly decreased in a mutant strain lacking the OpuA transport system. DNA sequence analysis revealed that the components of the OpuA system are encoded by anoperon (opuA) comprising three structural genes: opuAA, opuAB, and opuAC. The products of these genes exhibit features characteristic for binding protein-dependent transport systems and in particular show homology to the glycine betaine uptake system ProU from E. coli. Expression of the opuA operon is under osmotic control. The transcriptional initiation sites of opuA were mapped by high resolution primer extension analysis, and two opuA mRNAs were detected that differed by 38 base pairs at their 5' ends. Synthesis of the shorter transcript was strongly increased in cells grown at high osmolarity, whereas the amount of the longer transcript did not vary in response to medium osmolarity. Physical and genetic mapping experiments allowed the positioning the opuA operon at 25 degrees on the genetic map of B. subtilis.

The osmoprotectant proline betaine is a major substrate for the binding-protein-dependent transport system ProU of Escherichia coli K-12

The ProP and ProU transport systems of Escherichia coli mediate the uptake of several osmoprotectants including glycine betaine. Here we report that both ProP and ProU are involved in the transport of the potent osmoprotectant proline betaine. A set of isogenic E. coli strains carrying deletions in either the proP or proU loci was constructed. The growth properties of these mutants in high osmolarity minimal media containing 1 mM proline betaine demonstrated that the osmoprotective effect of this compound was dependent on either an intact ProP or ProU uptake system. Proline betaine competes with glycine betaine for binding to the proU-encoded periplasmic substrate binding protein (ProX) and we estimate a KD of 5.2 microM for proline betaine binding. This value is similar to the binding constant of the ProX protein determined previously for the binding of glycine betaine (KD of 1.4 microM). Our results thus demonstrate that the binding-protein-dependent ProU transport system of E. coli mediates the efficient uptake of the osmoprotectants glycine betaine and proline betaine.

pOSEX: vectors for osmotically controlled and finely tuned gene expression in Escherichia coli

Expression of the proU operon of Escherichia coli is directly proportional to the osmolarity of the growth medium. The basal level of proU transcription is very low, but a large increase is triggered by a sudden rise in the external osmolarity. This increased expression is maintained for as long as the osmotic stimulus persists. We have capitalized upon these regulatory features of the proU operon and have constructed a series of expression vectors (pOSEX) permitting osmotically controlled expression of heterologous genes governed by regulatory signals of proU. The pOSEX vectors carry the proU promoter, an upstream region required for high-level expression, and part of the first structural gene (proV), which acts as a silencer and is necessary to maintain low-level expression in low osmolarity media. An extended multiple cloning site (MCS) positioned at the 3' end of proV' permits the cloning of heterologous genes into the pOSEX plasmids, and efficient transcription terminators derived from the rrnB operon prevent deleterious read-through transcription into the vector portion. The properties of the pOSEX expression vectors were tested by positioning a promoterless lacZ (encoding beta-galactosidase) gene from E. coli and the gcdA (encoding carboxytransferase) gene from the Gram+ bacterium Acidaminococcus fermentans under the control of the proU regulatory region. Efficient, osmo-regulated and finely tuned expression of both lacZ and gcdA was achieved, and the amount of beta-galactosidase and carboxytransferase synthesized were simply controlled by adjusting the osmolarity of the growth medium with various concentrations of NaCl.

The nucleoid-associated DNA-binding protein H-NS is required for the efficient adaptation of Escherichia coli K-12 to a cold environment

The hns gene is a member of the cold-shock regulon, indicating that the nucleoid-associated, DNA-binding protein H-NS plays an important role in the adaptation of Escherichia coli to low temperatures. We show here that the ability to cope efficiently with a cold environment (12 degrees C and 25 degrees C) is strongly impaired in E. coli strains carrying hns mutations. Growth inhibition is much more pronounced in strains carrying the hns-206 allele (an ampicillin resistance cassette inserted after codon 37) than in those carrying the hns-205 mutation (a Tn10 insertion located in codon 93). A protein fragment (H-NS*) is synthesized in strains carrying the hns-205::Tn10 mutation, suggesting that this truncated polypeptide is partially functional in the cold adaptation process. Analysis of the growth properties of strains harbouring four different low-copy-number plasmid-encoded hns' genes that result in the production of C-terminally truncated H-NS proteins supports this proposal. H-NS* proteins composed of 133, 117 or 94 amino-terminal amino acids partially complemented the severe cold-sensitive growth phenotype of the hns-206 mutant. In contrast, synthesis of a truncated H-NS protein with only 75 amino-terminal amino acids was insufficient to restore growth at low temperature.