Biomarker panels for characterizing microbial community biofilm formation as composite molecular process.

Microbial consortia execute collaborative molecular processes with contributions from individual species, on such basis enabling optimized molecular function. Such collaboration and synergies benefit metabolic flux specifically in extreme environmental conditions as seen in acid mine drainage, with biofilms as relevant microenvironment. However, knowledge about community species composition is not sufficient for deducing presence and efficiency of composite molecular function. For this task molecular resolution of the consortium interactome is to be retrieved, with molecular biomarkers particularly suited for characterizing composite molecular processes involved in biofilm formation and maintenance. A microbial species set identified in 18 copper environmental sites provides a data matrix for deriving a cross-species molecular process model of biofilm formation composed of 191 protein coding genes contributed from 25 microbial species. Computing degree and stress centrality of biofilm molecular process nodes allows selection of network hubs and central connectors, with the top ranking molecular features proposed as biomarker candidates for characterizing biofilm homeostasis. Functional classes represented in the biomarker panel include quorum sensing, chemotaxis, motility and extracellular polysaccharide biosynthesis, complemented by chaperones. Abundance of biomarker candidates identified in experimental data sets monitoring different biofilm conditions provides evidence for the selected biomarkers as sensitive and specific molecular process proxies for capturing biofilm microenvironments. Topological criteria of process networks covering an aggregate function of interest support the selection of biomarker candidates independent of specific community species composition. Such panels promise efficient screening of environmental samples for presence of microbial community composite molecular function.

Interaction networks for identifying coupled molecular processes in microbial communities.

BACKGROUND: Microbial communities adapt to environmental conditions for optimizing metabolic flux. Such adaption may include cooperative mechanisms eventually resulting in phenotypic observables as emergent properties that cannot be attributed to an individual species alone. Understanding the molecular basis of cross-species cooperation adds to utilization of microbial communities in industrial applications including metal bioleaching and bioremediation processes. With significant advancements in metagenomics the composition of microbial communities became amenable for integrative analysis on the level of entangled molecular processes involving more than one species, in turn offering a data matrix for analyzing the molecular basis of cooperative phenomena. METHODS: We present an analysis framework aligned with a dynamical hierarchies concept for unraveling emergent properties in microbial communities, and exemplify this approach for a co-culture setting of At. ferrooxidans and At. thiooxidans. This minimum microbial community demonstrates a significant increase in bioleaching efficiency compared to the activity of individual species, involving mechanisms of the thiosulfate, the polysulfide and the iron oxidation pathway. RESULTS: Populating gene-centric data structures holding rich functional annotation and interaction information allows deriving network models at the functional level coupling energy production and transport processes of both microbial species. Applying a network segmentation approach on the interaction network of ortholog genes covering energy production and transport proposes a set of specific molecular processes of relevance in bioleaching. The resulting molecular process model essentially involves functionalities such as iron oxidation, nitrogen metabolism and proton transport, complemented by sulfur oxidation and nitrogen metabolism, as well as a set of ion transporter functionalities. At. ferrooxidans-specific genes embedded in the molecular model representation hold gene functions supportive for ammonia utilization as well as for biofilm formation, resembling key elements for effective chalcopyrite bioleaching as emergent property in the co-culture situation. CONCLUSIONS: Analyzing the entangled molecular processes of a microbial community on the level of segmented, gene-centric interaction networks allows identification of core molecular processes and functionalities adding to our mechanistic understanding of emergent properties of microbial consortia.

A WD-FYVE protein binds to the kinases Akt and PKCzeta/lambda.

WD (tryptophan-aspartic acid dipeptide)-repeat proteins play a central role in signal transduction cascades by co-ordinating the interaction of key signalling molecules. We identified a novel propeller-FYVE [domain identified in Fab1p, YOTB, Vac1p and EEA1 (early endosome antigen 1)] protein, ProF, which is expressed in various cell lines and tissues and consists of seven WD-repeats and a FYVE domain. WD-repeat proteins offer a platform for protein-protein interactions by folding into a seven-bladed propeller-like structure, while the FYVE domain binds to phosphatidylinositol 3-phosphate present mainly on intracellular membranes. The ProF protein partially co-localizes with EEA1 on vesicular structures and binds to the protein kinases Akt and PKCzeta/lambda (protein kinase Czeta/lambda) via its WD-repeat propeller. ProF interacts more strongly with the kinases after hormonal stimulation. Endogenously expressed ProF and the two kinases interact in brain and in the preadipocyte cell line 3T3-L1, suggesting a role in secretory vesicular processes. In summary, we describe a new binding partner for kinases, located on vesicular structures in specialized cells, which may play a role for the spatial organization of signalling cascades.

Cooperation of Ras- and c-Myc-dependent pathways in regulating the growth and invasiveness of synovial fibroblasts in rheumatoid arthritis.

OBJECTIVE: To study the specific contribution of MAP kinase activator c-Raf-1 and one of its downstream transcription factors, c-Myc, to the growth and invasive behavior of rheumatoid arthritis synovial fibroblasts (RASFs). METHODS: RASFs were transduced with retroviral constructs expressing dominant-negative mutants of c-Raf-1 or c-Myc (DN c-Raf-1 or DN c-Myc, respectively) or with the mock vector. The expression of wild-type and mutant proteins was confirmed by Western blotting. Growth curves of RASFs were recorded, and apoptosis was measured by flow cytometry. Invasiveness of RASFs was assessed in the SCID mouse model of RA. Immunohistochemistry was used to study the effects of DN c-Raf-1 on phosphorylated c-Jun and matrix metalloproteinase 1 (MMP-1) in RASFs implanted into SCID mice. The phosphorylation of ERK and JNK in DN c-Raf-1- and mock-transduced RASFs was determined in vitro by Western blotting. The levels of MMPs in these cells were measured by quantitative polymerase chain reaction (PCR). RESULTS: Neither DN c-Raf-1 alone nor DN c-Myc alone significantly altered proliferation or apoptosis of RASFs, but both mutants together rapidly induced apoptosis. Inhibition of c-Raf-1 or c-Myc significantly reduced the invasiveness of RASFs in the SCID mouse model. DN c-Raf-1 decreased the phosphorylation of ERK and JNK in vitro and reduced the in vivo expression of phosphorylated c-Jun as well as the expression of disease-relevant MMPs. As determined by quantitative PCR, the inhibition was most pronounced for MMP-1 and MMP-3. CONCLUSION: The data demonstrate that Ras- and c-Myc-dependent signaling events cooperate to regulate the growth and invasiveness of RASFs. Targeting of both c-Raf-1 and c-Myc may constitute an interesting therapeutic approach in RA.

Linear closed mini DNA generated by the prokaryotic cleaving-joining enzyme TelN is functional in mammalian cells.

For application of DNA in gene medicine plasmid or viral DNA is usually used as a vector for the gene of interest. To generate DNA with a minimum of foreign DNA sequences, we used the prokaryotic telomerase, protelomerase TelN, of bacteriophage N15. This is a novel enzyme with cleaving-joining activity, which is required for the formation of linear prophage DNA with closed ends in lysogenic bacteria. Acting on a telomere resolution site telRL, the protelomerase converts circular plasmid DNA into linear covalently closed dumbbell-shaped molecules ("doggybones") in a single-step enzyme reaction. Two such sites were inserted into an expression plasmid flanking a gene of interest. This is cleaved and joined by means of the protelomerase, yielding linear closed mini DNA coding for green fluorescent protein (EGFP) or interleukin-12 (IL-12). Upon transient transfection of human embryonal kidney cells, EGFP was expressed at higher levels from linear closed molecules than from linear open molecules generated by restriction endonucleases for comparison. The level of transcription was comparable to that observed for the parental plasmid DNA. To test whether the linear closed mini DNA molecules are functional in vivo the B16F10/C57BL/6 melanoma metastasis model was applied, where injection of IL-12-expressing DNA inhibits metastasis formation in the lung. The anti-metastatic effect of the IL-12-expressing linear closed DNA was equal or higher than that of the parental plasmid DNA. Therefore, the TelN/ telRL system is well suited to generate linear closed mini DNA with high stability and a minimum of foreign nucleotide sequences.

Regulation of Raf-Akt Cross-talk.

We have recently shown that the Ras-Raf-MEK-ERK and phosphatidylinositol 3-kinase (PI3K)-Akt signaling pathways can cross-talk in the human breast cancer cell line MCF-7. High Raf activity induces growth arrest and differentiation in these cells, whereas high PI3K/Akt activity correlates with cell survival and proliferation. Here we show that the Raf-Akt cross-talk is regulated in a concentration- and ligand-dependent manner. High doses of insulin-like growth factor I (IGF-I) activate Akt quickly and strongly enough to suppress Raf kinase activity via phosphorylation of Ser-259, whereas low doses of IGF-I do not trigger this cross-talk but are still mitogenic. Phorbol 12-myristate 13-acetate, a differentiation-inducing stimulus, potently activates the Ras-Raf-MEK-ERK pathway but only weakly activates PI3K/Akt and does not trigger the cross-talk. Thus, the herein analyzed parameters such as ligand type, concentration, and time course may contribute to the cellular response of either proliferation or differentiation. This is highly relevant to understanding cellular transformation and may be of use in areas like tissue engineering.