Application of an Escherichia coli triple reporter strain for at-line monitoring of single-cell physiology during L-phenylalanine production

Biotechnological production processes are sustainable approaches for the production of biobased components such as amino acids for food and feed industry. Scale-up from ideal lab-scale bioreactors to large-scale processes is often accompanied by loss in productivity. This may be related to population heterogeneities of cells originating from isogenic cultures that arise due to dynamic non-ideal conditions in the bioreactor. To better understand this phenomenon, deeper insights into single-cell physiologies in bioprocesses are mandatory before scale-up. Here, a triple reporter strain (3RP) was developed by chromosomally integrating the fluorescent proteins mEmerald, CyOFP1, and mTagBFP2 into the L-phenylalanine producing Escherichia coli strain FUS4 (pF81_kan) to allow monitoring of growth, oxygen availability, and general stress response of the single cells. Functionality of the 3RP was confirmed in well-mixed lab-scale fed-batch processes with glycerol as carbon source in comparison to the strain without fluorescent proteins, leading to no difference in process performance. Fluorescence levels could successfully reflect the course of related process state variables, revealed population heterogeneities during the transition between different process phases and potentially subpopulations that exhibit superior process performance. Furthermore, indications were found for noise in gene expression as regulation strategy against environmental perturbation.     

Novel Miscanthus hybrids: Modelling productivity on marginal land in Europe using dynamics of canopy development determined by light interception

New biomass crop hybrids for bioeconomic expansion require yield projections to determine their potential for strategic land use planning in the face of global challenges. Our biomass growth simulation incorporates radiation interception and conversion efficiency. Models often use leaf area to predict interception which is demanding to determine accurately, so instead we use low-cost rapid light interception measurements using a simple laboratory-made line ceptometer and relate the dynamics of canopy closure to thermal time, and to measurements of biomass. We apply the model to project the European biomass potentials of new market-ready hybrids for 2020–2030. Field measurements are easier to collect, the calibration is seasonally dynamic and reduces influence of weather variation between field sites. The model obtained is conservative, being calibrated by crops of varying establishment and varying maturity on less productive (marginal) land. This results in conservative projections of miscanthus hybrids for 2020–2030 based on 10% land use conversion of the least (productive) grassland and arable for farm diversification, which show a European potential of 80.7–89.7 Mt year⁻¹ biomass, with potential for 1.2–1.3 EJ year⁻¹ energy and 36.3–40.3 Mt year⁻¹ carbon capture, with seeded Miscanthus sacchariflorus × sinensis displaying highest yield potential. Simulated biomass projections must be viewed in light of the field measurements on less productive land with high soil water deficits. We are attempting to model the results from an ambitious and novel project combining new hybrids across Europe with agronomy which has not been perfected on less productive sites. Nevertheless, at the time of energy sourcing issues, seed-propagated miscanthus hybrids for the upscaled provision of bioenergy offer an alternative source of renewable energy. If European countries provide incentives for growers to invest, seeded hybrids can improve product availability and biomass yields over the current commercial miscanthus variety.     

Migratory Orientation of Blackcaps (Sylvia atricapilla): Population-specific Shifts of Direction during the Autumn

The population-specific orientation of two groups of blackcaps (Sylvia atricapilla), one from southwest Germany, the other from easternmost Austria, was studied outdoors in Emlen funnels. We investigated whether a seasonal shift in the migratory direction — as expected for the Austrian birds from ringing recoveries — occurs under experimental conditions and in a seasonally constant magnetic field. The West German birds, for which no shift was expected, oriented southwest during the entire season. The Austrian birds oriented southeast in October and southsouthwest in November. The clockwise shift by about 60° occurred within a 10-day period. The results indicate that in this species seasonal changes of migratory direction are probably based on an endogenous program, occur without the birds actually migrating and are independent of changes in the magnetic field. Our results provide further evidence that directional shifts in Sylvia warblers may be controlled by a different mechanism than in pied flycatchers (Ficedula hypoleuca).     

Accurate detection of very sparse sequence motifs.

Protein sequence alignments are more reliable the shorter the evolutionary distance. Here, we align distantly related proteins using many closely spaced intermediate sequences as stepping stones. Such transitive alignments can be generated between any two proteins in a connected set, whether they are direct or indirect sequence neighbors in the underlying library of pairwise alignments. We have implemented a greedy algorithm, MaxFlow, using a novel consistency score to estimate the relative likelihood of alternative paths of transitive alignment. In contrast to traditional profile models of amino acid preferences, MaxFlow models the probability that two positions are structurally equivalent and retains high information content across large distances in sequence space. Thus, MaxFlow is able to identify sparse and narrow active-site sequence signatures which are embedded in high-entropy sequence segments in the structure based multiple alignment of large diverse enzyme superfamilies. In a challenging benchmark based on the urease superfamily, MaxFlow yields better reliability and double coverage compared to available sequence alignment software. This promises to increase information returns from functional and structural genomics, where reliable sequence alignment is a bottleneck to transferring the functional or structural characterization of model proteins to entire protein superfamilies.     

A unique variant of streptococcal group O-antigen (C-polysaccharide) that lacks phosphocholine.

Streptococcus mitis strain SK598, which represents a subgroup of biovar 1, possesses a unique variant of the C-polysaccharide found in the cell wall of all strains of Streptococcus pneumoniae and in some strains of S. mitis. This new variant lacks the choline methyl groups in contrast to the previously characterized forms of C-polysaccharide, which all contain one or two choline residues per repeat. The following structure of the repeating unit of the SK598 polysaccharide was established: where AAT is 2-acetamido-4-amino-2,4,6-trideoxy-d-galactose. This structure is identical to the double choline-substituted form of C-polysaccharide, except that it is substituted with ethanolamine instead of choline. This extends the number of recognized C-polysaccharide variants to four.     

Tumor necrosis factor-alpha converting enzyme is processed by proprotein-convertases to its mature form which is degraded upon phorbol ester stimulation.

Tumor necrosis factor-alpha converting enzyme (TACE or ADAM17) is a member of the ADAM (a disintegrin and metalloproteinase) family of type I membrane proteins and mediates the ectodomain shedding of various membrane-anchored signaling and adhesion proteins. TACE is synthesized as an inactive zymogen, which is subsequently proteolytically processed to the catalytically active form. We have identified the proprotein-convertases PC7 and furin to be involved in maturation of TACE. This maturation is negatively influenced by the phorbol ester phorbol-12-myristate-13-acetate (PMA), which decreases the cellular amount of the mature form of TACE in PMA-treated HEK293 and SH-SY5Y cells. Furthermore, we found that stimulation of protein kinase C or protein kinase A signaling pathways did not influence long-term degradation of mature TACE. Interestingly, PMA treatment of furin-deficient LoVo cells did not affect the degradation of mature TACE. By examination of furin reconstituted LoVo cells we were able to exclude the possibility that PMA modulates furin activity. Moreover, the PMA dependent decrease of the mature enzyme form is specific for TACE, as the amount of mature ADAM10 was unaffected in PMA-treated HEK293 and SH-SY5Y cells. Our results indicate that the activation of TACE by the proprotein-convertases PC7 and furin is very similar to the maturation of ADAM10 although there is a significant difference in the cellular stability of the mature enzyme forms after phorbol ester treatment.     

INTERLEUKIN 10 PROTECTS ACTIVATED HUMAN T LYMPHOCYTES AGAINST GROWTH FACTOR WITHDRAWAL-INDUCED CELL DEATH BUT ONLY ANTI-FAS ANTIBODY CAN PREVENT ACTIVATION-INDUCED CELL DEATH

Interleukin 10 (IL-10) is a pleiotropic T cell-derived cytokine best known for its negative regulatory effects on T cell immunity. It inhibits responses indirectly by downregulating expression of major histocompatibility complex (MHC) molecules and co-stimulatory molecules such as CD80 on antigen presenting cells as well as directly via its effects on responding cells. On the other hand, IL-10 has been shown to protect activated T cells against apoptosis caused by withdrawal of the major growth factor, IL-2, and allow proliferation of T cells in the absence of IL-2. However, we show here that this IL-10-dependent, IL-2 independent proliferative response is short-lived, and that IL-10-responsive T cells cannot multiply in its presence. Moreover, inclusion of exogenous IL-10 in clonal cultures propagated with IL-2 results in suppression of their growth. These findings, together with the observation that IL-10 fails to protect T cells against activation-induced cell death (a fas/fas-ligand-dependent phenomenon blocked only by certain antagonistic anti-fas reagents), suggest that the negative regulatory effects of IL-10 outweigh the upregulated proliferation observed on some T cell clones (TCC) in the absence of IL-2.     

Widely Used Enhancer of Eukaryotic Expression Vectors Is Strongly and Differentially Regulated in Fibroblast, Myoblast, and Teratocarcinoma Cell Lines

The expression of transgenes in eukaryotic cells is a powerful approach in cell biology. In most cases, it is based on the activity of strong and constitutive viral cis-acting elements in eukaryotic expression vectors. Here we show that a widely used such element derived from an early gene of human cytomegalovirus is strongly and differentially regulated in mouse cell lines. We analyzed cytomegalovirus promoter-driven expression of stably transfected transgenes in growing, confluent, and differentiating mouse 3T3 fibroblasts, C2C12 myoblasts, and P19 teratocarcinoma cells. In the fibroblasts, transgene expression was strongly downregulated in confluent cultures and was upregulated in growing or confluent cultures by phorbol ester. In contrast, no downregulation by confluency, nor upregulation by phorbol ester, was detected in C2C12 cells. In addition, while marked upregulation was detected in differentiating myotubes, transgene expression was downregulated when differentiating teratocarcinoma cells assumed a neuronal phenotype. These results demonstrate the existence of drastic differences in the regulation of transgene expression in different types of cell lines, indicating that when studying transgene function in cells that are not growing exponentially, viral promoter-driven expression should not be taken for granted.