Genetic analysis of 15 protein folding factors and proteases of the Escherichia coli cell envelope

Each cell hosts thousands of proteins that vary greatly in abundance, structure, and chemical properties. To ensure that all proteins are biologically active and properly localized, efficient quality control systems have evolved. While the structure, function, and regulation of some individual protein folding factors and proteases were resolved up to atomic resolution, others remain poorly characterized. In addition, little is known about which factors are required for viability under specific stress conditions. We therefore determined the physiological implications of 15 factors of the E. coli cell envelope by an integrated genetic approach comprising phenotypic analyses. Our data indicate that surA and tsp null mutations are a lethal combination in rich medium, that surA dsbA and surA dsbC double mutants are temperature sensitive, and that surA ptrA, surA yfgC, dsbA fkpA, degP tsp, degP ppiD, tsp ppiD, and degP dsbA double mutants are temperature sensitive in rich medium containing 0.5 M NaCl, while degP dsbA, degP yfgC, tsp ydgD, and degP tsp double mutants do not grow in the presence of SDS/EDTA. Furthermore, we show that in degP dsbA, degP tsp, and degP yfgC double mutants a subpopulation of LamB exists as unfolded monomers. In addition, dsbA null mutants expressed lower levels of the outer membrane proteins LptD, LamB, FhuA, and OmpW while FhuA levels were reduced in surA single and degP ppiD double mutants. Lower FhuA levels in degP ppiD strains depend on Tsp, since in a tsp degP ppiD triple mutant FhuA levels are restored.     

Detecting and investigating substrate cycles in a genome-scale human metabolic network

Substrate cycles, also known as futile cycles, are cyclic metabolic routes that dissipate energy by hydrolysing cofactors such as ATP. They were first described to occur in the muscles of bumblebees and brown adipose tissue in the 1970s. A popular example is the conversion of fructose?6-phosphate to fructose?1,6-bisphosphate and back. In the present study, we analyze a large number of substrate cycles in human metabolism that consume ATP and discuss their statistics. For this purpose, we use two recently published methods (i.e. EFMEvolver and the K-shortest EFM method) to calculate samples of 100?000 and 15?000 substrate cycles, respectively. We find an unexpectedly high number of substrate cycles in human metabolism, with up to 100 reactions per cycle, utilizing reactions from up to six different compartments. An analysis of tissue-specific models of liver and brain metabolism shows that there is selective pressure that acts against the uncontrolled dissipation of energy by avoiding the coexpression of enzymes belonging to the same substrate cycle. This selective force is particularly strong against futile cycles that have a high flux as a result of thermodynamic principles.     

Design of simple synthetic RNA thermometers for temperature-controlled gene expression in Escherichia coli

RNA thermometers are thermosensors that regulate gene expression by temperature-induced changes in RNA conformation. Naturally occurring RNA thermometers exhibit complex secondary structures which are believed to undergo a series of gradual structural changes in response to temperature shifts. Here, we report the de novo design of considerably simpler RNA thermometers that provide useful RNA-only tools to regulate bacterial gene expression by a shift in the growth temperature. We show that a single small stem-loop structure containing the ribosome binding site is sufficient to construct synthetic RNA thermometers that work efficiently at physiological temperatures. Our data suggest that the thermometers function by a simple melting mechanism and thus provide minimum size on/off switches to experimentally induce or repress gene expression by temperature.     

Regulatory RNAs in Haloferax volcanii

In organisms of all three domains of life, a plethora of sRNAs (small regulatory RNAs) exists in addition to the well-known RNAs such as rRNAs, tRNAs and mRNAs. Although sRNAs have been well studied in eukaryotes and in bacteria, the sRNA population in archaea has just recently been identified and only in a few archaeal species. In the present paper, we summarize our current knowledge about sRNAs and their function in the halophilic archaeon Haloferax volcanii. Using two different experimental approaches, 111 intergenic and 38 antisense sRNAs were identified, as well as 42 tRFs (tRNA-derived fragments). Observation of differential expression under various conditions suggests that these sRNAs might be active as regulators in gene expression like their bacterial and eukaryotic counterparts. The severe phenotypes observed upon deletion and overexpression of sRNA genes revealed that sRNAs are involved in, and important for, a variety of biological functions in H. volcanii and possibly other archaea. Investigation of the Haloferax Lsm protein suggests that this protein is involved in the archaeal sRNA pathway.     

An immunohistochemical study of structure and development of the nervous system in the brine shrimp Artemia salina Linnaeus, 1758 (Branchiopoda, Anostraca) with remarks on the evolution of the arthropod brain

Brain morphology is an important character in the discussion of arthropod relationships. While a large body of literature is available on the brains of Hexapoda and Malacostraca, the structure of the brain has been rarely studied in representatives of the Entomostraca. This account examines the morphology and development of the nervous system in the brine shrimp Artemia salina Linnaeus, 1758 (Crustacea, Branchiopoda, Anostraca) by classical histology and immunohistochemistry against synaptic proteins (synapsins), and the neurotransmitters serotonin and histamine. The results indicate that the shape of the developing larval brain in A. salina (a circumstomodeal ring of neuropil) closely resembles that in malacostracan embryos. Furthermore, the organization of the central complex as well as the tritocerebral innervation pattern of the labrum is homologous in this species and in Malacostraca. Nevertheless, differences exist in the layout of the deutocerebrum, specifically in the absence of olfactory glomeruli in A. salina while the glomerular organization of the olfactory lobe is a character in the ground pattern of Malacostraca. These findings are compared to the brain structure in other Euarthropoda and possible phylogenetic implications are discussed.     

Automatic image recognition to determine morphological development and secondary metabolite accumulation in hairy root networks

This study focuses on the morphological development and secondary metabolite production of the red pigments from the group of betacyanins in hairy roots of Beta vulgaris. We demonstrate a working, medium throughput, customized, automatic image recognition solution for hairy roots on agar plates including the evaluation of 12 experimental samples. Image acquisition is conducted under comparable para‐meters using a tripod with light emitting diode background lighting and a digital single lens reflex camera. The server‐based image recognition system developed together with Wimasis GmbH, Munich, Germany helps to obtain not only quantitative values for morphological parameters, such as segment lengths and widths or metabolite concentrations, but also global parameters of root growth, such as total root length or the number of branching points. Using timed diagrams the development of the total root length, the total number of branching points, and the mean pigment concentration during the cultivation period were determined. The generated data present the basis for detailed mathematical modeling in order to achieve a structured growth model for hairy roots. A mathematical model for growth of hairy roots can be used to decrease experimental efforts as well as to optimize cultivation conditions and the bioreactor design.