Protein re-surfacing of E. coli L-Asparaginase to evade pre-existing anti-drug antibodies and hypersensitivity responses.

The optimal use of many biotherapeutics is restricted by Anti-drug antibodies (ADAs) and hypersensitivity responses which can affect potency and ability to administer a treatment. Here we demonstrate that Re-surfacing can be utilized as a generalizable approach to engineer proteins with extensive surface residue modifications in order to avoid binding by pre-existing ADAs. This technique was applied to E. coli Asparaginase (ASN) to produce functional mutants with up to 58 substitutions resulting in direct modification of 35% of surface residues. Re-surfaced ASNs exhibited significantly reduced binding to murine, rabbit and human polyclonal ADAs, with a negative correlation observed between binding and mutational distance from the native protein. Reductions in ADA binding correlated with diminished hypersensitivity responses in an in vivo mouse model. By using computational design approaches to traverse extended distances in mutational space while maintaining function, protein Re-surfacing may provide a means to generate novel or second line therapies for life-saving drugs with limited therapeutic alternatives.

Ocean acidification impacts sperm swimming performance and pHi in the New Zealand sea urchin Evechinus chloroticus.

In sea urchins, spermatozoa are stored in the gonads in hypercapnic conditions (pH<7.0). During spawning, sperm are diluted in seawater of pH>8.0, and there is an alkalinization of the sperm's internal pH (pHi) through the release of CO2 and H+. Previous research has shown that when pHi is above 7.2-7.3, the dynein ATPase flagellar motors are activated, and the sperm become motile. It has been hypothesized that ocean acidification (OA), which decreases the pH of seawater, may have a narcotic effect on sea urchin sperm by impairing the ability to regulate pHi, resulting in decreased motility and swimming speed. Here, we used data collected from the same individuals to test the relationship between pHi and sperm motility/performance in the New Zealand sea urchin Evechinus chloroticus under near-future (2100) and far-future (2150) atmospheric PCO2 conditions (RCP 8.5: pH 7.77, 7.51). Decreasing seawater pH significantly negatively impacted the proportion of motile sperm, and four of the six computer-assisted sperm analysis (CASA) sperm performance measures. In control conditions, sperm had an activated pHi of 7.52. Evechinus chloroticus sperm could not defend pHi in future OA conditions; there was a stepped decrease in the pHi at pH 7.77, with no significant difference in mean pHi between pH 7.77 and 7.51. Paired measurements in the same males showed a positive relationship between pHi and sperm motility, but with a significant difference in the response between males. Differences in motility and sperm performance in OA conditions may impact fertilization success in a future ocean.

Repeated measurement of Mo2 in small aquatic organisms: a manual intermittent flow respirometer using off-the-shelf components.

Measurement of rates of oxygen consumption ( Mo2) in small aquatic embryos or larvae (<1 mm) in response to altered environmental conditions has traditionally been challenging. Here, using modifications of a commercially available fluorescent optode flow-through cell (FTC; PreSens FTC-PSt3) and routine laboratory supplies (syringes, stopcocks, tubing), we have constructed a manual intermittent flow respirometer (MIFR) that allows measurement of Mo2 in small numbers of individuals when sequentially exposed to different environmental conditions (e.g., changes in seawater pH) through a gravity-driven media replacement perfusion system. We first show that the FTC can be used in "static" mode while incubating small numbers of embryos/larvae contained within the planar oxygen sensor (POS) chamber with Nitex filters. We then demonstrate the use of the MIFR by exposing larval echinoderms ( Fellaster zelandiae, Evechinus chloroticus, and Centrostephanus rodgersii) to seawater equilibrated with elevated CO2 and measured Mo2 during acute and chronic exposure to hypercapnia. This MIFR method will allow investigators to address questions regarding the respiratory physiology of small aquatic animals, such as the thresholds for metabolic depression in embryonic and larval forms. NEW & NOTEWORTHY A manual intermittent flow respirometer (MIFR), allowing media exchange in a flow-through cell containing small aquatic organisms, permits repeated measurement of Mo2 of individuals not only in a single medium (e.g., technical replication), but also in different media (here, high CO2-equilibrated seawater), enabling measurement of acute physiological responses to changed conditions. This versatile technique has wide-ranging implications for the study of the Mo2 response of aquatic organisms in the face of climate change.

High-quality binary protein interaction map of the yeast interactome network.

Current yeast interactome network maps contain several hundred molecular complexes with limited and somewhat controversial representation of direct binary interactions. We carried out a comparative quality assessment of current yeast interactome data sets, demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information. Because a large fraction of the yeast binary interactome remains to be mapped, we developed an empirically controlled mapping framework to produce a "second-generation" high-quality, high-throughput Y2H data set covering approximately 20% of all yeast binary interactions. Both Y2H and affinity purification followed by mass spectrometry (AP/MS) data are of equally high quality but of a fundamentally different and complementary nature, resulting in networks with different topological and biological properties. Compared to co-complex interactome models, this binary map is enriched for transient signaling interactions and intercomplex connections with a highly significant clustering between essential proteins. Rather than correlating with essentiality, protein connectivity correlates with genetic pleiotropy.

Identification of differentially expressed proteins in ovarian cancer using high-density protein microarrays.

Ovarian cancer is a leading cause of deaths, yet many aspects of the biology of the disease and a routine means of its detection are lacking. We have used protein microarrays and autoantibodies from cancer patients to identify proteins that are aberrantly expressed in ovarian tissue. Sera from 30 cancer patients and 30 healthy individuals were used to probe microarrays containing 5,005 human proteins. Ninety-four antigens were identified that exhibited enhanced reactivity from sera in cancer patients relative to control sera. The differential reactivity of four antigens was tested by using immunoblot analysis and tissue microarrays. Lamin A/C, SSRP1, and RALBP1 were found to exhibit increased expression in the cancer tissue relative to controls. The combined signals from multiple antigens proved to be a robust test to identify cancerous ovarian tissue. These antigens were also reactive with tissue from other types of cancer and thus are not specific to ovarian cancer. Overall our studies identified candidate tissue marker proteins for ovarian cancer and demonstrate that protein microarrays provide a powerful approach to identify proteins aberrantly expressed in disease states.

High-throughput methods of regulatory element discovery.

With the number of organisms whose genomes have been sequenced, a vast amount of information concerning the genetic structure of an organism's genome has been collected. However, effective experiment means to study how this information is accessed have only recently been developed. In this review, three basic methods for identifying regions of protein-DNA interaction will be introduced. The first two, chromatin immunoprecipitation (ChIP)-chip and ChIP-PET (for paired-end ditag), rely on the enrichment provided by chromosomal immunoprecipitation to interrogate the genomic sequence for the interaction sites of a protein of interest. In contrast, protein microarrays allow the identification of DNA binding protein that interacts with a DNA sequence of interest. These complementary methods of exploring protein-DNA interactions will increase our fundamental knowledge of how the information contained within the genome sequence is accessed and processed.

The SapB morphogen is a lantibiotic-like peptide derived from the product of the developmental gene ramS in Streptomyces coelicolor.

SapB is a morphogenetic peptide that is important for aerial mycelium formation by the filamentous bacterium Streptomyces coelicolor. Production of SapB commences during aerial mycelium formation and depends on most of the genes known to be required for the morphogenesis of aerial hyphae. Furthermore, the application of purified SapB to mutants blocked in morphogenesis restores their capacity to form aerial hyphae. Here, we present evidence that SapB is a lantibiotic-like peptide that is derived by posttranslational modification from the product of a gene (ramS) in the four-gene ram operon, which is under the control of the regulatory gene ramR. We show that the product of another gene in the operon (ramC) contains a region that is similar to enzymes involved in the biosynthesis of lantibiotics, suggesting that it might be involved in the posttranslational processing of RamS. We conclude that SapB is derived from RamS through proteolytic cleavage and the introduction of four dehydroalanine residues and two lanthionine bridges. We provide an example of a morphogenetic role for an antibiotic-like molecule.

Dimerization of the RamC morphogenetic protein of Streptomyces coelicolor.

RamC is required for the formation of spore-forming cells called aerial hyphae by the bacterium Streptomyces coelicolor. This protein is membrane associated and has an amino-terminal protein kinase-like domain, but little is known about its mechanism of action. In this study we found that the presence of multiple copies of a defective allele of ramC inhibits morphogenesis in S. coelicolor, consistent with either titration of a target or formation of inactive RamC multimers. We identified a domain in RamC that is C terminal to the putative kinase domain and forms a dimer with a K(d) of approximately 0.1 micro M. These data suggest that RamC acts as a dimer in vivo.

Membrane association and kinase-like motifs of the RamC protein of Streptomyces coelicolor.

The protein RamC is required for the production of the spore-forming cells called aerial hyphae by the filamentous bacterium Streptomyces coelicolor. We showed that RamC, which contains several weakly predicted membrane-spanning sequences, is located exclusively in the S. coelicolor membrane. By constructing site-directed mutants in the cloned ramC gene and complementing a ramC null mutant, we showed that protein kinase-like sequence motifs in the amino-terminal half of the protein are required for function in vivo. These data suggest that RamC is a membrane-associated receptor kinase.