Bacterial Antagonists of Aspergillus flavus

In order to search for bacteria capable of reducing the aflatoxin contamination of cottonseed, 892 indigenous bacterial isolates, including 11 that were endophytic to cotton, were screened for their ability to inhibit the growth of Aspergillus flavus on cottonseed in an in vitro bioassay. Only six isolates partially or totally inhibited fungal growth. All antagonistic isolates were recovered from boll, lint or seed surface or from the lint of mature bolls. One was retrieved from mature seeds. None of the endophytic isolates showed activity. In four field trials, the incidence of A. flavus -induced damage to locules inoculated simulteously with A. flavus plus the most A. flavus plus the most effective antagonistic isolate (D1) was reduced by 41-100% relative to locules inoculated with A. flavus alone. The severity of damage to locules inoculated simultaneously with A. flavus and with D1 was reduced by 60-l00% relative to locules inoculated with A. flavus alone. Isolate D1, identified as Pseudomonas cepacia, completely inhibited the growth of A. flavus on synthetic media.     

Tailoring translational strength using Kozak sequence variants improves bispecific antibody assembly and reduces product-related impurities in CHO cells

Optimal production of bispecific antibodies (bsAb) requires efficient and tailored co-expression and assembly of two distinct heavy and two distinct light chains. Here, we describe a novel technology to modulate the translational strength of antibody chains via Kozak sequence variants to produce bsAb in a single cell line. In this study, we designed and screened a large Kozak sequence library to identify 10 independent variants that can modulate protein expression levels from approximately 0.2 to 1.3-fold compared with the wild-type sequence in transient transfection. We used a combination of several of these variants, covering a wide range of translational strength, to develop stable single cell Chinese hamster ovary bispecific cell lines and compared the results with those obtained from the wild-type sequence. A significant increase in bispecific antibody assembly with a concomitant reduction in the level of product-related impurities was observed. Our findings suggest that for production of bsAb it can be advantageous to modify translational strength for selected protein chains to improve overall yield and product quality. By extension, tuning of translational strength can also be applied to improving the production of a wide variety of heterologous proteins.     

Utilizing a regulated targeted integration cell line development approach to systematically investigate what makes an antibody difficult to express

Chinese hamster ovary (CHO) cells are conventionally used to generate therapeutic cell lines via random integration (RI), where desired transgenes are stably integrated into the genome. Targeted integration (TI) approaches, which involve integration of a transgene into a specific locus in the genome, are increasingly utilized for CHO cell line development (CLD) in recent years. None of these CLD approaches, however, are suitable for expression of toxic or difficult-to-express molecules, or for determining the underlying causes for poor expression of some molecules. Here we introduce a regulated target integration (RTI) system, where the desired transgene is integrated into a specific locus and transcribed under a regulated promoter. This system was used to determine the underlying causes of low protein expression for a difficult-to-express antibody (mAb-A). Interestingly, we observed that both antibody heavy chain (HC) and light chain (LC) subunits of mAb-A independently contributed to its low expression. Analysis of RTI cell lines also revealed that while mAb-A LC triggered accumulation of intracellular BiP, its HC displayed impaired degradation and clearance. RTI pools, generated by swapping the WT or point-mutant versions of difficult-to-express antibody HC and LC with that of an average antibody, were instrumental in understanding the contribution of HC and LC subunits to the overall antibody expression. The ability to selectively turn off the expression of a target transgene in an RTI system could help to directly link expression of a transgene to an observed adverse effect. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2772, 2019.     

Structure of the ubiquitin hydrolase UCH-L3 complexed with a suicide substrate

Ubiquitin C-terminal hydrolases (UCHs) comprise a family of small ubiquitin-specific proteases of uncertain function. Although no cellular substrates have been identified for UCHs, their highly tissue-specific expression patterns and the association of UCH-L1 mutations with human disease strongly suggest a critical role. The structure of the yeast UCH Yuh1-ubiquitin aldehyde complex identified an active site crossover loop predicted to limit the size of suitable substrates. We report the 1.45 A resolution crystal structure of human UCH-L3 in complex with the inhibitor ubiquitin vinylmethylester, an inhibitor that forms a covalent adduct with the active site cysteine of ubiquitin-specific proteases. This structure confirms the predicted mechanism of the inhibitor and allows the direct comparison of a UCH family enzyme in the free and ligand-bound state. We also show the efficient hydrolysis by human UCH-L3 of a 13-residue peptide in isopeptide linkage with ubiquitin, consistent with considerable flexibility in UCH substrate size. We propose a model for the catalytic cycle of UCH family members which accounts for the hydrolysis of larger ubiquitin conjugates.     

Responses of guayule (Parthenium argentatum) seedlings to plant growth promoting fluorescent pseudomonads

Summary The potential of a number of fluorescent pseudomonad strains to promote growth of guayule plants in the greenhouse and in the field was studied. A number of bacterial strains collected from guayule roots and rhizospheres promoted growth of greenhouse-grown plants but not field-grown plants. Percent increase in shoot dry weight of 12-week-old, greenhouseinoculated guayule plants ranged from 17 to 75 nine weeks after inoculation compared to non-inoculated plants. The increased growth of plants in the greenhouse could reduce production cost by shortening the time required to maintain plants in the nursery prior to transplanting to the field.Journal Series Article no 3816 of the Arizona Agricultural Experiment Station.     

NLRP3/Cryopyrin Is Necessary for Interleukin-1�� (IL-1��) Release in Response to Hyaluronan, an Endogenous Trigger of Inflammation in Response to Injury

Inflammation under sterile conditions is a key event in autoimmunity and following trauma. Hyaluronan, a glycosaminoglycan released from the extracellular matrix after injury, acts as an endogenous signal of trauma and can trigger chemokine release in injured tissue. Here, we investigated whether NLRP3/cryopyrin, a component of the inflammasome, participates in the inflammatory response to injury or the cytokine response to hyaluronan. Mice with a targeted deletion in cryopyrin showed a normal increase in Cxcl2 in response to sterile injuries but had decreased inflammation and release of interleukin-1β (IL-1β). Similarly, the addition of hyaluronan to macrophages derived from cryopyrin-deficient mice increased release of Cxcl2 but did not increase IL-1β release. To define the mechanism of hyaluronan-mediated activation of cryopyrin, elements of the hyaluronan recognition process were studied in detail. IL-1β release was inhibited in peritoneal macrophages derived from CD44-deficient mice, in an MH-S macrophage cell line treated with antibodies to CD44, or by inhibitors of lysosome function. The requirement for CD44 binding and hyaluronan internalization could be bypassed by intracellular administration of hyaluronan oligosaccharides (10–18-mer) in lipopolysaccharide-primed macrophages. Therefore, the action of CD44 and subsequent hyaluronan catabolism trigger the intracellular cryopyrin → IL-1β pathway. These findings support the hypothesis that hyaluronan works through IL-1β and the cryopyrin system to signal sterile inflammation.Inflammation, as defined by changes in vascular permeability and leukocyte recruitment, is an essential step for the control of microbial invasion. Specific microbial products trigger this process through a diverse array of innate immune pattern recognition receptors. However, an inflammatory response independent of infection is also an important process for maintenance of biological homeostasis. For example, normal wound healing requires a controlled inflammatory response to enable the recruitment of monocytes and the release of growth factors required for repair. This response can occur in the absence of microbial stimuli. Furthermore, inflammation and the release of proinflammatory mediators is also associated with many diseases such as rheumatoid arthritis and Crohn disease (1). These diseases are not well understood in terms of their triggers but rather are described by the subsequent release of proinflammatory mediators. Identification of the triggers of sterile inflammation represents an important goal with immediate diagnostic and therapeutic significance.Recent work has begun to elucidate pathways of inflammation that occur in the absence of microbial stimuli. Stress signals such as heat-shock proteins, intracellular components of necrotic cells not normally seen by immune cells, and components of the extracellular matrix have all been implicated as endogenous triggers of injury (2–4). Among this group is the glycosaminoglycan hyaluronan (HA),⁶ an important structural component of the extracellular matrix that is also a common component of bacterial surfaces. HA is synthesized at the cell surface and typically exists as a high molecular mass polymer greater than 10⁶ Da and composed of repeating disaccharide units of N-acetylglucosamine and glucuronic acid (5, 6). Unlike other glycosaminoglycans such as heparan sulfate or chondroitin sulfates that encode specific activity by use of a diverse disaccharide sequence, HA is not sulfated or epimerized, and only changes in HA size, concentration, and location affect function.We have previously developed murine models of sterile injury to identify the innate elements that recognize and mediate sterile inflammation (7). Our results demonstrated that (a) the initiation of a sterile intrinsic inflammatory process is dependent on TLR4 activation, (b) sterile injury induces HA accumulation at the injured site, and (c) sterile intrinsic inflammation resembles signaling events that are activated by HA. Furthermore, we have defined a novel alternative recognition complex for HA that involves TLR4, MD-2, and CD44 (7). Taken together with other work associating HA and innate pattern recognition (4, 8–10), these observations have provided new insight into mechanisms responsible for sterile inflammation.Recently, the NLR (nucleotide-binding domain and leucine rich repeat-containing) family has been extensively analyzed as a group of intracellular pattern recognition receptors (11). NLRs have a leucine-rich repeat that recognizes pathogen-associated molecular patterns including bacterial cell wall components and viral nucleic acids. NOD2 and NLR family, pyrin containing 3 (NLRP3)/cryopyrin are two of the best characterized NLRs. NOD2 recognizes the bacterial peptidoglycan-derived molecule muramyl dipeptide and activates the NF-κB pathway to induce inflammatory responses (12). Mutations of the NOD2 gene were identified in individuals with chronic inflammatory disorders such as Crohn disease (13, 14) and Blau syndrome (15). Mouse knockin mutants of NOD2, which have the same mutation in NOD2 as human patients with Crohn disease, showed elevated proinflammatory cytokines following muramyl dipeptide challenge or dextran sodium sulfate-induced bowel inflammation (16). NLRP3, also known as cyropyrin, CIAS1, NALP3, PYPAF1, forms an “inflammasome” with ASC (apoptosis-associated speck-like protein containing a CARD) and caspase-1 to convert pro-IL-1β to active IL-1β (17). Mutations in NLRP3 were identified in individuals with familial cold autoinflammatory syndrome (FCAS), Muckle-Wells syndrome, and neonatal onset multisystem inflammatory disease (18–20). These individuals have recurrent or chronic inflammatory symptoms, including fever, arthritis, and a urticaria-like eruption characterized by neutrophilic infiltration. In FCAS, symptoms can be elicited by cold provocation by a mechanism that appears to be mediated through the skin (15, 21).Because disorders associated with mutations in NLRP3 are examples of inflammation under sterile conditions and HA has been shown to be a trigger of sterile inflammation, we sought to further understand the mechanism of the response to HA by examining the role of cryopyrin during injury and after exposure to HA. Our results show that cryopyrin and IL-1β are integral to sterile inflammation and the response to HA. These observations provide new insight into the function of HA as a “danger signal” of injury.     

Chlamydia trachomatis-derived deubiquitinating enzymes in mammalian cells during infection

Chlamydia trachomatis is an obligate intracellular bacterium that causes a variety of diseases in humans. C. trachomatis has a complex developmental cycle that depends on host cells for replication, during which gene expression is tightly regulated. Here we identify two C. trachomatis proteases that possess deubiquitinating and deneddylating activities. We have designated these proteins ChlaDub1 and ChlaDub2. The genes encoding ChlaDub1 and ChlaDub2 are present in all Chlamydia species except for Chlamydia pneumoniae, and their catalytic domains bear similarity to the catalytic domains of other eukaryotic ubiquitin-like proteases (Ulp). The C. trachomatis DUBs react with activity-based probes and hydrolyse ubiquitinated and neddylated substrates. ChlaDub1 and ChlaDub2 represent the first known bacterial DUBs that possess both deubiquitinating and deneddylating activities.