An E. coli display method for characterization of peptide-sensor kinase interactions

Bacteria use two-component system (TCS) signaling pathways to sense and respond to peptides involved in host defense, quorum sensing and inter-bacterial warfare. However, little is known about the broad peptide-sensing capabilities of TCSs. In this study, we developed an Escherichia coli display method to characterize the effects of human antimicrobial peptides (AMPs) on the pathogenesis-regulating TCS PhoPQ of Salmonella Typhimurium with much higher throughput than previously possible. We found that PhoPQ senses AMPs with diverse sequences, structures and biological functions. We further combined thousands of displayed AMP variants with machine learning to identify peptide sub-domains and biophysical features linked to PhoPQ activation. Most of the newfound AMP activators induce PhoPQ in S. Typhimurium, suggesting possible roles in virulence regulation. Finally, we present evidence that PhoPQ peptide-sensing specificity has evolved across commensal and pathogenic bacteria. Our method enables new insights into the specificities, mechanisms and evolutionary dynamics of TCS-mediated peptide sensing in bacteria.

Guiding Ethical Principles in Engineering Biology Research

Engineering biology is being applied toward solving or mitigating some of the greatest challenges facing society. As with many other rapidly advancing technologies, the development of these powerful tools must be considered in the context of ethical uses for personal, societal, and/or environmental advancement. Researchers have a responsibility to consider the diverse outcomes that may result from the knowledge and innovation they contribute to the field. Together, we developed a Statement of Ethics in Engineering Biology Research to guide researchers as they incorporate the consideration of long-term ethical implications of their work into every phase of the research lifecycle. Herein, we present and contextualize this Statement of Ethics and its six guiding principles. Our goal is to facilitate ongoing reflection and collaboration among technical researchers, social scientists, policy makers, and other stakeholders to support best outcomes in engineering biology innovation and development.

Rewiring bacterial two-component systems by modular DNA-binding domain swapping

Two-component systems (TCSs) are the largest family of multi-step signal transduction pathways and valuable sensors for synthetic biology. However, most TCSs remain uncharacterized or difficult to harness for applications. Major challenges are that many TCS output promoters are unknown, subject to cross-regulation, or silent in heterologous hosts. Here, we demonstrate that the two largest families of response regulator DNA-binding domains can be interchanged with remarkable flexibility, enabling the corresponding TCSs to be rewired to synthetic output promoters. We exploit this plasticity to eliminate cross-regulation, un-silence a gram-negative TCS in a gram-positive host, and engineer a system with over 1,300-fold activation. Finally, we apply DNA-binding domain swapping to screen uncharacterized Shewanella oneidensis TCSs in Escherichia coli, leading to the discovery of a previously uncharacterized pH sensor. This work should accelerate fundamental TCS studies and enable the engineering of a large family of genetically encoded sensors with diverse applications.

Effects of nitrogen fertilization and dried distillers grains supplementation: nitrogen use efficiency

In a 3-yr study, 135 crossbred steers (330 ± 10 kg) were used in a randomized complete block design to evaluate corn dried distillers grains plus solubles (DDGS) fed to yearling steers as a substitute for forage and N fertilizer and its effect on N use efficiency in yearling steers grazing smooth bromegrass pastures. Steers were initially stocked at 6.8 animal unit months (AUM)/ha on nonfertilized smooth bromegrass pastures (CONT), at 9.9 AUM/ha on smooth bromegrass pastures fertilized with 90 kg of N/ha (FERT), or at 9.9 AUM/ha on nonfertilized smooth bromegrass pastures with 2.3 kg (DM) of DDGS supplemented daily per steer (SUPP). Paddock was the experimental unit, with 3 replications per treatment per year for 3 yr. Paddocks were strip-grazed, and put-and-take cattle were used to maintain similar grazing pressure among treatment paddocks during the 160-d grazing season. Steers consumed less forage (P < 0.01), but total N intake for SUPP was greater (P < 0.01) per steer and per hectare than for FERT, and both were greater (P < 0.01) than for CONT. Nitrogen retention for steers in the SUPP treatment was increased (P < 0.01) by 31% compared with N retention in the CONT and FERT treatments. Nitrogen retention per hectare for SUPP was 30 and 98% greater (P < 0.01) than N retention per hectare for FERT and CONT, respectively. Nitrogen excretion per steer and per hectare were also greater (P < 0.01) for SUPP than FERT, and both were increased (P < 0.01) compared with CONT. Animal N use efficiency was similar (P = 0.29) for steers in the CONT, FERT, and SUPP treatments. However, system-based N use improved (P < 0.01) by 144% for SUPP compared with FERT. The DDGS increased N intake and N excretion in yearling steers. However, because of improvements in BW gain and increases in stocking rate of pastures, DDGS can be a useful tool to increase the efficiency of N use in smooth bromegrass grazing systems.