The yaq project: Standardized software enabling flexible instrumentation.

Modern instrumentation development often involves the incorporation of many dissimilar hardware peripherals into a single unified instrument. The increasing availability of modular hardware has brought greater instrument complexity to small research groups. This complexity stretches the capability of traditional, monolithic orchestration software. In many cases, a lack of software flexibility leads creative researchers to feel frustrated, unable to perform experiments they envision. Herein, we describe Yet Another acQuisition (yaq), a software project defining a new standardized way of communicating with diverse hardware peripherals. yaq encourages a highly modular approach to experimental software development that is well suited to address the experimental flexibility needs of complex instruments. yaq is designed to overcome hardware communication barriers that challenge typical experimental software. A large number of hardware peripherals are already supported, with tooling available to expand support. The yaq standard enables collaboration among multiple research groups, increasing code quality while lowering development effort.

Engineered Chimeras Unveil Swappable Modular Features of Fatty Acid and Polyketide Synthase Acyl Carrier Proteins.

The strategic redesign of microbial biosynthetic pathways is a compelling route to access molecules of diverse structure and function in a potentially environmentally sustainable fashion. The promise of this approach hinges on an improved understanding of acyl carrier proteins (ACPs), which serve as central hubs in biosynthetic pathways. These small, flexible proteins mediate the transport of molecular building blocks and intermediates to enzymatic partners that extend and tailor the growing natural products. Past combinatorial biosynthesis efforts have failed due to incompatible ACP-enzyme pairings. Herein, we report the design of chimeric ACPs with features of the actinorhodin polyketide synthase ACP (ACT) and of the Escherichia coli fatty acid synthase (FAS) ACP (AcpP). We evaluate the ability of the chimeric ACPs to interact with the E. coli FAS ketosynthase FabF, which represents an interaction essential to building the carbon backbone of the synthase molecular output. Given that AcpP interacts with FabF but ACT does not, we sought to exchange modular features of ACT with AcpP to confer functionality with FabF. The interactions of chimeric ACPs with FabF were interrogated using sedimentation velocity experiments, surface plasmon resonance analyses, mechanism-based cross-linking assays, and molecular dynamics simulations. Results suggest that the residues guiding AcpP-FabF compatibility and ACT-FabF incompatibility may reside in the loop I, α-helix II region. These findings can inform the development of strategic secondary element swaps that expand the enzyme compatibility of ACPs across systems and therefore represent a critical step toward the strategic engineering of "un-natural" natural products.