A cell-free transcription-translation pipeline for recreating methylation patterns boosts DNA transformation in bacteria.

The bacterial world offers diverse strains for understanding medical and environmental processes and for engineering synthetic biological chassis. However, genetically manipulating these strains has faced a long-standing bottleneck: how to efficiently transform DNA. Here, we report imitating methylation patterns rapidly in TXTL (IMPRINT), a generalized, rapid, and scalable approach based on cell-free transcription-translation (TXTL) to overcome DNA restriction, a prominent barrier to transformation. IMPRINT utilizes TXTL to express DNA methyltransferases from a bacterium's restriction-modification systems. The expressed methyltransferases then methylate DNA in vitro to match the bacterium's DNA methylation pattern, circumventing restriction and enhancing transformation. With IMPRINT, we efficiently multiplex methylation by diverse DNA methyltransferases and enhance plasmid transformation in gram-negative and gram-positive bacteria. We also develop a high-throughput pipeline that identifies the most consequential methyltransferases, and we apply IMPRINT to screen a ribosome-binding site library in a hard-to-transform Bifidobacterium. Overall, IMPRINT can enhance DNA transformation, enabling the use of sophisticated genetic manipulation tools across the bacterial world.

Characterization of Cas12a nucleases reveals diverse PAM profiles between closely-related orthologs.

CRISPR-Cas systems comprise diverse adaptive immune systems in prokaryotes whose RNA-directed nucleases have been co-opted for various technologies. Recent efforts have focused on expanding the number of known CRISPR-Cas subtypes to identify nucleases with novel properties. However, the functional diversity of nucleases within each subtype remains poorly explored. Here, we used cell-free transcription-translation systems and human cells to characterize six Cas12a single-effector nucleases from the V-A subtype, including nucleases sharing high sequence identity. While these nucleases readily utilized each other's guide RNAs, they exhibited distinct PAM profiles and apparent targeting activities that did not track based on phylogeny. In particular, two Cas12a nucleases encoded by Prevotella ihumii (PiCas12a) and Prevotella disiens (PdCas12a) shared over 95% amino-acid identity yet recognized distinct PAM profiles, with PiCas12a but not PdCas12a accommodating multiple G's in PAM positions -2 through -4 and T in position -1. Mutational analyses transitioning PiCas12a to PdCas12a resulted in PAM profiles distinct from either nuclease, allowing more flexible editing in human cells. Cas12a nucleases therefore can exhibit widely varying properties between otherwise related orthologs, suggesting selective pressure to diversify PAM recognition and supporting expansion of the CRISPR toolbox through ortholog mining and PAM engineering.

Modular one-pot assembly of CRISPR arrays enables library generation and reveals factors influencing crRNA biogenesis.

CRISPR-Cas systems inherently multiplex through CRISPR arrays-whether to defend against different invaders or mediate multi-target editing, regulation, imaging, or sensing. However, arrays remain difficult to generate due to their reoccurring repeat sequences. Here, we report a modular, one-pot scheme called CRATES to construct CRISPR arrays and array libraries. CRATES allows assembly of repeat-spacer subunits using defined assembly junctions within the trimmed portion of spacers. Using CRATES, we construct arrays for the single-effector nucleases Cas9, Cas12a, and Cas13a that mediated multiplexed DNA/RNA cleavage and gene regulation in cell-free systems, bacteria, and yeast. CRATES further allows the one-pot construction of array libraries and composite arrays utilized by multiple Cas nucleases. Finally, array characterization reveals processing of extraneous CRISPR RNAs from Cas12a terminal repeats and sequence- and context-dependent loss of RNA-directed nuclease activity via global RNA structure formation. CRATES thus can facilitate diverse multiplexing applications and help identify factors impacting crRNA biogenesis.

Mucins and Their Sugars. Critical Mediators of Hyperreactivity and Inflammation.

Excessive mucus causes severe airflow obstruction in fatal asthma. It is also present in mild to moderate disease, but is poorly understood and treated. Mucus overproduction is associated with dysregulated expression of the mucins MUC5AC and MUC5B. Whereas increased MUC5AC is a consistent finding, MUC5B varies-remaining stably produced in some patients but strongly repressed in others (>90%). Patients with lower MUC5B display worsened asthma phenotypes including airway hyperreactivity (AHR) to methacholine (MCh) and eosinophilic inflammation. To better understand the roles of mucins in asthma, we generated Muc5ac and Muc5b knockout ((-/-)) mice. AHR to MCh was abolished in antigen-challenged Muc5ac(-/-) mice, due to prevention of heterogeneous mucous plugging that occurred in allergic wild-type mice during MCh-induced bronchoconstriction. Thus, in addition to the established role of smooth muscle-mediated airway narrowing, Muc5ac is an essential noncontractile AHR component. We also found that, unlike Muc5ac(-/-) mice, Muc5b-deficient mice were not protected from asthma phenotypes. Furthermore, whereas inflammation was unaffected by Muc5ac deficiency, it was exaggerated in the absence of Muc5b. On the basis of these differential effects, we are now determining how asthma phenotypes are regulated by mucin isoform specificity. Glycosylation is dramatically different: Muc5ac is heavily fucosylated whereas Muc5b is mainly sialylated. Fucosylation increases mucus viscoelasticity, and FUT2, the enzyme that catalyzes mucin α1,2-fucosylation, is associated with severe asthma exacerbation risk. Sialylation is required for binding to siglec (sialic acid-binding immunoglobulin-like lectin) receptors on leukocytes. Eosinophils express Siglec-F (mouse) or Siglec-8 (human). Engagement by sialoside ligands induces eosinophil apoptosis, and Muc5b via sialylated termini that require the α2,3-sialyltransferase ST3Gal3 for synthesis binds Siglec-F and induces apoptosis in mouse eosinophils. Because Muc5b is required for host defense in mouse lungs, inhibiting MUC5AC while preserving or enhancing MUC5B functions may be effective for treating asthma.

The polymeric mucin Muc5ac is required for allergic airway hyperreactivity.

In asthma, airflow obstruction is thought to result primarily from inflammation-triggered airway smooth muscle (ASM) contraction. However, anti-inflammatory and smooth muscle-relaxing treatments are often temporary or ineffective. Overproduction of the mucin MUC5AC is an additional disease feature that, while strongly associated pathologically, is poorly understood functionally. Here we show that Muc5ac is a central effector of allergic inflammation that is required for airway hyperreactivity (AHR) to methacholine (MCh). In mice bred on two well-characterized strain backgrounds (C57BL/6 and BALB/c) and exposed to two separate allergic stimuli (ovalbumin and Aspergillus extract), genetic removal of Muc5ac abolishes AHR. Residual MCh responses are identical to unchallenged controls, and although inflammation remains intact, heterogeneous mucous occlusion decreases by 74%. Thus, whereas inflammatory effects on ASM alone are insufficient for AHR, Muc5ac-mediated plugging is an essential mechanism. Inhibiting MUC5AC may be effective for treating asthma and other lung diseases where it is also overproduced.