The second messenger cyclic diguanylate (c-di-GMP) controls diverse cellular processes among bacteria. Diguanylate cyclases synthesize c-di-GMP, whereas it is degraded by c-di-GMP–specific phosphodiesterases (PDEs). Nearly 80% of these PDEs are predicted to depend on the catalytic function of glutamate-alanine-leucine (EAL) domains, which hydrolyze a single phosphodiester group in c-di-GMP to produce 5ʹ-phosphoguanylyl-(3ʹ,5ʹ)-guanosine (pGpG). However, to degrade pGpG and prevent its accumulation, bacterial cells require an additional nuclease, the identity of which remains unknown. Here we identify oligoribonuclease (Orn)—a 3ʹ→5ʹ exonuclease highly conserved among Actinobacteria, Beta-, Delta- and Gammaproteobacteria—as the primary enzyme responsible for pGpG degradation in Pseudomonas aeruginosa cells. We found that a P. aeruginosa Δorn mutant had high intracellular c-di-GMP levels, causing this strain to overexpress extracellular polymers and overproduce biofilm. Although recombinant Orn degraded small RNAs in vitro, this enzyme had a proclivity for degrading RNA oligomers comprised of two to five nucleotides (nanoRNAs), including pGpG. Corresponding with this activity, Δorn cells possessed highly elevated pGpG levels. We found that pGpG reduced the rate of c-di-GMP degradation in cell lysates and inhibited the activity of EAL-dependent PDEs (PA2133, PvrR, and purified recombinant RocR) from P. aeruginosa. This pGpG-dependent inhibition was alleviated by the addition of Orn. These data suggest that elevated levels of pGpG exert product inhibition on EAL-dependent PDEs, thereby increasing intracellular c-di-GMP in Δorn cells. Thus, we propose that Orn provides homeostatic control of intracellular pGpG under native physiological conditions and that this activity is fundamental to c-di-GMP signal transduction.

Protein post-translational modifications mediate dynamic cellular processes with broad implications in human disease pathogenesis. There is a large demand for highthroughput technologies supporting post-translational modifications research, and both mass spectrometry and protein arrays have been successfully utilized for this purpose. Protein arrays override the major limitation of target protein abundance inherently associated with MS analysis. This technology, however, is typically restricted to pre-purified proteins spotted in a fixed composition on chips with limited life-time and functionality. In addition, the chips are expensive and designed for a single use, making complex experiments cost-prohibitive. Combining microfluidics with in situ protein expression from a cDNA microarray addressed these limitations. Based on this approach, we introduce a modular integrated microfluidic platform for multiple post-translational modifications analysis of freshly synthesized protein arrays (IMPA). The system's potency, specificity and flexibility are demonstrated for tyrosine phosphorylation and ubiquitination in quasicellular environments. Unlimited by design and protein composition, and relying on minute amounts of biological material and cost-effective technology, this unique approach is applicable for a broad range of basic, biomedical and biomarker research. Molecular

We uncovered interlocking mechanisms regulating the temporal proteolysis of the transcriptional repressor E2F8 in cycling cells including SCFCyclin F in G2, dephosphorylation of Cdk1 sites, and activation of APC/CCdh1, but not APC/CCdc20 during mitotic exit and G1. Differential stabilization under limited APC/C activity allows E2F8 to reaccumulate during late G1 and coregulate S-phase entry.

Autophosphorylation of receptor and non-receptor tyrosine kinases is a common molecular switch with broad implications for pathogeneses and therapy of cancer and other human diseases. Technologies for large-scale discovery and analysis of autophosphorylation are limited by the inherent difficulty to distinguish between phosphorylation and autophosphorylation in vivo and by the complexity associated with functional assays of receptors kinases in vitro. Here, we report a method for the direct detection and analysis of tyrosine autophosphorylation using integrated microfluidics and freshly synthesized protein arrays. We demonstrate the efficacy of our platform in detecting autophosphorylation activity of soluble and transmembrane tyrosine kinases, and the dependency of in vitro autophosphorylation assays on membranes. Our method, Integrated Microfluidics for Autophosphorylation Discovery (IMAD), is high-throughput, requires low reaction volumes and can be applied in basic and translational research settings. To our knowledge, it is the first demonstration of posttranslational modification analysis of membrane protein arrays.

19E2F8 is a transcriptional repressor that antagonizes the canonical cell cycle 20 transcription factor E2F1. Despite the importance of this atypical E2F family member in cell 21 cycle, apoptosis and cancer, we lack a complete description of the mechanisms that control 22 its dynamics. To address this question, we developed a complementary set of static and 23 dynamic cell-free systems of human origin, which recapitulate inter-mitotic and G1 phases, 24 and a full transition from pro-metaphase to G1. This revealed an interlocking molecular 25 switch controlling E2F8 degradation at mitotic exit, involving dephosphorylation of Cdk1 26 sites in E2F8 and the activation of APC/C Cdh1 , but not APC/C Cdc20 . Further, we revealed a 27 differential stability of E2F8, accounting for its accumulation in late G1 while APC/C Cdh1 is 28 still active and suggesting a key role for APC/C in controlling G1-S transcription. Finally, we 29 identified SCF-Cyclin F as the ubiquitin ligase controlling E2F8 in G2-phase. Altogether, our 30 data provide new insights into the regulation of E2F8 throughout the cell cycle, illuminating 31 an extensive coordination between phosphorylation, ubiquitination and transcription in 32 promoting orderly cell cycle progression. 33 34 35 36 37 38 39 40 41 42 Ran et al., 2008, Ouseph, Li et al., 2012). Despite being part of the 'repressive' branch of E2F 57proteins, E2F7 and E2F8 belong to the pro-proliferative gene network underlying cell 58 proliferation (Cohen, Vecsler et al., 2013). 59 E2F1, as well as E2F7 and E2F8, are regulated post-translationally via temporal 60 proteolysis. The anaphase-promoting complex/cyclosome (APC/C) is a multi-subunit cell 61 cycle ubiquitin ligase and core component of the cell cycle machinery (King, Peters et al., 62 1995, Sudakin, Ganoth et al., 1995. The APC/C uses two related co-activators termed Cdc20 63 and Cdh1, which bind substrates and recruit them to the APC/C for ubiquitination and 64 subsequent degradation (Kernan, Bonacci et al., 2018). We previously identified both E2F7 65 and E2F8 as targets of the Cdh1-bound form of APC/C (APC/C Cdh1 ) (Cohen et al., 2013). 66These findings, together with other supporting studies (Boekhout, Yuan et al., 2016), shifted 67 the model by which the E2F1-E2F7-E2F8 circuitry communicates with the cell cycle clock to 68 regulate the transition from the G1-phase of the cell cycle into S-phase. Nevertheless, the 69 exact inter-dynamics of E2F1-E2F7-E2F8 circuitry throughout G1 and the mechanism by 70 which they are achieved are not entirely resolved. No less obscure is the interplay between 71 E2F1 and atypical E2Fs during G2-phase and mitosis. Dissecting these complex signaling 72 circuits is important for understanding the decision making mechanisms at two critical 73 points in the life of a proliferating cell -commitment to DNA replication and division. 74Cell-free systems are known for their capacity to reproduce complex cellular 75 processes in vitro while maintaining a physiologically relevant context, bridging the gap 76...