HflX is a GTPase that controls hypoxia-induced replication arrest in slow-growing mycobacteria.

GTPase high frequency of lysogenization X (HflX) is highly conserved in prokaryotes and acts as a ribosome-splitting factor as part of the heat shock response in Escherichia coli. Here we report that HflX produced by slow-growing Mycobacterium bovis bacillus Calmette-Guérin (BCG) is a GTPase that plays a critical role in the pathogen's transition to a nonreplicating, drug-tolerant state in response to hypoxia. Indeed, HflX-deficient M. bovis BCG (KO) replicated markedly faster in the microaerophilic phase of a hypoxia model that resulted in premature entry into dormancy. The KO mutant displayed hallmarks of nonreplicating mycobacteria, including phenotypic drug resistance, altered morphology, low intracellular ATP levels, and overexpression of Dormancy (Dos) regulon proteins. Mice nasally infected with HflX KO mutant displayed increased bacterial burden in the lungs, spleen, and lymph nodes during the chronic phase of infection, consistent with the higher replication rate observed in vitro in microaerophilic conditions. Unlike fast growing mycobacteria, M. bovis BCG HlfX was not involved in antibiotic resistance under aerobic growth. Proteomics, pull-down, and ribo-sequencing approaches supported that mycobacterial HflX is a ribosome-binding protein that controls translational activity of the cell. With HflX fully conserved between M. bovis BCG and M. tuberculosis, our work provides further insights into the molecular mechanisms deployed by pathogenic mycobacteria to adapt to their hypoxic microenvironment.

Structural basis of human full-length kindlin-3 homotrimer in an auto-inhibited state.

Kindlin-1, -2, and -3 directly bind integrin ß cytoplasmic tails to regulate integrin activation and signaling. Despite their functional significance and links to several diseases, structural information on full-length kindlin proteins remains unknown. Here, we report the crystal structure of human full-length kindlin-3, which reveals a novel homotrimer state. Unlike kindlin-3 monomer, which is the major population in insect and mammalian cell expression systems, kindlin-3 trimer does not bind integrin ß cytoplasmic tail as the integrin-binding pocket in the F3 subdomain of 1 protomer is occluded by the pleckstrin homology (PH) domain of another protomer, suggesting that kindlin-3 is auto-inhibited upon trimer formation. This is also supported by functional assays in which kindlin-3 knockout K562 erythroleukemia cells reconstituted with the mutant kindlin-3 containing trimer-disrupting mutations exhibited an increase in integrin-mediated adhesion and spreading on fibronectin compared with those reconstituted with wild-type kindlin-3. Taken together, our findings reveal a novel mechanism of kindlin auto-inhibition that involves its homotrimer formation.

pSILAC-Based Determination of Cellular Protein Sorting into Extracellular Vesicles.

The protein cargo of extracellular vesicles (EVs) determines their impact on recipient cell types and the downstream effects on biological function. Environmental cues can modify EV loading with proteins derived from the plasma membrane via endocytosis, obtained from the preexisting cytosolic pool via active sorting, or packaging with newly synthesized proteins drawn from trans-golgi networks. Given the major impact these pathways exert on EV content and functional potential, it is important to study how defined stimuli influence protein sorting into these vesicles for dispersal. To this end, pSILAC-based approaches can be used to pulse/trace the origins of EV protein content and thereby provide valuable insight into vesicle biology and likely effects on intercellular communication in diverse settings.

Proteomic Profiling of the Secretome of Trichoderma reesei.

Trichoderma reesei (T. reesei) is the workhorse for the production of industrial cellulolytic enzyme cocktails for cellulose hydrolysis. However, the current industrial process using enzyme cocktails is not efficient enough for the cost-effective generation of cellulosic sugar. Here, we describe a protocol for the application of a state-of-the-art LC-MS/MS-based proteomics method for studying the T. reesei secretome. A protein-free minimal chemically defined cell culture medium must be used for a successful secretome analysis. A lignocellulose substrate can be added to this minimal medium to stimulate the fungal secretion of enzymes specific to that substrate. The secretory proteins in the conditioned medium can be purified for quantitative proteomics profiling. T. reesei secretes several hundred enzymes including cellulases, hemicellulases, pectinases, proteases, oxidoreductases, and many putative proteins when it is stimulated with lignocellulose. By combining an understanding of the basic biomass hydrolytic mechanisms with the discovery of novel enzymes, more effective enzyme cocktails can be designed for a sustainable biochemical-based biorefinery.

A systematic assessment of mycobacterial F1 -ATPase subunit ε's role in latent ATPase hydrolysis.

In contrast to most bacteria, the mycobacterial F1 FO -ATP synthase (α3 :ß3 :γ:δ:ε:a:b:b':c9 ) does not perform ATP hydrolysis-driven proton translocation. Although subunits α, γ and ε of the catalytic F1 -ATPase component α3 :ß3 :γ:ε have all been implicated in the suppression of the enzyme's ATPase activity, the mechanism remains poorly defined. Here, we brought the central stalk subunit ε into focus by generating the recombinant Mycobacterium smegmatis F1 -ATPase (MsF1 -ATPase), whose 3D low-resolution structure is presented, and its ε-free form MsF1 αßγ, which showed an eightfold ATP hydrolysis increase and provided a defined system to systematically study the segments of mycobacterial ε's suppression of ATPase activity. Deletion of four amino acids at ε's N terminus, mutant MsF1 αßγεΔ2-5 , revealed similar ATP hydrolysis as MsF1 αßγ. Together with biochemical and NMR solution studies of a single, double, triple and quadruple N-terminal ε-mutants, the importance of the first N-terminal residues of mycobacterial ε in structure stability and latency is described. Engineering ε's C-terminal mutant MsF1 αßγεΔ121 and MsF1 αßγεΔ103-121 with deletion of the C-terminal residue D121 and the two C-terminal ɑ-helices, respectively, revealed the requirement of the very C terminus for communication with the catalytic α3 ß3 -headpiece and its function in ATP hydrolysis inhibition. Finally, we applied the tools developed during the study for an in silico screen to identify a novel subunit ε-targeting F-ATP synthase inhibitor.