A metabolite binding protein moonlights as a bile- responsive chaperone

Bile salts are secreted into the gastrointestinal tract to aid in the absorption of lipids. In addition, bile salts show potent antimicrobial activity in part by mediating bacterial protein unfolding and aggregation. Here, using a protein folding sensor, we made the surprising discovery that the Escherichia coli periplasmic glycerol- 3- phosphate (G3P)- binding protein UgpB can serve, in the absence of its substrate, as a potent molecular chaperone that exhibits anti- aggregation activity against bile salt- induced protein aggregation. The substrate G3P, which is known to accumulate in the later compartments of the digestive system, triggers a functional switch between UgpB’s activity as a molecular chaperone and its activity as a G3P transporter. A UgpB mutant unable to bind G3P is constitutively active as a chaperone, and its crystal structure shows that it contains a deep surface groove absent in the G3P- bound wild- type UgpB. Our work illustrates how evolution may be able to convert threats into signals that first activate and then inactivate a chaperone at the protein level in a manner that bypasses the need for ATP.SynopsisThe periplasmic glycerol- 3- phosphate binding protein, UgpB, was found to have dual functions, as a metabolite binding protein and as a bile- responsive molecular chaperone. Stomach- acid induced stripping of its glycerol- 3- phosphate substrate functions as a switch that activates the chaperone activity of UgpB.A tripartite periplasmic protein folding sensor and Tn- Seq uncover UgpB as a new chaperone.UgpB prevents bile- induced protein aggregation when in its G3P- free form.Stomach acid- induced G3P stripping activates UgpB chaperone function.Crystal structure of a G3P- nonbinding variant of UgpB reveals opening of a deep surface groove when compared to the structure of G3P- bound wild- type UgpB.A periplasmic folding sensor reveals a mechanism by which stomach acid- induced G3P stripping remodels UgpB into a chaperone that prevents bile- induced bacterial protein aggregation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/163430/6/embj2019104231.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163430/5/embj2019104231-sup-0002-EVFigs.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163430/4/embj2019104231-sup-0006-SDataFig3.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163430/3/embj2019104231.reviewer_comments.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163430/2/embj2019104231_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/163430/1/embj2019104231-sup-0005-SDataFig2.pd

Adaptive Evolution in Zinc Finger Transcription Factors

The majority of human genes are conserved among mammals, but some gene families have undergone extensive expansion in particular lineages. Here, we present an evolutionary analysis of one such gene family, the poly–zinc-finger (poly-ZF) genes. The human genome encodes approximately 700 members of the poly-ZF family of putative transcriptional repressors, many of which have associated KRAB, SCAN, or BTB domains. Analysis of the gene family across the tree of life indicates that the gene family arose from a small ancestral group of eukaryotic zinc-finger transcription factors through many repeated gene duplications accompanied by functional divergence. The ancestral gene family has probably expanded independently in several lineages, including mammals and some fishes. Investigation of adaptive evolution among recent paralogs using dN/dS analysis indicates that a major component of the selective pressure acting on these genes has been positive selection to change their DNA-binding specificity. These results suggest that the poly-ZF genes are a major source of new transcriptional repression activity in humans and other primates

Folding while Bound to Chaperones

Chaperones are important in preventing protein aggregation and aiding protein folding. How chaperones aid protein folding remains a key question in understanding their mechanism. The possibility of proteins folding while bound to chaperones was reintroduced recently with the chaperone Spy, many years after the phenomenon was first reported with the chaperones GroEL and SecB. In this review, we discuss the salient features of folding while bound in the cases for which it has been observed and speculate about its biological importance and possible occurrence in other chaperones

MAPK Phosphatase AP2C3 Induces Ectopic Proliferation of Epidermal Cells Leading to Stomata Development in Arabidopsis

In plant post-embryonic epidermis mitogen-activated protein kinase (MAPK) signaling promotes differentiation of pavement cells and inhibits initiation of stomata. Stomata are cells specialized to modulate gas exchange and water loss. Arabidopsis MAPKs MPK3 and MPK6 are at the core of the signaling cascade; however, it is not well understood how the activity of these pleiotropic MAPKs is constrained spatially so that pavement cell differentiation is promoted only outside the stomata lineage. Here we identified a PP2C-type phosphatase termed AP2C3 (Arabidopsis protein phosphatase 2C) that is expressed distinctively during stomata development as well as interacts and inactivates MPK3, MPK4 and MPK6. AP2C3 co-localizes with MAPKs within the nucleus and this localization depends on its N-terminal extension. We show that other closely related phosphatases AP2C2 and AP2C4 are also MAPK phosphatases acting on MPK6, but have a distinct expression pattern from AP2C3. In accordance with this, only AP2C3 ectopic expression is able to stimulate cell proliferation leading to excess stomata development. This function of AP2C3 relies on the domains required for MAPK docking and intracellular localization. Concomitantly, the constitutive and inducible AP2C3 expression deregulates E2F-RB pathway, promotes the abundance and activity of CDKA, as well as changes of CDKB1;1 forms. We suggest that AP2C3 downregulates the MAPK signaling activity to help maintain the balance between differentiation of stomata and pavement cells