Permeability profiling of all 13 Arabidopsis PIP aquaporins using a high throughput yeast approach

Plant aquaporins have many more functions than just transporting water. Within the diversity of plant aquaporins are isoforms capable of transporting signaling molecules, nutrients, metalloids and gases. It is established that aquaporin substrate discrimination depends on combinations of factors such as solute size, pore size and polarity, and post-translational protein modifications. But our understanding of the relationships between variation in aquaporin structures and the implications for permeability is limited. High-throughput yeast-based assays were developed to assess diverse substrate permeabilities to water, H2O2, boric acid, urea and Na+. All 13 plasma membrane intrinsic proteins (PIPs) from Arabidopsis (AtPIPs) were permeable to both water and H2O2, although their effectiveness varied, and none were permeable to urea. AtPIP2 isoforms were more permeable to water than AtPIP1s, while AtPIP1s were more efficient at transporting H2O2 with AtPIP1;3 and AtPIP1;4 being the most permeable. Among the AtPIP2s, AtPIP2;2 and AtPIP2;7 were also permeable to boric acid and Na+. Linking AtPIP substrate profiles with phylogenetics and gene expression data enabled us to align substrate preferences with known biological roles of AtPIPs and importantly guide towards unidentified roles hidden by functional redundancy at key developmental stages and within tissue types. This analysis positions us to more strategically test in planta physiological roles of AtPIPs in order to unravel their complex contributions to the transport of important substrates, and secondly, to resolve links between aquaporin protein structure, substrate discrimination, and transport efficiency.

Substrate discrimination and quality control require each catalytic activity of TRAMP and the nuclear RNA exosome

Quality control requires discrimination between functional and aberrant species to selectively target aberrant substrates for destruction. Nuclear RNA quality control in Saccharomyces cerevisiae includes the TRAMP complex that marks RNA for decay via polyadenylation followed by helicase-dependent 3′ to 5′ degradation by the RNA exosome. Using reconstitution biochemistry, we show that polyadenylation and helicase activities of TRAMP cooperate with processive and distributive exoribonuclease activities of the nuclear RNA exosome to protect stable RNA from degradation while selectively targeting and degrading less stable RNA. Substrate discrimination is lost when the distributive exoribonuclease activity of Rrp6 is inactivated, leading to degradation of stable and unstable RNA species. These data support a proofreading mechanism in which deadenylation by Rrp6 competes with Mtr4-dependent degradation to protect stable RNA while selectively targeting and degrading unstable RNA.

Involvement of a Membrane-Bound Amphiphilic Helix in Substrate Discrimination and Binding by an Escherichia coli S2P Peptidase RseP

Intramembrane proteases (IMPs) are a unique class of proteases that catalyze the proteolysis within the membrane and regulate diverse cellular processes in various organisms. RseP, an Escherichia coli site-2 protease (S2P) family IMP, is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-σE) protein RseA. Extracytoplasmic stresses trigger a sequential cleavage of RseA, in which first DegS cleaves off its periplasmic domain, and RseP catalyzes the second cleavage of RseA. The two tandem-arranged periplasmic PDZ (PDZ tandem) domains of RseP serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP IMP domain. However, RseP’s substrate recognition mechanism is not fully understood. Here, we found that a periplasmic region of RseP, located downstream of the PDZ tandem, contains a segment (named H1) predicted to form an amphiphilic helix. Bacterial S2P homologs with various numbers of PDZ domains have a similar amphiphilic helix in the corresponding region. We demonstrated that the H1 segment forms a partially membrane-embedded amphiphilic helix on the periplasmic surface of the membrane. Systematic and random mutagenesis analyses revealed that the H1 helix is important for the stability and proteolytic function of RseP and that mutations in the H1 segment can affect the PDZ-mediated substrate discrimination. Cross-linking experiments suggested that H1 directly interacts with the DegS-cleaved form of RseA. We propose that H1 acts as an adaptor required for proper arrangement of the PDZ tandem domain to perform its filter function and for substrate positioning for its efficient cleavage.

Structural basis for substrate discrimination byE. colirepair enzyme, AlkB

Positive charge on methylated nucleotides is a prime criterion for substrate recognition byE. coliAlkB.

Signal and Specificity of Protein Ubiquitination for Proteasomal Degradation

The eukaryotic ubiquitin system regulates essential cell events such as DNA repair, protein homeostasis, and signal transduction. Like many biochemical processes, ubiquitination must ensure signaling efficiency and in the meantime maintain substrate specificity. We examine this signal-specificity relationship by theoretical models of polyubiquitinations that tag proteins for the proteasomal degradation. Parsimonious models provide explicit formulas to key measurable quantities and offer guiding insights into the signal-specificity tradeoffs under varying structures and kinetics. Models with measured kinetics from two primary cell-cycle ligases (SCF and APC) explain mechanisms of chain initiation, elongation slowdown, chain-length dependence of E3-substrate affinity, and deubiquitinases. We find that substrate discrimination over ubiquitin transfer rates is consistently more efficient than over substrate-E3 ligase binding energy, regardless of circuit structure, parameter value, and dynamics. E3-associated substrate deubiquitination increases the discrimination over the former and in the meantime decreases the latter, further widening their difference. Both discrimination strategies might be simultaneously explored by an E3 system to effectively proofread substrates as we demonstrated by analyzing experimental data from the CD4-Vpu-SCF system. We also identify that sequential deubiquitination circuit may act as a specificity switch, by which a modest change in deubiquitination and/or processivity can greatly increase substrate discrimination without much compromise in degradation signal. This property may be utilized as a gatekeeper mechanism to direct a temporal polyubiquitination and thus degradation order of substrates with small biochemical differences.