Translation Initiation Rate Determines the Impact of Ribosome Stalling on Bacterial Protein Synthesis

Ribosome stalling during translation can be caused by a number of characterized mechanisms. However, the impact of elongation stalls on protein levels is variable, and the reasons for this are often unclear. To investigate this relationship, we examined the bacterial translation elongation factor P (EF-P), which plays a critical role in rescuing ribosomes stalled at specific amino acid sequences including polyproline motifs. In previous proteomic analyses of both Salmonella and Escherichia coli efp mutants, it was evident that not all proteins containing a polyproline motif were dependent on EF-P for efficient expression in vivo . The α- and β-subunits of ATP synthase, AtpA and AtpD, are translated from the same mRNA transcript, and both contain a PPG motif; however, proteomic analysis revealed that AtpD levels are strongly dependent on EF-P, whereas AtpA levels are independent of EF-P. Using these model proteins, we systematically determined that EF-P dependence is strongly influenced by elements in the 5′-untranslated region of the mRNA. By mutating either the Shine-Dalgarno sequence or the start codon, we find that EF-P dependence correlates directly with the rate of translation initiation where strongly expressed proteins show the greatest dependence on EF-P. Our findings demonstrate that polyproline-induced stalls exert a net effect on protein levels only if they limit translation significantly more than initiation. This model can be generalized to explain why sequences that induce pauses in translation elongation to, for example, facilitate folding do not necessarily exact a penalty on the overall production of the protein

Archeological and Bioarcheological Investigations at Campbell’s Bayou Cemetery Galveston County, Texas

This report documents the removal of individuals buried within Campbell’s Bayou Cemetery (41GV171) to avoid potential impact to the remains during implementation of remediation activities at the Malone Service Company Superfund Site (Site) in Texas City, TX. An oil recovery and waste processing facility had operated at the Site for more than 30 years, ending in the mid1990s. The facility had stored, processed, and disposed of industrial solid wastes and hazardous wastes. In July 2012, a group of companies known as the Malone Cooperating Parties (MCP) entered into a Consent Decree with the U.S. Government, the U.S. Environmental Protection Agency, and the State of Texas to implement a remedial design and remedial action at the Site. It was determined that if the remains in the cemetery were not relocated, there was the potential that remediation activities could impact the cemetery. Archival research, review of historic maps and aerial photographs, and reconnaissance survey revealed the extent of potential remains at the cemetery, and, given the location of the cemetery and the scope of the planned remediation activities, it was deemed impractical for the environmental remediation contractors to work around the cemetery. (41GV171). The MCP consulted with EPA, Campbell family descendants, the Galveston County Historical Commission, and the Texas Historical Commission and developed a plan to relocate the remains to a perpetual care cemetery in accordance with Texas state law and associated rules and procedures. In accordance with Texas Health and Safety Code §711.004, the landowner Land Navigator, Ltd., on behalf of the MCP, petitioned the Galveston County Judicial District Court for removal of the dedication of the cemetery and the transfer of the human remains to the perpetual care cemetery operated by Forest Park East Funeral Home and Cemetery (FPE), 21620 Gulf Freeway, Webster, TX 77598. On February 11, 2014, Land Navigator was granted a Summary Judgment allowing Land Navigator to disinter and relocate the remains to FPE. Versar, Inc. (formerly Geo-Marine, Inc.), on behalf of the MCP, provided all archeological and human osteological expertise for the disinterment and analysis of the human remains. Disinterment permits from the State Registrar of the Vital Statistics Unit of the Department of State Health Services, as required by Texas Administrative Code, Title 13, Chapter 22 (Texas Historical Commission, Cemeteries), were obtained for each burial. The disinterment excavations at Campbell’s Bayou Cemetery revealed 34 burials from which 35 individuals were excavated. No graves were marked by headstones. It is the professional judgment of Versar that, of the 35 individual sets of remains identified, 11 were determined to be adults (5 male and 3 female; 3 of indeterminate sex), and 24 were determined to be children. The majority of children at Campbell’s Bayou Cemetery (n=18) are under 5 years of age and six are premature infants aged 30–40 weeks. Burials could not be associated conclusively with any individuals identified by the descendants; however, the combination of bioarcheological analysis, coffin hardware analysis, census data, and descendant identifications resulted in a list of individuals that may have been interred in certain graves. Some of the interments include James and Mary Campbell, Charlie Meyers, Benjamin Ninnie Dick, Phoebe Rutlage, and Shelby McNeil, Jr. Children were difficult to identify; however, there is good potential the graves of Frank Campbell, Mary Jane Campbell, Charles Munson, and Grace Dick were identified. Data are conclusive that the children Levi and Joseph (Joe) Parr were both interred together in Burial 6, the concrete crypt with brick covering. Grace Dick was the last individual interred at the cemetery in 1904

Divergent Protein Motifs Direct EF-P Mediated Translational Regulation in \u3cem\u3eSalmonella\u3c/em\u3e and \u3cem\u3eEscherichia coli\u3c/em\u3e

Elongation factor P (EF-P) is a universally conserved bacterial translation factor homologous to eukaryotic/archaeal initiation factor 5A. In Salmonella, deletion of the efp gene results in pleiotropic phenotypes, including increased susceptibility to numerous cellular stressors. Only a limited number of proteins are affected by the loss of EF-P, and it has recently been determined that EF-P plays a critical role in rescuing ribosomes stalled at PPP and PPG peptide sequences. Here we present an unbiased in vivo investigation of the specific targets of EF-P by employing stable isotope labeling of amino acids in cell culture (SILAC) to compare the proteomes of wild-type and efp mutant Salmonella. We found that metabolic and motility genes are prominent among the subset of proteins with decreased production in the Δefp mutant. Furthermore, particular tripeptide motifs are statistically overrepresented among the proteins downregulated in efp mutant strains. These include both PPP and PPG but also additional motifs, such as APP and YIRYIR, which were confirmed to induce EF-P dependence by a translational fusion assay. Notably, we found that many proteins containing polyproline motifs are not misregulated in an EF-P-deficient background, suggesting that the factors that govern EF-P-mediated regulation are complex. Finally, we analyzed the specific region of the PoxB protein that is modulated by EF-P and found that mutation of any residue within a specific GSCGPG sequence eliminates the requirement for EF-P. This work expands the known repertoire of EF-P target motifs and implicates factors beyond polyproline motifs that are required for EF-P-mediated regulation

Rho Kinase Pathway Alterations in the Brain and Leukocytes in Huntington’s Disease

Huntington’s disease (HD) is a fatal neurodegenerative disease caused by an expanded polyglutamine tract in the huntingtin gene. Therapeutic approaches targeting mutant huntingtin (mtHtt) or its downstream toxic consequences are under development, including Rho kinase pathway inhibition. We investigated the messenger RNA (mRNA) expression of Rho kinase pathway genes, including RhoA (Ras homolog family member A), ROCK1 (Rho-associated kinase1), PRK2 (protein kinase C-related protein kinase 2), Profilin1, cofilin1, MYPT1 (myosin phosphatase target subunit 1), and LIMK1 (LIM domain kinase 1) in HD human blood leukocytes, postmortem brain, and in R6/2 HD mouse brain tissue using qPCR. RhoA, ROCK1, PRK2, Profilin1, cofilin1, and MYPT1 were significantly increased in HD blood compared to controls. In frontal cortex of HD postmortem brain tissue, the expression of RhoA, ROCK1, PRK2, Profilin1, and MYPT1 were also significantly increased. In the brain from 4-week-old R6/2 mice, the expression of Rock1, Prk2, Cofilin1, and MYPT1 was significantly increased while RhoA, Rock1, Profilin1, Cofilin1, and Mypt1 were increased and Limk1 mRNA decreased in 13-week-old R6/2 mice. Western blot analysis using human postmortem tissues for ROCK1 and Profilin1 demonstrated significantly increased protein levels, which correlated with the mRNA increases. Collectively, we have shown the panel of Rho kinase pathway genes to be highly altered in human HD blood, postmortem brain tissue, and in R6/2 mice. These studies confirm that HD upregulates the Rho kinase pathway and identifies mRNAs that could serve as peripheral markers in HD patients and translational markers in HD mouse models

Mechanisms of Copper Ion Mediated Huntington's Disease Progression

Huntington's disease (HD) is caused by a dominant polyglutamine expansion within the N-terminus of huntingtin protein and results in oxidative stress, energetic insufficiency and striatal degeneration. Copper and iron are increased in the striata of HD patients, but the role of these metals in HD pathogenesis is unknown. We found, using inductively-coupled-plasma mass spectroscopy, that elevations of copper and iron found in human HD brain are reiterated in the brains of affected HD transgenic mice. Increased brain copper correlated with decreased levels of the copper export protein, amyloid precursor protein. We hypothesized that increased amounts of copper bound to low affinity sites could contribute to pro-oxidant activities and neurodegeneration. We focused on two proteins: huntingtin, because of its centrality to HD, and lactate dehydrogenase (LDH), because of its documented sensitivity to copper, necessity for normoxic brain energy metabolism and evidence for altered lactate metabolism in HD brain. The first 171 amino acids of wild-type huntingtin, and its glutamine expanded mutant form, interacted with copper, but not iron. N171 reduced Cu(2+) in vitro in a 1∶1 copper∶protein stoichiometry indicating that this fragment is very redox active. Further, copper promoted and metal chelation inhibited aggregation of cell-free huntingtin. We found decreased LDH activity, but not protein, and increased lactate levels in HD transgenic mouse brain. The LDH inhibitor oxamate resulted in neurodegeneration when delivered intra-striatially to healthy mice, indicating that LDH inhibition is relevant to neurodegeneration in HD. Our findings support a role of pro-oxidant copper-protein interactions in HD progression and offer a novel target for pharmacotherapeutics

The mTOR kinase inhibitor Everolimus decreases S6 kinase phosphorylation but fails to reduce mutant huntingtin levels in brain and is not neuroprotective in the R6/2 mouse model of Huntington's disease

<p>Abstract</p> <p>Background</p> <p>Huntington's disease (HD) is a progressive neurodegenerative disorder caused by a CAG repeat expansion within the huntingtin gene. Mutant huntingtin protein misfolds and accumulates within neurons where it mediates its toxic effects. Promoting mutant huntingtin clearance by activating macroautophagy is one approach for treating Huntington's disease (HD). In this study, we evaluated the mTOR kinase inhibitor and macroautophagy promoting drug everolimus in the R6/2 mouse model of HD.</p> <p>Results</p> <p>Everolimus decreased phosphorylation of the mTOR target protein S6 kinase indicating brain penetration. However, everolimus did not activate brain macroautophagy as measured by LC3B Western blot analysis. Everolimus protected against early declines in motor performance; however, we found no evidence for neuroprotection as determined by brain pathology. In muscle but not brain, everolimus significantly decreased soluble mutant huntingtin levels.</p> <p>Conclusions</p> <p>Our data suggests that beneficial behavioral effects of everolimus in R6/2 mice result primarily from effects on muscle. Even though everolimus significantly modulated its target brain S6 kinase, this did not decrease mutant huntingtin levels or provide neuroprotection.</p

Crystal structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine

ClpX is a AAA+ machine that uses the energy of ATP binding and hydrolysis to unfold native proteins and translocate unfolded polypeptides into the ClpP peptidase. The crystal structures presented here reveal striking asymmetry in ring hexamers of nucleotide-free and nucleotide-bound ClpX. Asymmetry arises from large changes in rotation between the large and small AAA+ domains of individual subunits. These differences prevent nucleotide binding to two subunits, generate a staggered arrangement of ClpX subunits and pore loops around the hexameric ring, and provide a mechanism for coupling conformational changes caused by ATP binding or hydrolysis in one subunit to flexing motions of the entire ring. Our structures explain numerous solution studies of ClpX function, predict mechanisms for pore elasticity during translocation of irregular polypeptides, and suggest how repetitive conformational changes might be coupled to mechanical work during the ATPase cycle of ClpX and related molecular machines.National Institutes of Health (U.S.) (Grant number AI-15706