The RACK1 signal anchor protein from Trypanosoma brucei associates with eukaryotic elongation factor 1A: a role for translational control in cytokinesis

RACK1 is a WD-repeat protein that forms signal complexes at appropriate locations in the cell. RACK1 homologues are core components of ribosomes from yeast, plants and mammals. In contrast, a cryo-EM analysis of trypanosome ribosomes failed to detect RACK1, thus eliminating an important translational regulatory mechanism. Here we report that TbRACK1 from Trypanosoma brucei associates with eukaryotic translation elongation factor-1a (eEF1A) as determined by tandem MS of TAP-TbRACK1 affinity eluates, co-sedimentation in a sucrose gradient, and co-precipitation assays. Consistent with these observations, sucrose gradient purified 80S monosomes and translating polysomes each contained TbRACK1. When RNAi was used to deplete cells of TbRACK1, a shift in the polysome profile was observed, while the phosphorylation of a ribosomal protein increased. Under these conditions, cell growth became hypersensitive to the translational inhibitor anisomycin. The kinetoplasts and nuclei were misaligned in the postmitotic cells, resulting in partial cleavage furrow ingression during cytokinesis. Overall, these findings identify eEF1A as a novel TbRACK1 binding partner and establish TbRACK1 as a component of the trypanosome translational apparatus. The synergy between anisomycin and TbRACK1 RNAi suggests that continued translation is required for complete ingression of the cleavage furrow.     

Predicting the three-dimensional folding of transfer RNA with a computer modeling protocol

We have developed a computer modeling protocol that can be used to predict the three-dimensional folding of a ribonucleic acid on the basis of limited amounts of secondary and tertiary data. This protocol extends the use of distance geometry beyond the domain of NMR data in which it is usually applied. The use of this algorithm to fold the molecule eliminates operator subjectivity and reproducibly predicts the overall dimensions and shape of the transfer RNA molecule. By use of a replacement pseudoatom set based on helical substructures, a series of transfer RNA foldings have been completed that utilize only the primary structure, the phylogenetically deduced secondary structure, and five long-range interactions that were determined without reference to the crystal structure. In a control set of foldings, all the interactions suspected to exist in 1969 have been included. In all cases, the modeling process consistently predicts the global arrangement of the helical domains and to a lesser extent the general path of the backbone of transfer RNA.     

Glycerophospholipid variation in choline and inositol auxotrophs of Neurospora crassa. Internal compensation among zwitterionic and anionic species.

The glycerophospholipids of cultures of Neurospora crassa were extracted, deacylated, and analyzed. In addition to a wild-type strain, several auxotrophic mutant strains were examined: chol-1 (defective S-adenosylmethionine: phosphatidylethanolamine methyltransferase), chol-2 (defective S-adenosyl methionine:phosphatidylmonomethylethanolamine (dimethylethanolamine) methyltransferase), and inos (defective myoinositol-1-phosphate phosphatase). In addition, a double mutant strain, chol-1;chol-2, was constructed. Cultures of the mutant strains grown with concentrations of supplement(s) just adequate to support growth had bizarre phospholipid compositions. By appropriate choice of mutant and supplement(s), it was possible to vary the relative level of every phospholipid of the organism, with the exception of cardiolipin. The maximum ranges encountered for the zwitterionic species, expressed as per cent of total phospholipid phosphorus, were lecithin (0.9 to 53.1%), phosphatidyldimethylethanolamine (0.0 to 55.5%), phosphatidylmonomethylethanolamine (0.0 to 53.9%), and phosphatidylethanolamine (9.8 to 43.3%). For the anionic species, the ranges were phosphatidylserine (1.7 to 10.4%) and phosphatidylinositol (3.6 to 25.1%). Despite the wide variation of the relative proportions of the individual phospholipid species, five quantities remained constant: the cardiolipin content, the total phospholipid content, the total content of the zwitterionic species, the total content of the anionic species, and the ratio of the zwitterionic to anionic totals. The data suggest the existence of an internal compensation mechanism, the net effect of which is maintenance of a fairly constant contribution by the phospholipid components to the over-all membrane charge.     

Dynamics of four rat liver plasma membrane proteins and polymeric IgA receptor. Rates of synthesis and selective loss into the bile.

We have determined the half-lives and amounts per hepatocyte of the polymeric IgA receptor (pIgA-R) and four rat hepatocyte plasma membrane proteins and subsequently have predicted their rates of synthesis and possible routes of degradation. Using in vivo pulse-chase metabolic labeling with L-[35S]cysteine, we found that the pIgA-R had an apparent half-life of 1.1 h. Additional metabolic labeling experiments showed that CE9, HA4, and HA321 had apparent half-lives of 4-5 days, and dipeptidyl peptidase IV had an apparent half-life of 9 days. To quantify the amount of each protein per hepatocyte, homogenates and a standard curve of purified protein were compared by immunoblotting. We found that these proteins were present at 1-8 x 10(6) molecules/hepatocyte. The calculated rate of synthesis for pIgA-R was 1.6 x 10(6) molecules/hepatocyte/h, whereas the others were synthesized at much lower rates (0.9-5 x 10(4) molecules/hepatocyte/h). Using immunoblot analysis, we found that pIgA-R was released into bile at a rate of 30%/h (700%/day), whereas dipeptidyl peptidase IV and HA4 were released at a rate of 2-3%/day. While the majority of the loss of pIgA-R from hepatocytes occurred by release into the bile, less than 30% of the degradation of dipeptidyl peptidase IV and HA4 could be accounted for by this pathway, suggesting that the remaining molecules must be retrieved from the apical surface before degradation.     

Inferential biases linked to unobservable states in complex occupancy models

Modeling of species distributions has undergone a shift from relying on equilibrium assumptions to recognizing transient system dynamics explicitly. This shift has necessitated more complex modeling techniques, but the performance of these dynamic models has not yet been assessed for systems where unobservable states exist. Our work is motivated by the impacts of the emerging infectious disease chytridiomycosis, a disease of amphibians that is associated with declines of many species worldwide. Using this host‐pathogen system as a general example, we first illustrate how misleading inferences can result from failing to incorporate pathogen dynamics into the modeling process, especially when the pathogen is difficult or impossible to survey in the absence of a host species. We found that traditional modeling techniques can underestimate the effect of a pathogen on host species occurrence and dynamics when the pathogen can only be detected in the host, and pathogen information is treated as a covariate. We propose a dynamic multistate modeling approach that is flexible enough to account for the detection structures that may be present in complex multistate systems, especially when the sampling design is limited by a species’ natural history or sampling technology. When multistate occupancy models are used and an unobservable state is present, parameter estimation can be influenced by model complexity, data sparseness, and the underlying dynamics of the system. We show that, even with large sample sizes, many models incorporating seasonal variation in vital rates may not generate reasonable estimates, indicating parameter redundancy. We found that certain types of missing data can greatly hinder inference, and we make study design recommendations to avoid these issues. Additionally, we advocate the use of time‐varying covariates to explain temporal trends in the data, and the development of sampling techniques that match the biology of the system to eliminate unobservable states when possible.     

Discovery of heterocyclic replacements for the coumarin core of anti-tubercular FadD32 inhibitors

Previous work established a coumarin scaffold as a starting point for inhibition of Mycobacterium tuberculosis (Mtb) FadD32 enzymatic activity. After further profiling of the coumarin inhibitor 4 revealed chemical instability, we discovered that a quinoline ring circumvented this instability and had the advantage of offering additional substitution vectors to further optimize. Ensuing SAR studies gave rise to quinoline-2-carboxamides with potent anti-tubercular activity. Further optimization of ADME/PK properties culminated in 21b that exhibited compelling in vivo efficacy in a mouse model of Mtb infection.