The Crystal Structure and Small-Angle X-Ray Analysis of CsdL/TcdA Reveal a New tRNA Binding Motif in the MoeB/E1 Superfamily

Cyclic N⁶-threonylcarbamoyladenosine (‘cyclic t⁶A’, ct⁶A) is a non-thiolated hypermodification found in transfer RNAs (tRNAs) in bacteria, protists, fungi and plants. In bacteria and yeast cells ct⁶A has been shown to enhance translation fidelity and efficiency of ANN codons by improving the faithful discrimination of aminoacylated tRNAs by the ribosome. To further the understanding of ct⁶A biology we have determined the high-resolution crystal structures of CsdL/TcdA in complex with AMP and ATP, an E1-like activating enzyme from Escherichia coli, which catalyzes the ATP-dependent dehydration of t⁶A to form ct⁶A. CsdL/TcdA is a dimer whose structural integrity and dimer interface depend critically on strongly bound K⁺ and Na⁺ cations. By using biochemical assays and small-angle X-ray scattering we show that CsdL/TcdA can associate with tRNA with a 1:1 stoichiometry and with the proper position and orientation for the cyclization of t⁶A. Furthermore, we show by nuclear magnetic resonance that CsdL/TcdA engages in transient interactions with CsdA and CsdE, which, in the latter case, involve catalytically important residues. These short-lived interactions may underpin the precise channeling of sulfur atoms from cysteine to CsdL/TcdA as previously characterized. In summary, the combination of structural, biophysical and biochemical methods applied to CsdL/TcdA has afforded a more thorough understanding of how the structure of this E1-like enzyme has been fine tuned to accomplish ct⁶A synthesis on tRNAs while providing support for the notion that CsdA and CsdE are able to functionally interact with CsdL/TcdA.     

Generation of Food-Grade Recombinant Lactic Acid Bacterium Strains by Site-Specific Recombination

The construction of a delivery and clearing system for the generation of food-grade recombinant lactic acid bacterium strains, based on the use of an integrase (Int) and a resolvo-invertase (β-recombinase) and their respective target sites (attP-attB and six, respectively) is reported. The delivery system contains a heterologous replication origin and antibiotic resistance markers surrounded by two directly oriented six sites, a multiple cloning site where passenger DNA could be inserted (e.g., the cI gene of bacteriophage A2), the int gene, and the attP site of phage A2. The clearing system provides a plasmid-borne gene encoding β-recombinase. The nonreplicative vector-borne delivery system was transformed into Lactobacillus casei ATCC 393 and, by site-specific recombination, integrated as a single copy in an orientation- and Int-dependent manner into the attB site present in the genome of the host strain. The transfer of the clearing system into this strain, with the subsequent expression of the β-recombinase, led to site-specific DNA resolution of the non-food-grade DNA. These methods were validated by the construction of a stable food-grade L. casei ATCC 393-derived strain completely immune to phage A2 infection during milk fermentation.     

A BASIC microcomputer program to calculate the secondary structure of proteins from their circular dichroism spectrum

A BASIC program (CDPROT) has been developed to calculate thesecondary structure of proteins from their far UV circular dichroismspectrum. This implementation can use different reference spectra,calculated either from model polypeptides or proteins of knowntertiary structure. Apart from obtaining the a-helical, ß-structure,ß-turns or random percentages which would generatethe spectrum of best fit with respect to the experimental measures,CDPROT represents on screen both theoretical and experimentalspectra indicating the root-mean-square error. The provisionof additional reference spectra by the user is also considered,and another program (STOREREF) performs the editing in an adequateformat for CDPROT. Received on March 8, 1988; accepted on June 3, 1988     

CpG-induced tyrosine phosphorylation occurs via a TLR9-independent mechanism and is required for cytokine secretion

Toll-like receptors (TLRs) recognize molecular patterns preferentially expressed by pathogens. In endosomes, TLR9 is activated by unmethylated bacterial DNA, resulting in proinflammatory cytokine secretion via the adaptor protein MyD88. We demonstrate that CpG oligonucleotides activate a TLR9-independent pathway initiated by two Src family kinases, Hck and Lyn, which trigger a tyrosine phosphorylation–mediated signaling cascade. This cascade induces actin cytoskeleton reorganization, resulting in cell spreading, adhesion, and motility. CpG-induced actin polymerization originates at the plasma membrane, rather than in endosomes. Chloroquine, an inhibitor of CpG-triggered cytokine secretion, blocked TLR9/MyD88-dependent cytokine secretion as expected but failed to inhibit CpG-induced Src family kinase activation and its dependent cellular responses. Knock down of Src family kinase expression or the use of specific kinase inhibitors blocked MyD88-dependent signaling and cytokine secretion, providing evidence that tyrosine phosphorylation is both CpG induced and an upstream requirement for the engagement of TLR9. The Src family pathway intersects the TLR9–MyD88 pathway by promoting the tyrosine phosphorylation of TLR9 and the recruitment of Syk to this receptor.     

Conversion of olive tree biomass into fermentable sugars by dilute acid pretreatment and enzymatic saccharification

The production of fermentable sugars from olive tree biomass was studied by dilute acid pretreatment and further saccharification of the pretreated solid residues. Pretreatment was performed at 0.2%, 0.6%, 1.0% and 1.4% (w/w) sulphuric acid concentrations while temperature was in the range 170-210 degrees C. Attention is paid to sugar recovery both in the liquid fraction issued from pretreatment (prehydrolysate) and that in the water-insoluble solid (WIS). As a maximum, 83% of hemicellulosic sugars in the raw material were recovered in the prehydrolysate obtained at 170 degrees C, 1% sulphuric acid concentration, but the enzyme accessibility of the corresponding pretreated solid was not very high. In turn, the maximum enzymatic hydrolysis yield (76.5%) was attained from a pretreated solid (at 210 degrees C, 1.4% acid concentration) in which cellulose solubilization was detected; moreover, sugar recovery in the prehydrolysate was the poorest one among all the experiments performed. To take account of fermentable sugars generated by pretreatment and the glucose released by enzymatic hydrolysis, an overall sugar yield was calculated. The maximum value (36.3 g sugar/100 g raw material) was obtained when pretreating olive tree biomass at 180 degrees C and 1% sulphuric acid concentration, representing 75% of all sugars in the raw material. Dilute acid pretreatment improves results compared to water pretreatment.     

Genome Editing by CRISPR/Cas9: A Game Change in the Genetic Manipulation of Protists

Genome editing by CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR‐associated gene 9) system has been transformative in biology. Originally discovered as an adaptive prokaryotic immune system, CRISPR/Cas9 has been repurposed for genome editing in a broad range of model organisms, from yeast to mammalian cells. Protist parasites are unicellular organisms producing important human diseases that affect millions of people around the world. For many of these diseases, such as malaria, Chagas disease, leishmaniasis and cryptosporidiosis, there are no effective treatments or vaccines available. The recent adaptation of the CRISPR/Cas9 technology to several protist models will be playing a key role in the functional study of their proteins, in the characterization of their metabolic pathways, and in the understanding of their biology, and will facilitate the search for new chemotherapeutic targets. In this work we review recent studies where the CRISPR/Cas9 system was adapted to protist parasites, particularly to Apicomplexans and trypanosomatids, emphasizing the different molecular strategies used for genome editing of each organism, as well as their advantages. We also discuss the potential usefulness of this technology in the green alga Chlamydomonas reinhardtii.     

Seed bank versus seed rain in the regeneration of a tropical pioneer tree

Summary We used the tropical pioneer tree, Cecropia obtusifolia to evaluate the relative importance of different sources of seeds in the regeneration of species that depend on ephemeral sites. We studied seed production in a population established in a 5 ha plot, and dispersal, dormancy and seed predation in two recent treefall gaps (<1 year-old), two building or successional forest patches (10–15 since disturbed), and two mature forest patches (>35 years since disturbed) for a one year period at Los Tuxtlas (Mexico). Flowers and fruits were counted at monthly intervals. Annual fecundity per tree ranged from 1.4×10⁴ to 1.4×10⁷ seeds. Seeds were continuously available on the trees and on the ground. Average annual seed rain per m² (as measured by 0.5×0.5 m seed traps) varied from 184 to 1925 among the six sites. Distance to nearest seed source and patch type explained more than 60% of the seed rain variation among sites. Soil seed density, estimated by counting seeds from ten samples (78.5 cm²×10 cm deep) collected from each site in October and January, ranged among the six sites from 269 to 4485 seeds per m² in January and from 204 to 5073 in October. Soil seed viabilities were much lower (17.1% in October and 5.1% in January) than those of rain seeds (48.26%). Annual survivorships of 2.2% were estimated for seeds artificially sown on the soil surface of a gap and a mature patch, and 3.75% in a building patch. In two other experiments seed removal rates ranged from 27% to 98% in 4 days. Removal rates were significantly higher in gap and mature patches than in building patches. Ants (Paratrechina vividula) and grasshopper nymphs (Hygronemobius. sp.) were the main predators. We draw three main conclusions from our data: (1) Pathogens and predators determine low survivorship of C. obtusifolia's seeds in the soil and a rapid turnover rate (1.07 to 1.02 years) of its seed bank; (2) a continuous and copious seed production and an abundant and extensive seed rain replenish the soil seed pool in patches with different disturbance ages at least up to 86 m from nearest source; (3) more than 90% of the seeds contributing to C. obtusifolia seedling recruitment in gaps are less than one year-old. We discuss our results in the context of previous similar studies for tropical forests.     

Size‐based interactions and trophic transfer efficiency are modified by fish predation and cyanobacteria blooms in Lake Mývatn,Iceland

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Methods to account for spatial autocorrelation in the analysis of species distributional data: a review

Species distributional or trait data based on range map (extent‐of‐occurrence) or atlas survey data often display spatial autocorrelation, i.e. locations close to each other exhibit more similar values than those further apart. If this pattern remains present in the residuals of a statistical model based on such data, one of the key assumptions of standard statistical analyses, that residuals are independent and identically distributed (i.i.d), is violated. The violation of the assumption of i.i.d. residuals may bias parameter estimates and can increase type I error rates (falsely rejecting the null hypothesis of no effect). While this is increasingly recognised by researchers analysing species distribution data, there is, to our knowledge, no comprehensive overview of the many available spatial statistical methods to take spatial autocorrelation into account in tests of statistical significance. Here, we describe six different statistical approaches to infer correlates of species’ distributions, for both presence/absence (binary response) and species abundance data (poisson or normally distributed response), while accounting for spatial autocorrelation in model residuals: autocovariate regression; spatial eigenvector mapping; generalised least squares; (conditional and simultaneous) autoregressive models and generalised estimating equations. A comprehensive comparison of the relative merits of these methods is beyond the scope of this paper. To demonstrate each method's implementation, however, we undertook preliminary tests based on simulated data. These preliminary tests verified that most of the spatial modeling techniques we examined showed good type I error control and precise parameter estimates, at least when confronted with simplistic simulated data containing spatial autocorrelation in the errors. However, we found that for presence/absence data the results and conclusions were very variable between the different methods. This is likely due to the low information content of binary maps. Also, in contrast with previous studies, we found that autocovariate methods consistently underestimated the effects of environmental controls of species distributions. Given their widespread use, in particular for the modelling of species presence/absence data (e.g. climate envelope models), we argue that this warrants further study and caution in their use. To aid other ecologists in making use of the methods described, code to implement them in freely available software is provided in an electronic appendix.