The ancestor of Paulinella chromatophora established a symbiotic relationship with cyanobacteria related to the Prochloroccocus/Synechococcus clade. This event has been described as a second primary endosymbiosis leading to a plastid in the making. Based on the rate of pseudogene disintegration in the endosymbiotic bacteria Buchnera aphidicola, it was suggested that the chromatophore in P. chromatophora has a minimum age of ~60 Myr. Here we revisit this estimation by using a lognormal relaxed molecular clock on the 18S rRNA of P. chromatophora. Our time estimates show that depending on the assumptions made to calibrate the molecular clock, P. chromatophora diverged from heterotrophic Paulinella spp. ~ 90 to 140 Myr ago, thus establishing a maximum date for the origin of the chromatophore. Funding StatementBPZ wishes to thank CINVESTAV Irapuato for funding and support. The authors also declare that no competing interests exist.

The expression of some very short open reading frames (ORFs) in Escherichia coli results in peptidyltRNA accumulation that is lethal to cells defective in peptidyl-tRNA hydrolase activity. In an attempt to understand the factors that affect this phenotype, we have surveyed the toxicity of a complete set of two-codon ORFs cloned as minigenes in inducible expression vectors. The minigenes were tested in hydrolase-defective hosts and classified according to their degree of toxicity. In general, minigenes harboring codons belonging to the same box in the standard table of the genetic code mediated similar degrees of toxicity. Moreover, the levels of peptidyl-tRNA accumulation for synonymous minigenes decoded by the same tRNA were comparable. However, two exceptions were observed: (i) expression of minigenes harboring the Arg codons CGA, CGU, and CGC, resulted in the accumulation of different levels of the unique peptidyl-tRNA Arg-2 and (ii) the toxicity of minigenes containing CUG and UCU codons, each recognized by two different tRNAs, depended on peptidyltRNA accumulation of only one of them. Non-toxic, or partly toxic, minigenes prompted higher accumulation levels of peptidyl-tRNA upon deprivation of active RF1, implying that translation termination occurred efficiently. Our data indicate that the nature of the last decoding tRNA is crucial in the rate of peptidyl-tRNA release from the ribosome.Minigenes are DNA sequences present in bacterial chromosomes that may be expressed into functionally active oligopeptides. In Escherichia coli for example, translation of a peptide encoded in a minigene present in the 23 S rRNA, turns cells erythromycin resistant (1); also, peptides containing five to eight amino acid residues encoded in the attenuator sequence of genes, which confer resistance to chloramphenicol and erythromycin (catA86, cmlA and ermC), inhibit peptidyltransferase activity in bacteria (2).Translation of two-codon minigenes located in bacteriophage lambda chromosome bar regions is lethal to cells partly defective in peptidyl-tRNA hydrolase activity, but not to wild-type bacteria (3). Translation of bar minigene mRNAs results in premature release of peptidyl-tRNAs from ribosomes (a phenomenon called "drop-off "); under limited Pth 1 activity, these peptidyl-tRNAs accumulate in the cell. It has been proposed that lethality stems from the subsequent shortage in the pool of specific tRNAs for further involvement in protein synthesis (4). Recently, evidence that seems to support this inference has been obtained for a ribosome bypassing system (5), but the alternative explanation that peptidyl-tRNAs might be toxic per se has not been ruled out (6).Translation ends at the termination codon in an mRNA, when the ribosomal peptidyl-transferase presumably hydrolyzes the ester bond between the completed polypeptide chain and the last tRNA. The termination reaction requires the concurrence of the release factors RF-1 or RF-2 (depending on the nature of the termination codon) and other factors catalyzing the release of t...

The innate immune response of Anopheles gambiae involves the transcriptional upregulation of effector genes. Therefore, the cis-regulatory sequences and their cognate binding factors play essential roles in the mosquito’s immune response. However, the genetic control of the mosquito’s innate immune response is not yet fully understood. To gain further insight on the elements, the factors and the potential mechanisms involved, an open chromatin profiling was carried out on A. gambiae-derived immune-responsive cells. Here, we report the identification of cis-regulatory sites, immunity-related transcription factor binding sites, and cis-regulatory modules. A de novo motif discovery carried out on this set of cis-regulatory sequences identified immunity-related motifs and cis-regulatory modules. These modules contain motifs that are similar to binding sites for REL-, STAT-, lola- and Deaf1-type transcription factors. Sequence motifs similar to the binding sites for GAGA were found within a cis-regulatory module, together with immunity-related transcription factor binding sites. The presence of Deaf1- and lola-type binding sites, along with REL- and STAT-type binding sites, suggests that the immunity function of these two factors could have been conserved both in Drosophila and Anopheles gambiae.

The story of how preColumbian civilizations developed goes hand-in-hand with the process of plant domestication by Mesoamerican inhabitants. Here, we present the almost complete sequence of a mitochondrial genome and a partial chloroplast genome from an archaeological maize sample collected at the Valley of Tehuacán, México. Accelerator mass spectrometry dated the maize sample to be 5,040–5,300 years before present (95% probability). Phylogenetic analysis of the mitochondrial genome shows that the archaeological sample branches basal to the other Zea mays genomes, as expected. However, this analysis also indicates that fertile genotype NB is closely related to the archaeological maize sample and evolved before cytoplasmic male sterility genotypes (CMS-S, CMS-T, and CMS-C), thus contradicting previous phylogenetic analysis of mitochondrial genomes from maize. We show that maximum-likelihood infers a tree where CMS genotypes branch at the base of the tree when including sites that have a relative fast rate of evolution thus suggesting long-branch attraction. We also show that Bayesian analysis infer a topology where NB and the archaeological maize sample are at the base of the tree even when including faster sites. We therefore suggest that previous trees suffered from long-branch attraction. We also show that the phylogenetic analysis of the ancient chloroplast is congruent with genotype NB to be more closely related to the archaeological maize sample. As shown here, the inclusion of ancient genomes on phylogenetic trees greatly improves our understanding of the domestication process of maize, one of the most important crops worldwide.

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