No abstract

The first evidence for the emergence of land plants (embryophytes) consists of mid-Ordovician spore tetrads (approximately 476 Myr old). The identity of the early plants that produced these spores is unclear; they are sometimes claimed to be liverworts, but there are no associated megafossils, and similar spores can be produced by a diversity of plants. Indeed, the earliest unequivocal megafossils of land plants consist of early vascular plants and various plants of uncertain affinity. Different phylogenetic analyses have identified liverworts, hornworts and bryophytes as each being the first lineage of land plants; the consensus of these conflicting topologies yields an unresolved polychotomy at the base of land plants. Here we survey 352 diverse land plants and find that three mitochondrial group II introns are present, with occasional losses, in mosses, hornworts and all major lineages of vascular plants, but are entirely absent from liverworts, green algae and all other eukaryotes. These results indicate that liverworts are the earliest land plants, with the three introns having been acquired in a common ancestor of all other land plants, and have important implications concerning the early stages of plant evolution.

A quantitative description of the relationship between protein expression levels and open reading frame nucleotide sequences (ORFs) is important for understanding natural systems, designing synthetic systems, and optimizing heterologous expression. Codon identity, mRNA secondary structure, and nucleotide composition within ORFs markedly influence expression levels. Bioinformatic analysis of ORF sequences in 816 bacterial genomes revealed that these features show distinct regional trends. To investigate their effects on protein expression, we designed 285 synthetic genes and determined corresponding expression levels in vitro using E. coli extracts. We developed a mathematical function, parameterized using this synthetic gene dataset, which enables computation of protein expression levels from ORF nucleotide sequences. In addition to its practical application in the design of heterologous expression systems, this equation provides mechanistic insight into the factors that control translation efficiency. We found that expression is strongly dependent on the presence of high AU content and low secondary structure in the ORF 5′ region. Choice of high-frequency codons contributes to a lesser extent. The 3′ terminal AU content makes modest, but detectable contributions. We present a model for the effect of these factors on the three phases of ribosomal function: initiation, elongation, and termination.

In vitro selection can be used to generate nucleic acid ligands (aptamers) to target molecules ranging in size and structure from cations to cells. However, the selection process is repetitive and time-consuming. We have automated a protocol for in vitro selection using an augmented Beckman Biomek 2000 pipetting robot. The automated selection procedure requires the integration of four devices and the optimization of four molecular biology methods, and is one of the most complex automated protocols attempted to date. Initial attempts at selection yielded robust replication parasites, but optimization of the automated selection procedure suppressed the emergence of these parasites and led to the selection of true nucleic acid ligands. Automated selection can now be used to generate nucleic acid aptamers in days rather than weeks or months.