Revaluation of overselected stimuli: Emergence of control by underselected stimuli depends on degree of overselectivity.

Stimulus overselectivity describes strong control by one stimulus element at the expense of other equally relevant elements. Research suggests that control by underselected stimuli emerges following extinction of the overselected stimulus ("revaluation") and the emergence is larger when overselectivity is greater. We compared such revaluation effects with a control compound or condition in two experiments. Human participants chose between compound S+ and S- stimuli. Then, to assess control by compound-stimulus elements, participants chose between individual elements in a testing phase without feedback. The S+ element chosen most often (the overselected element) underwent revaluation, during which choice of that element was extinguished and choice of a novel element reinforced. Thereafter, participants completed a retesting phase. Revaluation reduced choice of the overselected element. Choice of the underselected element decreased for participants with low overselectivity but increased for participants with high overselectivity. This was not the case for a control compound that did not undergo revaluation (Experiments 1 and 2) or in a control condition in which the overselected element continued to be reinforced during revaluation (Experiment 2). These findings suggest that overselectivity levels may modulate revaluation effects, and they also highlight the importance of the contingency change in postrevaluation changes in stimulus control.

Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment.

Antibiotic resistance arising via chromosomal mutations is typically specific to a particular antibiotic or class of antibiotics. We have identified mutations in genes encoding ribosomal components in Mycobacterium smegmatis that confer resistance to several structurally and mechanistically unrelated classes of antibiotics and enhance survival following heat shock and membrane stress. These mutations affect ribosome assembly and cause large-scale transcriptomic and proteomic changes, including the downregulation of the catalase KatG, an activating enzyme required for isoniazid sensitivity, and upregulation of WhiB7, a transcription factor involved in innate antibiotic resistance. Importantly, while these ribosomal mutations have a fitness cost in antibiotic-free medium, in a multidrug environment they promote the evolution of high-level, target-based resistance. Further, suppressor mutations can then be easily acquired to restore wild-type growth. Thus, ribosomal mutations can serve as stepping-stones in an evolutionary path leading to the emergence of high-level, multidrug resistance.

New classes of self-cleaving ribozymes revealed by comparative genomics analysis.

Enzymes made of RNA catalyze reactions that are essential for protein synthesis and RNA processing. However, such natural ribozymes are exceedingly rare, as evidenced by the fact that the discovery rate for new classes has dropped to one per decade from about one per year during the 1980s. Indeed, only 11 distinct ribozyme classes have been experimentally validated to date. Recently, we recognized that self-cleaving ribozymes frequently associate with certain types of genes from bacteria. Herein we exploited this association to identify divergent architectures for two previously known ribozyme classes and to discover additional noncoding RNA motifs that are self-cleaving RNA candidates. We identified three new self-cleaving classes, which we named twister sister, pistol and hatchet, from this collection, suggesting that even more ribozymes remain hidden in modern cells.

An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism.

Over 30 years ago, ZTP (5-aminoimidazole-4-carboxamide riboside 5'-triphosphate), a modified purine biosynthetic intermediate, was proposed to signal 10-formyl-tetrahydrofolate (10f-THF) deficiency in bacteria. However, the mechanisms by which this putative alarmone or its precursor ZMP (5-aminoimidazole-4-carboxamide ribonucleotide, also known as AICAR) brings about any metabolic changes remain unexplained. Herein, we report the existence of a widespread riboswitch class that is most commonly associated with genes related to de novo purine biosynthesis and one-carbon metabolism. Biochemical data confirm that members of this riboswitch class selectively bind ZMP and ZTP with nanomolar affinity while strongly rejecting numerous natural analogs. Indeed, increases in the ZMP/ZTP pool, caused by folate stress in bacterial cells, trigger changes in the expression of a reporter gene fused to representative ZTP riboswitches in vivo. The wide distribution of this riboswitch class suggests that ZMP/ZTP signaling is important for species in numerous bacterial lineages.

A widespread self-cleaving ribozyme class is revealed by bioinformatics.

Ribozymes are noncoding RNAs that promote chemical transformations with rate enhancements approaching those of protein enzymes. Although ribozymes are likely to have been abundant during the RNA world era, only ten classes are known to exist among contemporary organisms. We report the discovery and analysis of an additional self-cleaving ribozyme class, called twister, which is present in many species of bacteria and eukarya. Nearly 2,700 twister ribozymes were identified that conform to a secondary structure consensus that is small yet complex, with three stems conjoined by internal and terminal loops. Two pseudoknots provide tertiary structure contacts that are critical for catalytic activity. The twister ribozyme motif provides another example of a natural RNA catalyst and calls attention to the potentially varied biological roles of this and other classes of widely distributed self-cleaving RNAs.

An engineered microbial platform for direct biofuel production from brown macroalgae.

Prospecting macroalgae (seaweeds) as feedstocks for bioconversion into biofuels and commodity chemical compounds is limited primarily by the availability of tractable microorganisms that can metabolize alginate polysaccharides. Here, we present the discovery of a 36-kilo-base pair DNA fragment from Vibrio splendidus encoding enzymes for alginate transport and metabolism. The genomic integration of this ensemble, together with an engineered system for extracellular alginate depolymerization, generated a microbial platform that can simultaneously degrade, uptake, and metabolize alginate. When further engineered for ethanol synthesis, this platform enables bioethanol production directly from macroalgae via a consolidated process, achieving a titer of 4.7% volume/volume and a yield of 0.281 weight ethanol/weight dry macroalgae (equivalent to ~80% of the maximum theoretical yield from the sugar composition in macroalgae).

Heterobimetallic coordination polymers incorporating [M(CN)(2)](-) (M = Cu, Ag) and [Ag(2)(CN)(3)](-) units: increasing structural dimensionality via M-M' and M...NC interactions.

A series of new heterometallic coordination polymers has been prepared from the reaction of metal-ligand cations and KAg(CN)(2) units. Many of these contain silver-silver (argentophilic) interactions, analogous to gold-gold interactions, which serve to increase supramolecular structural dimensionality. Compared to [Au(CN)(2)](-) analogues, these polymers display new trends specific to [Ag(CN)(2)](-), including the formation of [Ag(2)(CN)(3)](-) and the presence of Ag...N interactions. [Cu(en)(2)][Ag(2)(CN)(3)][Ag(CN)(2)] (1, en = ethylenediamine) forms 1-D chains of alternating [Ag(CN)(2)](-) and [Ag(2)(CN)(3)](-) units via argentophilic interactions of 3.102(1) A. These chains are connected into a 2-D array by strong cyano(N)-Ag interactions of 2.572(3) A. [Cu(dien)Ag(CN)(2)](2)[Ag(2)(CN)(3)][Ag(CN)(2)] (2, dien = diethylenetriamine) forms a 1-D chain of alternating [Cu(dien)](2+) and [Ag(CN)(2)](-) ions with the Cu(II) atoms connected in an apical/equatorial fashion. These chains are cross-linked by [Ag(2)(CN)(3)](-) units via argentophilic interactions of 3.1718(8) A and held weakly in a 3-D array by argentophilic interactions of 3.2889(5) A between the [Ag(CN)(2)](-) in the 2-D array and the remaining free [Ag(CN)(2)](-). [Ni(en)][Ni(CN)(4)].2.5H(2)O (4) was identified as a byproduct in the reaction to prepare the previously reported [Ni(en)(2)Ag(2)(CN)(3)][Ag(CN)(2)] (3). In [Ni(tren)Ag(CN)(2)][Ag(CN)(2)] (5, tren = tris(2-aminoethyl)amine), [Ni(tren)](2+) cations are linked in a cis fashion by [Ag(CN)(2)](-) anions to form a 1-D chain similar to the [Au(CN)(2)](-) analogue. [Cu(en)Cu(CN)(2)Ag(CN)(2)] (6) is a trimetallic polymer consisting of interpenetrating (6,3) nets stabilized by d(10)-d(10) interactions between Cu(I)-Ag(I) (3.1000(4) A). Weak antiferromagnetic coupling has been observed in 2, and a slightly stronger exchange has been observed in 6. The Ni(II) complexes, 4 and 5, display weak antiferromagnetic interactions as indicated by their relatively larger D values compared to that of 3. Magnetic measurements on isostructural [Ni(tren)M(CN)(2)][M(CN)(2)] (M = Ag, Au) show that Ag(I) is a more efficient mediator of magnetic exchange as compared to Au(I). The formation of [Ni(CN)(4)](2)(-), [Ag(2)(CN)(3)](-), and [Cu(CN)(2)](-) are all attributed to secondary reactions of the dissociation products of the labile KAg(CN)(2).