Are prions a relic of an early stage of peptide evolution?

The rather unique properties of prions and their presence in very different kinds of living species suggest that this type of molecule was created at a very early stage of evolution and may even represent a relic from a time where peptide evolution was ongoing and RNA/DNA did not yet exist. A comparison of the most frequently occurring amino acid sequences in known prions with the sequences preferentially formed in the salt-induced peptide formation reaction, the most simple mechanism enabling the formation of peptides under primitive earth conditions, shows a remarkable coincidence that strongly supports this hypothesis.     

Insulin secretion: Feed-forward control of insulin biosynthesis?

It has long been accepted wisdom that insulin secreted from islet beta cells has either no effect, or an inhibitory feedback effect, on insulin synthesis and secretion. Recent work suggests, instead, that secreted insulin acts directly on beta cells, via its own receptor, to enhance insulin production in an autocrine feed-forward loop.     

Aminoacylation of the anticodon stem by a tRNA-synthetase paralog: relic of an ancient code?

The activation and charging of amino acids onto the acceptor stems of their cognate tRNAs are the housekeeping functions of aminoacyl-tRNA synthetases. The availability of whole genome sequences has revealed the existence of synthetase-like proteins that have other functions linked to different aspects of cell metabolism and physiology. In eubacteria, a paralog of glutamyl-tRNA synthetase, which lacks the tRNA-binding domain, was found to aminoacylate tRNA(Asp) not on the 3'-hydroxyl group of the acceptor stem but on a cyclopentene diol of the modified nucleoside queuosine present at the wobble position of anticodon loop. This modified nucleoside might be a relic of an ancient code.     

Biochemical control of xylan biosynthesis - which end is up?

Xylans are major components of land plant secondary cell walls and are required for normal plant growth and development. Secondary walls also account for the bulk of lignocellulosic biomass, a potential feedstock for large-scale production of biofuels. Glucuronoxylan and arabinoxylan affect the conversion of lignocellulosic biomass to fermentable sugar, a crucial and expensive step in biofuel production. Thus, knowledge of xylan biosynthesis may provide tools to modify secondary cell wall structure and thereby improve the bioprocessing characteristics of biomass. Recent studies have shown that glucuronoxylan structure and biosynthesis are far more complex than previously appreciated and the number of glycosyltransferases implicated in this process continues to increase. New hypotheses regarding the mechanisms of glucuronoxylan biosynthesis challenge some widely held views.     

Using human brain lesions to infer function: a relic from a past era in the fMRI age?

Recent technological advances, such as functional imaging techniques, allow neuroscientists to measure and localize brain activity in healthy individuals. These techniques avoid many of the limitations of the traditional method for inferring brain function, which relies on examining patients with brain lesions. This has fueled the zeitgeist that the classical lesion method is an inferior and perhaps obsolescent technique. However, although the lesion method has important weaknesses, we argue that it complements the newer activation methods (and their weaknesses). Furthermore, recent developments can address many of the criticisms of the lesion method. Patients with brain lesions provide a unique window into brain function, and this approach will fill an important niche in future research.     

The sulfide binding function of annelid hemoglobins: relic of an old biosystem?

Invertebrates living in sulfide-rich environments have developed different strategies of coping with sulfide toxicity. Some bivalves and annelids have hemoglobins that are capable of binding sulfide for detoxification and/or transporting it to internal bacterial symbionts. Annelids living in the sulfide-rich environments have giant (approximately 3.6 MDa) hemoglobin, consisting of 144 globin chains arranged in a hexagonal bilayer structure held together by 36 nonglobin linker chains. Some globin chains contain either a free cysteine residue at positions Cys+1 or at position Cys+11 relative to the E7 distal residue in the E helix and EF interhelical region, respectively, which bind sulfide. The hexagonal bilayer hemoglobins of annelids living in environments lacking sulfide, do not have the corresponding free cysteine residues and cannot bind sulphide. Given that the early stages of life occurred under anoxic conditions in the presence of sulfide, it is possible that the sulfide binding function from modern annelid globins inhabiting sulphide rich habitats is an evolutionary relic. This proposal seems supported by the recent finding of "protoglobins" which also have a corresponding cysteine residue in Archea known to exist in hyperthermophilic and sulfide-rich environments.     

Rubisco activase: an enzyme with a temperature‐dependent dual function?

Heat treatment of intact spinach leaves was found to induce a unique thylakoid membrane association of an approximately 40 kDa stromal protein. This protein was identified as rubisco activase. Most of the rubisco activase was sequestered to the thylakoid membrane, particularly to the stroma-exposed regions, during the first 10 min of heat treatment at 42 degrees C. At lower temperatures (38-40 degrees C) the association of rubisco activase with the thylakoid membrane occurred more slowly. The temperature-dependent association of rubisco activase with the thylakoid membrane was due to a conformational change in the rubisco activase itself, not to heat-induced alterations in the thylakoid membrane. Association of the 41 kDa isoform of rubisco activase occurred first, followed by the binding of the 45 kDa isoform to the thylakoid membrane. Fractionation of thylakoid membranes revealed a specific association of rubisco activase with thylakoid-bound polysomes. Our results suggest a temperature-dependent dual function for rubisco activase. At optimal temperatures it functions in releasing inhibitory sugar phosphates from the active site of Rubisco. During a sudden and unexpected exposure of plants to heat stress, rubisco activase is likely to manifest a second role as a chaperone in association with thylakoid-bound ribosomes, possibly protecting, as a first aid, the thylakoid associated protein synthesis machinery against heat inactivation.     

Allosteric control of mammalian DNA methyltransferases – a new regulatory paradigm

In mammals, DNA methylation is introduced by the DNMT1, DNMT3A and DNMT3B methyltransferases, which are all large multi-domain proteins containing a catalytic C-terminal domain and an N-terminal part with regulatory functions. Recently, two novel regulatory principles of DNMTs were uncovered. It was shown that their catalytic activity is under allosteric control of N-terminal domains with autoinhibitory function, the RFT and CXXC domains in DNMT1 and the ADD domain in DNMT3. Moreover, targeting and activity of DNMTs were found to be regulated in a concerted manner by interactors and posttranslational modifications (PTMs). In this review, we describe the structures and domain composition of the DNMT1 and DNMT3 enzymes, their DNA binding, catalytic mechanism, multimerization and the processes controlling their stability in cells with a focus on their regulation and chromatin targeting by PTMs, interactors and chromatin modifications. We propose that the allosteric regulation of DNMTs by autoinhibitory domains acts as a general switch for the modulation of the function of DNMTs, providing numerous possibilities for interacting proteins, nucleic acids or PTMs to regulate DNMT activity and targeting. The combined regulation of DNMT targeting and catalytic activity contributes to the precise spatiotemporal control of DNMT function and genome methylation in cells.     

The discovery of Rubisco activase – yet another story of serendipity

A brief history of Rubisco (ribulose bisphosphate carboxylase oxygenase) research and the events leading to the discovery and initial characterization of Rubisco activase are described. Key to the discovery was the chance isolation of a novel Arabidopsis photosynthesis mutant. The characteristics of the mutant suggested that activation of Rubisco was not a spontaneous process in vivo, but involved a heritable factor. The search for the putative factor by 2D electrophoresis identified two polypeptides, genetically linked to Rubisco activation, that were missing in chloroplasts from the mutant. An assay for the activity of these polypeptides, which were given the name Rubisco activase, was developed after realizing the importance of including ribulose bisphosphate (RuBP) in the assay. The requirement for ATP and the subsequent identification of activase as an ATPase came about fortuitously, the result of a RuBP preparation that was contaminated with adenine nucleotides. Finally, the ability of activase to relieve inhibition of the endogenous Rubisco inhibitor, 2-carboxyarabinitol 1-phosphate, provided an early indication of the mechanism by which activase regulates Rubisco. This revised version was published online in June 2006 with corrections to the Cover Date.     

Unique biosynthesis of dehydroquinic acid?

A search of the genomic sequences of the thermophilic microorganisms Aquifex aeolicus, Archaeoglobus fulgidus, Methanobacterium thermoautotrophicum, and Methanococcus jannaschii for the first seven enzymes (aroG, B, D, E, K, A, and C ) involved in the shikimic acid biosynthetic pathway reveal two key enzymes are missing. The first enzyme in the pathway, 3-deoxy-d-arabino-heptulosonic acid 7-phosphate synthase (aroG) and the second enzyme in the pathway, 5-dehydroquinic acid synthase (aroB) are "missing." The remaining five genes for the shikimate pathway in these organism are present and are similar to the corresponding Escherichia coli genes. The genomic sequences of the thermophiles Pyrococcus abyssi and Thermotoga maritima contain the aroG and aroB genes. Several fungi such as Aspergillus fumigatus, Aspergillus nidulans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Pneumocystis carinii f. sp. carinii, and Neurospora crassa contain the gene aroM, a pentafunctional enzyme whose overall activity is equivalent to the combined catalytic activities of proteins expressed by aroB, D, E, K, and A genes. Two of these fungi also lack an aroG gene. A discussion of potential reasons for these missing enzymes is presented.     

Why are the genomes of endosymbiotic bacteria so stable?

The comparative analysis of three strains of the endosymbiotic bacterium Buchnera aphidicola has revealed high genome stability associated with an almost complete absence of chromosomal rearrangements and horizontal gene transfer events during the past 150 million years. The loss of genes involved in DNA uptake and recombination in the initial stages of endosymbiosis probably underlies this stability. Gene loss, which was extensive during the initial steps of Buchnera evolution, has continued in the different Buchnera lineages since their divergence.     

Subunit structure and gene control of mouse NADP—malate dehydrogenase

The NADP-dependent malate dehydrogenase (MDH) in the supernatant fraction of mouse tissues is known to occur in two allelic forms which are electrophoretically distinguishable; each produces a single band in starch gel. We have investigated the subunit structure and synthesis of NADP—MDH through electrophoretic patterns obtained from several experimental sources. (1) Heterozygotes containing both alleles yield a five-banded pattern. The bands are in an approximate frequency of 1:4:6:4:1; the two extremes correspond to the pure types and the three intermediates are presumably hybrid enzymes. The NADP—MDH molecule therefore appears to be a tetramer. (2) In muscle heterokaryons of allophenic mice (with homozygous nuclei of each genotype within a common cytoplasm), hybrid enzymes are formed; they are not formed in other allophenic tissues. Therefore the gene at this locus codes only for monomeric subunits and the tetramer is assembled in a second step in the cytoplasm. Also, both genes must function in a nucleus when the locus is active (e.g., in F₁ uninucleated cells). (3) Dissociation in vitro of mixtures of both pure types of enzymes, followed by reassociation among fragments, leads to a three-banded pattern, even after repeated cycles. Thus the tetramer must cleave in a fixed plane, to form dimers, which reassociate, rather than in a random fashion to form monomers. The most likely interpretation is that mouse NADP—MDH is an example of the type of tetramer postulated by Monod et al. (1965) and termed isologous. The dimers are held symmetrically in the tetrameric conformation by relatively weak forces; the monomeric subunits comprising the dimer are held together by stronger forces.These investigations were supported by U.S.P.H.S. grants No. HD-01646, CA-06927, and FR-05539, and by an appropriation from the Commonwealth of Pennsylvania.     

Is a genome a codeword of an error-correcting code?

Since a genome is a discrete sequence, the elements of which belong to a set of four letters, the question as to whether or not there is an error-correcting code underlying DNA sequences is unavoidable. The most common approach to answering this question is to propose a methodology to verify the existence of such a code. However, none of the methodologies proposed so far, although quite clever, has achieved that goal. In a recent work, we showed that DNA sequences can be identified as codewords in a class of cyclic error-correcting codes known as Hamming codes. In this paper, we show that a complete intron-exon gene, and even a plasmid genome, can be identified as a Hamming code codeword as well. Although this does not constitute a definitive proof that there is an error-correcting code underlying DNA sequences, it is the first evidence in this direction.