New insights into the molecular mechanisms of evolution: stress increases genetic diversity

The mechanisms of stress-induced mutagenesis in prokaryotes and realization of reserved (preaccumulated) genetic variation in eukaryotes are considered. In prokaryotes, replication becomes error-prone in stress because of the induction of the SOS response and the inactivation of the mismatch repair system; stress also increases the transposition rate and the efficiency of interspecific gene transfer. In eukaryotes, chaperone HSP90, which restores the native folding of mutant proteins (e.g., signal transduction and morphogenetic proteins) in normal conditions, fails to do so in stress, which leads to abrupt expression of multiple mutations earlier reserved in the corresponding genes. The role of these mechanisms in the evolution of prokaryotes and eukaryotes is discussed.     

Seeking the determinants of the elusive functions of Sco proteins

Sco proteins are present in all types of organisms, including the vast majority of eukaryotes and many prokaryotes. It is well established that Sco proteins in eukaryotes are involved in the assembly of the Cu(A) cofactor of mitochondrial cytochrome c oxidase; however their precise role in this process has not yet been elucidated at the molecular level. In particular, some but not all eukaryotes including humans possess two Sco proteins whose individual functions remain unclear. There is evidence that eukaryotic Sco proteins are also implicated in other cellular processes such as redox signalling and regulation of copper homeostasis. The range of physiological functions of Sco proteins appears to be even wider in prokaryotes, where Sco-encoding genes have been duplicated many times during evolution. While some prokaryotic Sco proteins are required for the biosynthesis of cytochrome c oxidase, others are most likely to take part in different processes such as copper delivery to other enzymes and protection against oxidative stress. The detailed understanding of the multiplicity of roles ascribed to Sco proteins requires the identification of the subtle determinants that modulate the two properties central to their known and potential functions, i.e. copper binding and redox properties. In this review, we provide a comprehensive summary of the current knowledge on Sco proteins gained by genetic, structural and functional studies on both eukaryotic and prokaryotic homologues, and propose some hints to unveil the elusive molecular mechanisms underlying their functions.     

Oxidative Stress and Mechanisms of Protection Against It in Bacteria

In the review contemporary data on the effects of oxidative stresses of various kinds in bacteria are summarized. A general theory of oxidative stress, peculiarities of oxidative stress in eukaryotes and prokaryotes, and natural and induced oxidative stresses are described. Data on the mechanisms of protection against oxidative stress are given, including prevention of the generation of oxidative stress, prevention of propagation of free radical chain reactions, and the mechanisms of repair of damaged DNA. The regulation of effector genes via redox-sensitive iron-containing proteins is analyzed. Special attention is given to the expression of so-called antioxidant and associated enzymes as protection mechanisms and to the space–time organization of the response of bacteria to oxidative stress.     

Comparing function and structure between entire proteomes

More than 30 organisms have been sequenced entirely. Here, we applied a variety of simple bioinformatics tools to analyze 29 proteomes for representatives from all three kingdoms: eukaryotes, prokaryotes, and archaebacteria. We confirmed that eukaryotes have relatively more long proteins than prokaryotes and archaes, and that the overall amino acid composition is similar among the three. We predicted that approximately 15%-30% of all proteins contained transmembrane helices. We could not find a correlation between the content of membrane proteins and the complexity of the organism. In particular, we did not find significantly higher percentages of helical membrane proteins in eukaryotes than in prokaryotes or archae. However, we found more proteins with seven transmembrane helices in eukaryotes and more with six and 12 transmembrane helices in prokaryotes. We found twice as many coiled-coil proteins in eukaryotes (10%) as in prokaryotes and archaes (4%-5%), and we predicted approximately 15%-25% of all proteins to be secreted by most eukaryotes and prokaryotes. Every tenth protein had no known homolog in current databases, and 30%-40% of the proteins fell into structural families with >100 members. A classification by cellular function verified that eukaryotes have a higher proportion of proteins for communication with the environment. Finally, we found at least one homolog of experimentally known structure for approximately 20%-45% of all proteins; the regions with structural homology covered 20%-30% of all residues. These numbers may or may not suggest that there are 1200-2600 folds in the universe of protein structures. All predictions are available at http://cubic.bioc.columbia.edu/genomes.     

Reverse genetic approaches in plants and yeast suggest a role for novel,evolutionarily conserved,selenoprotein-related genes in oxidative stress defense

Oxidation of methionine residues during periods of oxidative stress can lead to loss of protein function. Organisms have developed defense strategies to minimize such damage. The PilB protein, which is involved in pilus formation in the pathogen Neisseria gonorrhoeae, is composed of three functional protein domains (I-III) with putative roles in oxidative stress defense. These domains are evolutionarily conserved and homologs have been discovered in diverse prokaryotes and eukaryotes. Domain III shows similarities to selenoproteins which contain selenium instead of sulfur in a conserved cysteine residue. The substitution of selenium for sulfur alters the redox properties of such proteins. Knock-out mutants were used to elucidate the function of these novel selenoprotein-like domains in yeast and in Arabidopsis thaliana. We show that organisms with non-functional genes for selenoprotein-like polypeptides accumulate higher levels of oxidized methionine residues on exposure to oxidative stress. The behavior of the mutants suggests that these novel selenoprotein-like gene products are part of a ubiquitous detoxification system that interacts with other redox-related proteins such as the thioredoxin-related protein and methionine sulfoxide reductase which are encoded by domains I and II of PilB. These proteins may be encoded by one gene as in the case of several prokaryotes, or by separate genes as in the eukaryotes examined here.     

New Role for an Old Rule: N-end Rule-Mediated Degradation of Ethylene Responsive Factor Proteins Governs Low Oxygen Response in Plants

The N-end rule pathway regulates protein degradation, which depends on exposed N-terminal sequences in prokaryotes and eukaryotes. In plants, conserved and specific enzymes stimulate selective proteolysis. Although a number of developmental and growth phenotypes have been reported for mutants in the N-end rule, its function has remained unrelated to specific physiological pathways. The first report of the direct involvement of the N-end rule in stress responses focused on hypoxic signaling and how the oxygen-dependent oxidation of cystein promotes the N-end rule-mediated degradation of ethylene responsive factor (ERF)-VII proteins, the master regulators of anaerobic responses. It has beensuggested that plants have evolved specific mechanisms to tune ERF-VII availability in the nucleus. In this review, we speculate that ERF-VII proteins are reversibly protected from degradation via membrane sequestration. The oxidative response in plants subjected to anoxic conditions suggests that reactive oxygen and nitrogen species (reactive oxygen species and reactive nitrogen species) may interact or interfere with the N-end rule pathway-mediated response to hypoxia.     

mRNA decay in prokaryotes and eukaryotes: different approaches to a similar problem

Over the past 15 years considerable progress has been made in understanding the molecular mechanisms of mRNA decay in both prokaryotes and eukaryotes. Interestingly, unlike other important biological reactions such as DNA replication and repair, many features of mRNA decay differ between prokaryotes or eukaryotes. Even when a particular enzyme like poly(A) polymerase has been conserved, polyadenylation of mRNAs in prokaryotes appears to serve a very different function than it does in eukaryotes. Furthermore, while mRNA degrading multiprotein complexes have been identified in both prokaryotes and eukaryotes, their composition and biochemical mechanisms are significantly different. Accordingly, this review seeks to provide a concise comparison of our current knowledge regarding the pathways of mRNA decay in two model organisms, the prokaryote Escherichia coli and the eukaryote Saccharomyces cerevisiae.     

Glycoproteins in prokaryotes

Rather recently it has become clear that prokaryotes (Archaea and Bacteria) are able to glycosylate proteins. A literature survey revealed the different types of glycoproteins. They include mainly surface layer (S-layer) proteins, flagellins, and polysaccharide-degrading enzymes. Only in a few cases is structural information available. Many different structures have been observed that display much more variation than that observed in eukaryotes. A few studies have given evidence for the function of the prokaryotic glycoprotein glycans. Also from the biosynthetic point of view, information is rather scarce. Due to their different cell structure, prokaryotes have to use mechanisms different from those found in eukaryotes to glycosylate proteins. However, from the fragmented data available for the prokaryotic glycoproteins, similarities with the eukaryotic system can be noticed. Received: 24 February 1997 / Accepted: 13 May 1997     

"Anticipated" nucleosome positioning pattern in prokaryotes

Linguistic (word count) analysis of prokaryotic genome sequences, by Shannon N-gram extension, reveals that the dominant hidden motifs in A+T rich genomes are T(A)(T)A and G(A)(T)C with uncertain number of repeating A and T. Since prokaryotic sequences are largely protein-coding, the motifs would correspond to amphipathic alpha-helices with alternating lysine and phenylalanine as preferential polar and non-polar residues. The motifs are also known in eukaryotes, as nucleosome positioning patterns. Their existence in prokaryotes as well may serve for binding of histone-like proteins to DNA. In this case the above patterns in prokaryotes may be considered as "anticipated" nucleosome positioning patterns which, quite likely, existed in prokaryotic genomes before the evolutionary separation between eukaryotes and prokaryotes.     

Signs of Ancient and Modern Exon-Shuffling Are Correlated to the Distribution of Ancient and Modern Domains Along Proteins

Exon-shuffling is an important mechanism accounting for the origin of many new proteins in eukaryotes. However, its role in the creation of proteins in the ancestor of prokaryotes and eukaryotes is still debatable. Excess of symmetric exons is thought to represent evidence for exon-shuffling since the exchange of exons flanked by introns of the same phase does not disrupt the reading frame of the host gene. In this report, we found that there is a significant correlation between symmetric units of shuffling and the age of protein domains. Ancient domains, present in both prokaryotes and eukaryotes, are more frequently bounded by phase 0 introns and their distribution is biased towards the central part of proteins. Modern domains are more frequently bounded by phase 1 introns and are present predominantly at the ends of proteins. We propose a model in which shuffling of ancient domains mainly flanked by phase 0 introns was important in the ancestor of eukaryotes and prokaryotes, during the creation of the central part of proteins. Shuffling of modern domains, predominantly flanked by phase 1 introns, accounted for the origin of the extremities of proteins during eukaryotic evolution.     

Differential gene expression in Giardia lamblia under oxidative stress: Significance in eukaryotic evolution

Giardia lamblia is a unicellular, early branching eukaryote causing giardiasis, one of the most common human enteric diseases. Giardia, a microaerophilic protozoan parasite has to build up mechanisms to protect themselves against oxidative stress within the human gut (oxygen concentration 60 μM) to establish its pathogenesis. G. lamblia is devoid of the conventional mechanisms of the oxidative stress management system, including superoxide dismutase, catalase, peroxidase, and glutathione cycling, which are present in most eukaryotes. NADH oxidase is a major component of the electron transport chain of G. lamblia, which in concurrence with disulfide reductase, protects oxygen-labile proteins such as pyruvate: ferredoxin oxidoreductase against oxidative stress by sustaining a reduced intracellular environment. It also contains the arginine dihydrolase pathway, which occurs in a number of anaerobic prokaryotes, includes substrate level phosphorylation and adequately active to make a major contribution to ATP production.     

Cold shock and adaptation

Adaptation to environmental stresses, such as temperature fluctuation, is essential for the survival of all living organisms. Cellular responses in both prokaryotes and eukaryotes to high temperature include the synthesis of a set of highly conserved proteins known as the heat shock proteins. In contrast to the heat shock response, adaptation to low temperatures has not been as extensively studied. However, a family of cold-inducible proteins is evident in prokaryotes. In addition, most organisms have developed adaptive mechanisms that alter both membrane fluidity and the protein translation machinery at low temperature. This review addresses the different adaptive mechanisms used by a variety of organisms with a focus on the molecular mechanisms of cold adaptation that have recently been identified during the cold shock response in Escherichia coli. BioEssays 20:49–57, 1998. © 1998 John Wiley & Sons, Inc.     

Where is the root of the universal tree of life?

The currently accepted universal tree of life based on molecular phylogenies is characterised by a prokaryotic root and the sisterhood of archaea and eukaryotes. The recent discovery that each domain (bacteria, archaea, and eucarya) represents a mosaic of the two others in terms of its gene content has suggested various alternatives in which eukaryotes were derived from the merging of bacteria and archaea. In all these scenarios, life evolved from simple prokaryotes to complex eukaryotes. We argue here that these models are biased by overconfidence in molecular phylogenies and prejudices regarding the primitive nature of prokaryotes. We propose instead a universal tree of life with the root in the eukaryotic branch and suggest that many prokaryotic features of the information processing mechanisms originated by simplification through gene loss and non-orthologous displacement.     

Intracellular copper routing: the role of copper chaperones

Copper is required by all living systems. Cells have a variety of mechanisms to deal with this essential, yet toxic trace element. A recently discovered facet of homeostatic mechanisms is the protein-mediated, intracellular delivery of copper to target proteins. This routing is accomplished by a novel class of proteins, the 'copper chaperones'. They are a family of conserved proteins present in prokaryotes and eukaryotes, which suggests that copper chaperones are used throughout nature for intracellular copper routing.     

Death by protein damage in irradiated cells

A founding concept of radiobiology that deals with X-rays, γ-rays and ultraviolet light is that radiation indiscriminately damages cellular macromolecules. Mounting experimental evidence does not fit into this theoretical framework. Whereas DNA lesion-yields in cells exposed to a given dose and type of radiation appear to be fixed, protein lesion-yields are highly variable. Extremely radiation resistant bacteria such as Deinococcus radiodurans have evolved extraordinarily efficient antioxidant chemical defenses which specifically protect proteins and the functions they catalyze. In diverse prokaryotes, the lethal effects of radiation appear to be governed by oxidative protein damage, which inactivates enzymes including those needed to repair and replicate DNA. These findings offer fresh insight into the molecular mechanisms of radiation resistance and present themselves as new opportunities to study and control oxidative stress in eukaryotes, including mammalian cells and their cancer cell counterparts.     

Generalized electrostatic model of the wrapping of DNA around oppositely charged proteins

Histonelike proteins in prokaryotes and histone octamers in eukaryotes carry large positive charges, which are responsible of strong electrostatic interactions with DNA. As a result, DNA wraps around proteins and genetic information is condensed. We describe a generalized model of these electrostatic interactions mediated by salt that explains the wrapping of DNA around the nucleosome octamer, around remodeling factors in eukaryotes and around histonelike proteins in prokaryotes. It comes out that small changes in protein dimension and charge produce large effects in the supramolecular DNA-protein architecture.     

Microtubule Dynamics may Embody a Stationary Bipolarity Forming Mechanism Related to the Prokaryotic Division Site Mechanism (Pole-to-Pole Oscillations)

Cell division mechanisms in eukaryotes and prokaryotes have until recently been seen as being widely different. However, pole-to-pole oscillations of proteins like MinE in prokaryotes are now known to determine the division plane. These protein waves arise through spontaneous pattern forming reaction—diffusion mechanisms, based on cooperative binding of the proteins to a quasistationary matrix (like the cell membrane or DNA). Rather than waves, stationary bipolar pattern formation may arise as well. Some of the involved proteins have eukaryotic homologs (e.g. FtsZ and tubulin), pointing to a possible ancient shared mechanism. Tubulin polymerizes to microtubules in the spindle. Mitotic microtubules are in a highly dynamical state, frequently undergoing rapid shortening (catastrophe), and fragments formed from the microtubule ends are inferred to enhance the destabilization. Here, we show that cooperative binding of such fragments to microtubules may set up a similar pattern forming mechanism as seen in prokaryotes. The result is a spontaneously formed, well controllable, bipolar state of microtubule dynamics in the cell, which may contribute to defining the bipolar spindle.     

Structural disorder in eukaryotes

Based on early bioinformatic studies on a handful of species, the frequency of structural disorder of proteins is generally thought to be much higher in eukaryotes than in prokaryotes. To refine this view, we present here a comparative prediction study and analysis of 194 fully described eukaryotic proteomes and 87 reference prokaryotes for structural disorder. We found that structural disorder does distinguish eukaryotes from prokaryotes, but its frequency spans a very wide range in the two superkingdoms that largely overlap. The number of disordered binding regions and different Pfam domain types also contribute to distinguish eukaryotes from prokaryotes. Unexpectedly, the highest levels--and highest variability--of predicted disorder is found in protists, i.e. single-celled eukaryotes, often surpassing more complex eukaryote organisms, plants and animals. This trend contrasts with that of the number of domain types, which increases rather monotonously toward more complex organisms. The level of structural disorder appears to be strongly correlated with lifestyle, because some obligate intracellular parasites and endosymbionts have the lowest levels, whereas host-changing parasites have the highest level of predicted disorder. We conclude that protists have been the evolutionary hot-bed of experimentation with structural disorder, in a period when structural disorder was actively invented and the major functional classes of disordered proteins established.     

Protein export in prokaryotes and eukaryotes. Theme with variations.

Protein export in prokaryotes as well as in eukaryotes can be defined as protein transport across the plasma membrane. In both types of organisms there are various apparently ATP-dependent transport mechanisms which can be distinguished from one another and which show similarities when the prokaryotic mechanism is compared with the respective eukaryotic mechanism. First, one can distinguish between transport mechanisms which involve so-called signal or leader peptides and those which do not. The latter mechanisms seem to employ ATP-dependent transport systems which belong to the family of oligopeptide permeases and multiple drug resistance proteins. Second, in signal or leader peptide-dependent transport one can distinguish between transport mechanisms which involve ribonucleoparticles and those which employ molecular chaperones. Both mechanisms appear to converge at the level of ATP-dependent translocases.