The palirrhotrophic origin of energy metabolism

It is proposed that the earliest cellular organisms relied upon a novel type of energy transduction termed palirrhotrophy, which generates a high-energy currency chemiosmotically by exploiting the rhythmic variations in salinity which occur in the estuarine environment. Calculations based on estimates of contemporary chemiosmotic transduction efficiency suggest that such a mechanism could produce usable energy in high yield. The minimum polypeptide requirement for palirrhotrophy compares favorably with that of a fermentative pathway. It is suggested that palirrhotrophic organisms exist today but are difficult to detect.     

Monotreme IGF2 expression and ancestral origin of genomic imprinting

IGF2 (insulin-like growth factor 2) and M6P/IGF2R (mannose 6-phosphate/insulin-like growth factor 2 receptor) are imprinted in marsupials and eutherians but not in birds. These results along with the absence of M6P/IGF2R imprinting in the egg-laying monotremes indicate that the parental imprinting of fetal growth-regulatory genes may be unique to viviparous mammals. In this investigation, we have cloned IGF2 from two monotreme mammals, the platypus and echidna, to further investigate the origin of imprinting. We report herein that like M6P/IGF2R, IGF2 is not imprinted in monotremes. Thus, although IGF2 encodes for a highly conserved growth factor in chordates, it is only imprinted in therian mammals. These findings support a concurrent origin of IGF2 and M6P/IGF2R imprinting in the late Jurassic/early Cretaceous period. The absence of imprinting in monotremes, despite apparent interparental conflicts over maternal-offspring exchange, argues that a fortuitous congruency of genetic and epigenetic events may have limited the phylogenetic breadth of genomic imprinting to therian mammals. J. Exp. Zool. (Mol. Dev. Evol.) 291:205-212, 2001.     

The origin and evolution of modern metabolism

One fundamental goal of current research is to understand how complex biomolecular networks took the form that we observe today. Cellular metabolism is probably one of the most ancient biological networks and constitutes a good model system for the study of network evolution. While many evolutionary models have been proposed, a substantial body of work suggests metabolic pathways evolve fundamentally by recruitment, in which enzymes are drawn from close or distant regions of the network to perform novel chemistries or use different substrates. Here we review how structural and functional genomics has impacted our knowledge of evolution of modern metabolism and describe some approaches that merge evolutionary and structural genomics with advances in bioinformatics. These include mining the data on structure and function of enzymes for salient patterns of enzyme recruitment. Initial studies suggest modern metabolism originated in enzymes of nucleotide metabolism harboring the P-loop hydrolase fold, probably in pathways linked to the purine metabolic subnetwork. This gateway of recruitment gave rise to pathways related to the synthesis of nucleotides and cofactors for an ancient RNA world. Once the TIM beta/alpha-barrel fold architecture was discovered, it appears metabolic activities were recruited explosively giving rise to subnetworks related to carbohydrate and then amino acid metabolism. Remarkably, recruitment occurred in a layered system reminiscent of Morowitz's prebiotic shells, supporting the notion that modern metabolism represents a palimpsest of ancient metabolic chemistries.     

Mechanosensitive channels of bacteria and archaea share a common ancestral origin

The ubiquity of mechanosensitive (MS) ion channels set off a search for their functional homologues in archaea, the third domain of life. A new MS channel was identified in the archaeon Methanococcus jannaschii by using the TM1 transmembrane domain of the bacterial MS channel of large conductance, MscL, as a genetic probe to search the archaeal genomic database for MS channel homologues. The hypothetical protein MJ0170 (MscMJ) was found to harbor two MscL-like TM1 structural motifs and showed a high degree of se quence and secondary structure conservation with MscS (YggB) homologues. The alignment of sequences of MscL, MscS and MscMJ homologues further revealed that bacterial and archaeal channels form a phylogenetic tree composed of three main branches and share a common ancestral origin. This suggests the evolution of prokaryotic MS channels via gene duplication of a MscL-like progenitor gene followed by divergence, fur ther indicating that the common ancestor of the prokaryotic MS channels most likely resembled MscL. When expressed in E. coli and functionally examined by the patch clamp, the MscMJ protein behaved as a MS channel with a conductance of 270 pS in 200 mM KCl and a cation selectivity (PK/PC]) of approximately 6. The structural and functional homologue of MscMJ, MscMJLR, was identified as a second type of MS channel in M. jannaschii. The channel has a conductance of approximately 2 nS, rectifies with voltage and shares cation selectivity with MscMJ. The stoichiometry of both types of MS channels revealed that the free energy of activation, deltaG0 approximately 7kT, obtained for MscMJ matches the one calculated for MscS, deltaG0 approximately 5kT, whereas the free energy of activation approximately deltaG0 approximately 18kT of MscMJLR resembles more the deltaG0 = 14-19kT reported for MscL. The presence of two types of MS channels discovered in the cell envelope of M. jannaschii indicates that multiplicity of MS channels in prokaryotes is a necessary element for their survival in the habitats frequently challenged by sudden changes in osmolarity. Further functional and phylogenetic study of MS channels from all three domains of the universal phylogenetic tree may help to understand the evolution and common biophysical principles that govern mechanosensory transduction.     

The origin of greater-than-unit-length plasmids generated during bacterial conjugation

In Gram-negative bacteria, the general mechanism of conjugal plasmid transfer, which is probably similar for many different groups of plasmids, involves the transfer of a single plasmid DNA strand with 5′ to 3′ polarity. Transfer is initiated by nicking of the duplex DNA at a particular site, i.e. the origin of transfer (oriT). We constructed plasmids containing two directly repeated copies of oriT, derived from the broad-host-range plasmid R1162 and flanking the lac operator. The number of lacO copies in the plasmid after transfer could be determined from the colour of transconjugant colonies on medium containing X-Gal. When the oriTs were mutated to prevent initiation and termination of transfer at the same oriTs, almost all of the transconjugant cells contained greater-than-unit-length plasmids with two copies of lacO and three copies of oriT. We show that these molecules were generated by an intramolecular, conjugation dependent mechanism unlikely to depend solely on a pre-existing population of circular or linear multimers in donor cells. We propose that the greater-than-unit-length molecules were instead generated by a rolling-circle mechanism of DNA replication.     

An evolutionary perspective of the origin of males from unisexual ancestral females

正The urge to understand the cause and evolution of sex both scientifically and philosophically is the result of the development of human civilization and a fascination regarding the existing phenomenon of sexual reproduction.Theories regarding the evolution of sex have been developed by many scientists such as Aristotle,Charles Darwin,August Weismann,Hermann Henking,Nettie Stevens,John Maynard Smith,the Charlesworths,Sarah P.Otto,and A.S.Kondrashov(Maynard Smith,1978;Kondrashov,1993;Bachtrog et al.,2014).Many theories tried to provide reasons behind the maintenance of sex,but a sequence in the     

A hybrid bacterial replication origin

We constructed a hybrid replication origin that consists of the main part of oriC from Escherichia coli, the DnaA box region and the AT-rich region from Bacillus subtilis oriC. The AT-rich region could be unwound by E. coli DnaA protein, and the DnaB helicase was loaded into the single-stranded bubble. The results show that species specificity, i.e. which DnaA protein can do the unwinding, resides within the DnaA box region of oriC.     

The place of metabolism in the origin of life

Metabolism and replication are generally considered essential features of biological life. Workers in the field of the origin of life are mostly split into two groups, depending on which of these two functions is postulated to have occurred first. Because of difficulties encountered by the replication-first (or genetics-first) approach, some workers have postulated that a highly developed metabolism must have originated before replication and the formation of a genetic apparatus. However, as supporters of a replication-first approach have pointed out, and as is discussed in this article, the alternative metabolism-first approach has fundamental problems that have not been sufficiently addressed.     

Genomics and bacterial metabolism

The field of bacterial metabolism and physiology is arguably the oldest in microbiology. Much of our understanding of biological processes and molecular paradigms has its roots In early studies of prokaryotic physiology. After a period of declining interest in metabolic studies (prompted by the insurgence of molecular techniques), genomic technologies are revitalizing the study of bacterial metabolism and physiology. These new technologies bring a means to approach metabolic questions with a global perspective. When used in combination with classical and molecular techniques, emerging global technologies will make it feasible to understand the complex integration of metabolic processes that result in an efficient physiology. At the same time, without increased computational capabilities, the massive amounts of data generated by these technologies threaten to overwhelm, rather than facilitate, this work. For genomic technologies to reach their potential for increasing our understanding of bacterial metabolism, microbiologists must become more collaborative and multidisciplinary than at any time in our history.     

The primordial metabolism: an ancestral interconnection between leucine,arginine, and lysine biosynthesis

Background

It is generally assumed that primordial cells had small genomes with simple genes coding for enzymes able to react with a wide range of chemically related substrates, interconnecting different metabolic routes. New genes coding for enzymes with a narrowed substrate specificity arose by paralogous duplication(s) of ancestral ones and evolutionary divergence. In this way new metabolic pathways were built up by primordial cells. Useful hints to disclose the origin and evolution of ancestral metabolic routes and their interconnections can be obtained by comparing sequences of enzymes involved in the same or different metabolic routes. From this viewpoint, the lysine, arginine, and leucine biosynthetic routes represent very interesting study-models. Some of the lys, arg and leu genes are paralogs; this led to the suggestion that their ancestor genes might interconnect the three pathways. The aim of this work was to trace the evolutionary pathway leading to the appearance of the extant biosynthetic routes and to try to disclose the interrelationships existing between them and other pathways in the early stages of cellular evolution.

Results

The comparative analysis of the genes involved in the biosynthesis of lysine, leucine, and arginine, their phylogenetic distribution and analysis revealed that the extant metabolic "grids" and their interrelationships might be the outcome of a cascade of duplication of ancestral genes that, according to the patchwork hypothesis, coded for unspecific enzymes able to react with a wide range of substrates. These genes belonged to a single common pathway in which the three biosynthetic routes were highly interconnected between them and also to methionine, threonine, and cell wall biosynthesis. A possible evolutionary model leading to the extant metabolic scenarios was also depicted.

Conclusion

The whole body of data obtained in this work suggests that primordial cells synthesized leucine, lysine, and arginine through a single common metabolic pathway, whose genes underwent a set of duplication events, most of which can have predated the appearance of the last common universal ancestor of the three cell domains (Archaea, Bacteria, and Eucaryotes). The model proposes a relative timing for the appearance of the three routes and also suggests a possible evolutionary pathway for the assembly of bacterial cell-wall.

     

From The Origin of Species to the origin of bacterial flagella

In the recent Dover trial, and elsewhere, the 'Intelligent Design' movement has championed the bacterial flagellum as an irreducibly complex system that, it is claimed, could not have evolved through natural selection. Here we explore the arguments in favour of viewing bacterial flagella as evolved, rather than designed, entities. We dismiss the need for any great conceptual leaps in creating a model of flagellar evolution and speculate as to how an experimental programme focused on this topic might look.     

Direct screening of antibiotics-siderophores of bacterial origin

Antifungal activity of 275 strains belonging to 15 species of Pseudomonas was studied with using media containing no iron or supplemented with 100 micrograms/ml of FeCl3. 33 per cent of the cultures showed lower activity against phytopathogenic fungi in the presence of iron. Addition of this element did not influence the antifungal activity of phenazin and floroglucin derivatives isolated from Pseudomonas cultures. However, its addition markedly lowered the antifungal effect of some crude antibiotics and fluorescent pigments. A scheme for screening siderophore antibiotics with using Pseudomonas cultures is described.     

QS-type bacterial signal molecules of nonpeptide origin

This review classifies and analyzes the literature data on bacterial autoinducers (AI), the signal molecules produced and secreted by bacterial cells and responsible for intercellular communication (quorum sensing, QS). The most important families of nonpeptide AI are discussed, including N-acyl homoserine lactones, derivatives of 2-methyl-2,3,4,5-tetrahydroxy tetrahydrofuran, indole and quinoline derivatives, and adrenalinerelated compounds. The data is provided on the intracellular and membrane receptors specifically binding to AI, as well as on the effector systems that are activated by AI and mediate their regulatory effects. The possible role of some vertebrate hormones (adrenergic agonists, serotonin, etc.) as AI and their effect on bacterial activity are discussed. The data are presented suggesting a high efficiency of AI-based antibacterial preparations, which selectively disrupt the bacterial information network and thus suppress bacterial infections.     

Phospholipid metabolism during bacterial growth

Haemophilus parainfluenzae incorporates glycerol and phosphate into the membrane phospholipids without lag during logarithmic growth. In phosphatidyl glycerol (PG), the phosphate and unacylated glycerol moieties turn over and incorporate radioactivity much more rapidly than does the diacylated glycerol. At least half the radioactivity is lost from the phosphate and unacylated glycerol in about 1 doubling. The total fatty acids turn over slightly faster than the diacyl glycerol. In phosphatidyl ethanolamine (PE), which is the major lipid of the bacterium, ethanolamine and phosphate turn over and incorporate radioactivity at least half as fast as the phosphate in PG. The glycerol of PE did not turn over in 4 bacterial doublings. In phosphatidic acid the glycerol turns over at one-third the rate of phosphate turnover. By means of a modified method for the quantitative recovery of 1,3-glycerol diphosphate from cardiolipin, the phosphates and middle glycerol of cardiolipin were shown to turn over more rapidly than the acylated glycerols during bacterial growth. There is no randomization of the radioactivity in the 1- and 3-positions of the glycerol in the course of 1 doubling. The fatty acids of PG turn over faster than those in PE. In both lipids the 2-fatty acids turn over much faster than the 1-fatty acids. At both positions the individual fatty acids have their own rates of turnover. The distribution of fatty acids between the 1- and 2-positions is the same as in other organisms, with more monoenoic and long-chain fatty acids at the 2-position. The different rates of turnover and incorporation of radioactivity into different parts of the lipids suggest that exchange reactions may be important to phospholipid metabolism.     

A discrete model of bacterial metabolism

This paper describes a computer model of the intermediary metabolismof bacteria during steady-state growth and during adaptations,e g. to new carbon sources. Metabolic regulation is representedas a process of optimisation, in which the trend is towardsimproved metabolic performance. The model uses linear programmingtechniques for the optimisation The implementation falls intofour phases: (i) assembly of model parameters; (ii) calculations;(iii) storage of solutions and (iv) projection of solutions.The use of a commercial database and a commercial spreadsheethas proved to be of great assistance in the first and thirdphases. A metabolic map format, with the optional addition ofconversion values, names of enzymes or co-factors has been usedto project the results in a form convenient for inspection. Received on August 22, 1985; accepted on January 3, 1985