Millennial musings on molecular motors

In a universe that is dominated by increasing entropy, living organisms are a curious anomaly. The organization that distinguishes living organisms from their inanimate surroundings relies upon their ability to execute vectorial processes, such as directed movements and the assembly of macromolecules and organelle systems. Many of these phenomena are executed by molecular motors that harness chemical potential energy to perform mechanical work and unidirectional motion. This article explores how these remarkable protein machines might have evolved and what roles they could play in biological and medical research in the coming decades.     

Millennial musings on molecular motors

In a universe that is dominated by increasing entropy, living organisms are a curious anomaly. The organization that distinguishes living organisms from their inanimate surroundings relies upon their ability to execute vectorial processes, such as directed movements and the assembly of macromolecules and organelle systems. Many of these phenomena are executed by molecular motors that harness chemical potential energy to perform mechanical work and unidirectional motion. This article explores how these remarkable protein machines might have evolved and what roles they could play in biological and medical research in the coming decades.     

The Evolution of Oxygen As a Biosynthetic Reagent

The biosynthesis of certain cell constituents: monounsaturated fatty acids, tyrosine, and nicotinic acid, is oxygen-dependent in many higher organisms. The same compounds can be synthesized by different, oxygen-independent pathways in lower organisms. The general outlines of these pathways are described and the importance of the compounds synthesized is discussed. An examination of the distribution of these pathways among living organisms reveals that oxygen-dependent pathways replaced the "anaerobic" pathways at different branch points on the evolutionary tree. Other groups of compounds are discussed, which are not distributed as widely among living organisms, but are found in all higher organisms. These compounds have specialized functions and their biosynthesis requires molecular oxygen. The oxygen-dependent portions of the biosynthetic pathways leading to porphyrins, quinone coenzymes, carotenoids, sterols, and polyunsaturated fatty acids are summarized. The distribution and functions of these compounds are also considered and an attempt is made to place them in the framework of evolution. While sterols and polyunsaturated fatty acids are found exclusively in the higher Protista and multicellular organisms, carotenoids, porphyrins, and quinones are also found in bacteria. The possibility of oxygen-independent mechanisms for their biosynthesis is discussed.     

Bio-electrosprays: the next generation of electrified jets

Biological electrosprays are rapidly becoming a robust means by which to engineer living organisms for applications ranging from tissue repair to developmental biology. We previously reported the ability to electrospray living organisms without compromising their viability, but found it challenging to achieve stability in the jetting of these organisms as a result of the chemical properties of the living cellular suspensions. Jet stability is required for the generation of a near-mono distribution of droplets, which is necessary for the development of electrospray technology as a "drop and place" biotechnique. Recently, we determined the conditions needed to achieve jet stability and were able to generate droplets with a near-mono distribution (<50 microm). In this communication, we elucidate the relationship between jet behaviour and droplet size under stable jetting conditions, with a view to further reducing the droplet size to deposit a single living cell within a droplet. We believe that this level of resolution will make electrospray jetting superior amongst the jet-based biotechnologies presently being developed for the engineering of biological architectures comprised of living cells.     

Dimetrodon Is Not a Dinosaur: Using Tree Thinking to Understand the Ancient Relatives of Mammals and their Evolution

The line of descent that includes all living mammals extends back in time over 300 million years. Many of the ancient relatives of mammals that fall along this line are very different in appearance from living mammals and are frequently mistaken for reptiles such as dinosaurs. This misconception is reinforced by the fact that these animals are often referred to as “mammal-like reptiles,” a term reflecting outdated methods for classifying organisms. In reality, these ancient mammal-relatives, known as synapsids, are more closely related to living mammals than they are to any reptiles. Evolutionary trees, which depict patterns of descent from common ancestors among organisms, are very useful for understanding why this is the case and for reconstructing the evolutionary histories of many of the unique characters found in mammals. Here, I provide an introduction to evolutionary trees and their implications for understanding the relationships between mammals, synapsids, and reptiles. This is followed by a review of synapsid diversity and a discussion of how evolutionary trees can be used to investigate when in synapsid history different mammalian characteristics first appeared.     

Leishmania parasites: could we consider them as living organisms per se?

Over the last 10 years - in Microbes and Infection - the publications dealing with protozoan parasites were mainly providing insights on the pathogenic processes leading to the local or systemic damages in the mammals, these parasitic organisms exploit/subvert as hosts. As a result, many investigators introduced the objectives of their analysis by referring to "host-pathogen" interactions. Though we, as investigators, are all determined to decipher the pathogenic processes which can indeed be coupled to the parasite uncontrolled development, I think that the parasites - alike the living organisms they subvert as hosts - need to be considered as living organisms per se, instead of being considered as "pathogens". Such a conceptual frame will promote research on the processes on which relies their perpetuation whatever the level under investigations - individual and/or population level. Only the unicellular protozoan parasites of the genus Leishmania known to be hosted by blood-feeding insects and mammals will be further considered in this brief contribution.     

Comparative analysis of organophosphate degrading enzymes from diverse species

Different types of organophosphorous compounds constitute most potent pesticides. These chemicals attack the nervous system of living organisms causing death. Different organisms produce enzymes to degrade these chemicals. These enzymes are present in simple microorganisms from archaea, bacteria to complex eukaryotes like humans. A comparison of representative eight shortlisted enzymes involved in the degradation and inactivation of organophosphates from a wide range of organisms was performed to infer the basis of their common functionality. There is little sequence homology in these enzymes which results in divergent tertiary structures. The only feature that these enzymes seem to share is their amino acid composition. However, structural analysis has shown no significant similarities among this functionally similar group of organophosphate degrading enzymes.     

Adaptive significance of circadian clocks

Circadian clocks are ubiquitous and are found in organisms ranging from bacteria to mammals. This ubiquity of occurrence implies adaptive significance, but to date there has been no rigorous empirical evidence to support this. It is believed that an organism possessing circadian clocks gains fitness advantage in two ways: (i) by synchronizing its behavioral and physiological processes to cyclic environmental factors (extrinsic adaptive value); (ii) by coordinating its internal metabolic processes (intrinsic adaptive value). There is preliminary circumstantial evidence to support both. Several studies using organisms living in constant environments have shown that these organisms possess functional circadian clocks, suggesting that circadian clocks may have some intrinsic adaptive value. Studies to assess the adaptive value of circadian clocks in periodic environments suggest that organisms may have a fitness advantage in those periodic environments, which closely match their own intrinsic periodicity. Furthermore, evidence from organisms living in the wild, selection studies, and studies on latitudinal clines suggest that circadian clocks may have an extrinsic adaptive value as well. In this paper, I have presented several hypotheses for the emergence of circadian clocks and have reviewed some major empirical studies suggesting adaptive significance of circadian clocks.     

Adaptive Significance of Circadian Clocks

Circadian clocks are ubiquitous and are found in organisms ranging from bacteria to mammals. This ubiquity of occurrence implies adaptive significance, but to date there has been no rigorous empirical evidence to support this. It is believed that an organism possessing circadian clocks gains fitness advantage in two ways: (i) by synchronizing its behavioral and physiological processes to cyclic environmental factors (extrinsic adaptive value); (ii) by coordinating its internal metabolic processes (intrinsic adaptive value). There is preliminary circumstantial evidence to support both. Several studies using organisms living in constant environments have shown that these organisms possess functional circadian clocks, suggesting that circadian clocks may have some intrinsic adaptive value. Studies to assess the adaptive value of circadian clocks in periodic environments suggest that organisms may have a fitness advantage in those periodic environments, which closely match their own intrinsic periodicity. Furthermore, evidence from organisms living in the wild, selection studies, and studies on latitudinal clines suggest that circadian clocks may have an extrinsic adaptive value as well. In this paper, I have presented several hypotheses for the emergence of circadian clocks and have reviewed some major empirical studies suggesting adaptive significance of circadian clocks.     

To be or not to be rhythmic? A review of studies on organisms inhabiting constant environments

Abstract

Circadian clocks are endogenous time keeping mechanisms that drive near 24-h behavioural, physiological and metabolic rhythms in organisms. It is thought that organisms possess circadian clocks to facilitate coordination of essential biological events to the external day and night (extrinsic advantage) so as to enhance Darwinian fitness. However, on Earth, there are a number of habitats that are not subject to such robust daily cycling of geo-physical factors. Do organisms living under such conditions exhibit rhythmic behaviours that are driven by endogenous circadian clocks? We attempt to critically survey studies of rhythms (or the lack of them) in organisms living in a range of constant environments. Many such organisms do show rhythms in behaviour and/or physiological variables. We suggest that such presence of rhythms may be indicative of an underlying clock that facilitates, (a) internal synchrony among rhythms, and (b) temporal partitioning of incompatible cellular processes (intrinsic advantage). We then highlight reasons that limit our interpretations about the presence (or absence) of clocks in such organisms living under constant conditions, and suggest possible methods to conclusively test whether or not rhythms in these organisms are driven by endogenous circadian clocks with the hope that it may enhance our understanding of circadian clocks in organisms under constant environments.     

The lifestyle of prokaryotic organisms influences the repertoire of promiscuous enzymes

The metabolism of microbial organisms and its diversity are partly the result of an adaptation process to the characteristics of the environments that they inhabit. In this work, we analyze the influence of lifestyle on the content of promiscuous enzymes in 761 nonredundant bacterial and archaeal genomes. Promiscuous enzymes were defined as those proteins whose catalytic activities are defined by two or more different Enzyme Commission (E.C.) numbers. The genomes analyzed were categorized into four lifestyles for their exhaustive comparisons: free‐living, extremophiles, pathogens, and intracellular. From these analyses we found that free‐living organisms have larger genomes and an enrichment of promiscuous enzymes. In contrast, intracellular organisms showed smaller genomes and the lesser proportion of promiscuous enzymes. On the basis of our data, we show that the proportion of promiscuous enzymes in an organism is mainly influenced by the lifestyle, where fluctuating environments promote its emergence. Finally, we evidenced that duplication processes occur preferentially in metabolism of free‐living and extremophiles species. Proteins 2015; 83:1625–1631. © 2015 Wiley Periodicals, Inc.     

微量元素蛋白质组的比较基因组学研究

微量元素指需要量很少（人体中含量在0．01％以下）,但却是所有生物体所必需的元素。它们参与了生物体中各种复杂的生物过程,因此不同生物必须依赖相应的微量元素才能生存。过去大量的工作主要放在微量元素代谢通路和微量元素结合蛋白的实验研究上,由此凸显出微量元素对生命的重要性。然而,微量元素的计算生物学研究工作却非常有限。着重介绍当前利用比较基因组学的理论和方法来研究不同微量元素的利用、代谢、功能和进化方面问题的最新进展。对于所讨论的元素,大多数利用它们的蛋白已经基本确定,并且这些蛋白对于特定元素的依赖性也是非常保守的。通过比较基因组学分析,有助于帮助我们进一步认识微量元素领域很多基本问题（如在古菌、细菌和真核生物中的代谢、功能和动态进化规律等）及其重要特征。     

Multiple mechanisms controlling carbon metabolism in bacteria

Catabolite repression is a universal phenomenon, found in virtually all living organisms. These organisms range from the simplest bacteria to higher fungi, plants, and animals. A mechanism involving cyclic AMP and its receptor protein (CRP) in Escherichia coli was established years ago, and this mechanism has been assumed by many to serve as the prototype for catabolite repression in all organisms. However, recent studies have shown that this mechanism is restricted to enteric bacteria and their close relatives. Cyclic AMP-independent mechanisms of catabolite repression occur in other bacteria, yeast, plants, and even E. coli. In fact, single-celled organisms such as E. coli, Bacillus subtilis, and Saccharomyces cerevisiae exhibit multiple mechanisms of catabolite repression, and most of these are cyclic AMP-independent. The mechanistic features of the best of such characterized processes are briefly reviewed, and references are provided that will allow the reader to delve more deeply into these subjects.     

Distribution of the heavy isotope of carbon (13C) in biological systems

Causes conditioning fractionation of carbon isotopes in biological systems are considered. Concepts of E. M. Galimov are discussed. According to these concepts distribution of carbon isotopes between biomolecules and their fragments is quaziequilibrium, i. e. it differs from the equilibrium one by a constant multiplier, which is the same for all the biomolecules of an organism but different for various organisms. These concepts have no theoretical grounds and do not agree with the experimental evidence available. An analysis of experimental data, as well as theoretical considerations, indicate that the observed differences in isotope composition of metabolytes and their fragments in the living organisms are conditioned by the kinetic isotope effects of carbon at the stages of their enzymic transformations and by the portion of substances participating in the reaction. It means that these differences do not depend directly on the constants characterizing the equilibrium distribution of carbon isotopes between corresponding compounds and between different groups inside their molecules.     

Metagenomics: DNA sequencing of environmental samples

Although genomics has classically focused on pure, easy-to-obtain samples, such as microbes that grow readily in culture or large animals and plants, these organisms represent only a fraction of the living or once-living organisms of interest. Many species are difficult to study in isolation because they fail to grow in laboratory culture, depend on other organisms for critical processes, or have become extinct. Methods that are based on DNA sequencing circumvent these obstacles, as DNA can be isolated directly from living or dead cells in various contexts. Such methods have led to the emergence of a new field, which is referred to as metagenomics.     

Recent developments in the taxonomic affiliation and phylogenetic positioning of fungi: impact in applied microbiology and environmental biotechnology

The goal of modern taxonomy is to understand the relationships of living organisms in terms of evolutionary descent. Thereby, the relationships between living organisms are understood in terms of nested clades—every time a speciation event takes place, two new clades are produced. Life comprises three domains of living organisms, these are the Bacteria, the Archaea and the Eukaryota. Within the eukaryotic domain, the fungi form a monophyletic group of the eukaryotic crown group and are thus high up in the evolutionary hierarchy of life. Fungus-like organisms possess certain morphological features of fungi, such as the hyphal organization of the Oomycota or the spores and reproductive structures inside a fructification of plasmodiophorids (Plasmodiophoromycota) and slime moulds (Mycetozoa). The first group are algae which secondarily lost their plastids during evolution and contain cellulose in their cell walls. Both osmotrophic phyla, the Oomycota and the Plasmidiophoromycota belong to the Chromista and Rhizaria, respectively, whereas the last group, the cellular and plasmodial slime moulds (Mycetozoa) are phagotrophic amoeboid protists belonging to the Amoebozoa. These fungus-like organisms are not considered further in this review. The Fungi sensu stricto comprise a heterogenous, often inconspicuous group of microorganisms which (1) are primarily heterotrophic with an (2) osmotrophic style of nutrition containing (3) chitin and its derivatives in the cell wall. This review discusses species concepts and current strategies in fungal taxonomy, phylogenetic affiliations of miscellaneous fungus-like groups like the microsporidia, perspectives of fungal nomenclature, and their impact on natural product research.     

Culture collections in the twenty-first century

Culture collections conserve the living tools for biotechnology. Without them there would be no reference organisms, and no stocks of crucial or rare microorganisms that are so valuable for biotechnology and biomedical research. The expertise that drives these collections is under threat, but the collections themselves may survive by pooling their knowledge.