Life | March 2018 - Browse Articles

12 pages, 763 KiB

Open AccessReview

Reporting Key Features in Cold-Adapted Bacteria

by Paula M. Tribelli and Nancy I. López

Life 2018, 8(1), 8; https://doi.org/10.3390/life8010008 - 13 Mar 2018

Cited by 120 | Viewed by 10688

It is well known that cold environments are predominant over the Earth and there are a great number of reports analyzing bacterial adaptations to cold. Most of these works are focused on characteristics traditionally involved in cold adaptation, such as the structural adjustment [...] Read more.

It is well known that cold environments are predominant over the Earth and there are a great number of reports analyzing bacterial adaptations to cold. Most of these works are focused on characteristics traditionally involved in cold adaptation, such as the structural adjustment of enzymes, maintenance of membrane fluidity, expression of cold shock proteins and presence of compatible solutes. Recent works based mainly on novel “omic” technologies have presented evidence of the presence of other important features to thrive in cold. In this work, we analyze cold-adapted bacteria, looking for strategies involving novel features, and/or activation of non-classical metabolisms for a cold lifestyle. Metabolic traits related to energy generation, compounds and mechanisms involved in stress resistance and cold adaptation, as well as characteristics of the cell envelope, are analyzed in heterotrophic cold-adapted bacteria. In addition, metagenomic, metatranscriptomic and metaproteomic data are used to detect key functions in bacterial communities inhabiting cold environments. Full article

(This article belongs to the Special Issue Extremophiles and the Origin of Life)

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11 pages, 884 KiB

Open AccessPerspective

Potential Role of Inorganic Confined Environments in Prebiotic Phosphorylation

by Avinash Vicholous Dass, Maguy Jaber, André Brack, Frédéric Foucher, Terence P. Kee, Thomas Georgelin and Frances Westall

Life 2018, 8(1), 7; https://doi.org/10.3390/life8010007 - 5 Mar 2018

Cited by 25 | Viewed by 5857

Abstract

A concise outlook on the potential role of confinement in phosphorylation and phosphate condensation pertaining to prebiotic chemistry is presented. Inorganic confinement is a relatively uncharted domain in studies concerning prebiotic chemistry, and even more so in terms of experimentation. However, molecular crowding [...] Read more.

A concise outlook on the potential role of confinement in phosphorylation and phosphate condensation pertaining to prebiotic chemistry is presented. Inorganic confinement is a relatively uncharted domain in studies concerning prebiotic chemistry, and even more so in terms of experimentation. However, molecular crowding within confined dimensions is central to the functioning of contemporary biology. There are numerous advantages to confined environments and an attempt to highlight this fact, within this article, has been undertaken, keeping in context the limitations of aqueous phase chemistry in phosphorylation and, to a certain extent, traditional approaches in prebiotic chemistry. Full article

(This article belongs to the Special Issue Phosphorus (P) and the Origins of Life)

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11 pages, 835 KiB

Open AccessReview

The Prevailing Catalytic Role of Meteorites in Formamide Prebiotic Processes

by Raffaele Saladino, Lorenzo Botta and Ernesto Di Mauro

Life 2018, 8(1), 6; https://doi.org/10.3390/life8010006 - 22 Feb 2018

Cited by 20 | Viewed by 4771

Abstract

Meteorites are consensually considered to be involved in the origin of life on this Planet for several functions and at different levels: (i) as providers of impact energy during their passage through the atmosphere; (ii) as agents of geodynamics, intended both as starters [...] Read more.

Meteorites are consensually considered to be involved in the origin of life on this Planet for several functions and at different levels: (i) as providers of impact energy during their passage through the atmosphere; (ii) as agents of geodynamics, intended both as starters of the Earth’s tectonics and as activators of local hydrothermal systems upon their fall; (iii) as sources of organic materials, at varying levels of limited complexity; and (iv) as catalysts. The consensus about the relevance of these functions differs. We focus on the catalytic activities of the various types of meteorites in reactions relevant for prebiotic chemistry. Formamide was selected as the chemical precursor and various sources of energy were analyzed. The results show that all the meteorites and all the different energy sources tested actively afford complex mixtures of biologically-relevant compounds, indicating the robustness of the formamide-based prebiotic chemistry involved. Although in some cases the yields of products are quite small, the diversity of the detected compounds of biochemical significance underlines the prebiotic importance of meteorite-catalyzed condensation of formamide. Full article

(This article belongs to the Special Issue Meteorites and the Origin of Life)

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20 pages, 607 KiB

Open AccessArticle

Intrinsic Properties of tRNA Molecules as Deciphered via Bayesian Network and Distribution Divergence Analysis

by Sergio Branciamore, Grigoriy Gogoshin, Massimo Di Giulio and Andrei S. Rodin

Life 2018, 8(1), 5; https://doi.org/10.3390/life8010005 - 8 Feb 2018

Cited by 6 | Viewed by 4651

Abstract

The identity/recognition of tRNAs, in the context of aminoacyl tRNA synthetases (and other molecules), is a complex phenomenon that has major implications ranging from the origins and evolution of translation machinery and genetic code to the evolution and speciation of tRNAs themselves to [...] Read more.

The identity/recognition of tRNAs, in the context of aminoacyl tRNA synthetases (and other molecules), is a complex phenomenon that has major implications ranging from the origins and evolution of translation machinery and genetic code to the evolution and speciation of tRNAs themselves to human mitochondrial diseases to artificial genetic code engineering. Deciphering it via laboratory experiments, however, is difficult and necessarily time- and resource-consuming. In this study, we propose a mathematically rigorous two-pronged in silico approach to identifying and classifying tRNA positions important for tRNA identity/recognition, rooted in machine learning and information-theoretic methodology. We apply Bayesian Network modeling to elucidate the structure of intra-tRNA-molecule relationships, and distribution divergence analysis to identify meaningful inter-molecule differences between various tRNA subclasses. We illustrate the complementary application of these two approaches using tRNA examples across the three domains of life, and identify and discuss important (informative) positions therein. In summary, we deliver to the tRNA research community a novel, comprehensive methodology for identifying the specific elements of interest in various tRNA molecules, which can be followed up by the corresponding experimental work and/or high-resolution position-specific statistical analyses. Full article

(This article belongs to the Special Issue The Origin and Evolution of the Genetic Code: 100th Anniversary Year of the Birth of Francis Crick)

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15 pages, 4367 KiB

Open AccessArticle

The Diverging Routes of BORIS and CTCF: An Interactomic and Phylogenomic Analysis

by Kamel Jabbari, Peter Heger, Ranu Sharma and Thomas Wiehe

Life 2018, 8(1), 4; https://doi.org/10.3390/life8010004 - 30 Jan 2018

Cited by 8 | Viewed by 5643

Abstract

The CCCTC-binding factor (CTCF) is multi-functional, ubiquitously expressed, and highly conserved from Drosophila to human. It has important roles in transcriptional insulation and the formation of a high-dimensional chromatin structure. CTCF has a paralog called “Brother of Regulator of Imprinted Sites” (BORIS) or [...] Read more.

The CCCTC-binding factor (CTCF) is multi-functional, ubiquitously expressed, and highly conserved from Drosophila to human. It has important roles in transcriptional insulation and the formation of a high-dimensional chromatin structure. CTCF has a paralog called “Brother of Regulator of Imprinted Sites” (BORIS) or “CTCF-like” (CTCFL). It binds DNA at sites similar to those of CTCF. However, the expression profiles of the two proteins are quite different. We investigated the evolutionary trajectories of the two proteins after the duplication event using a phylogenomic and interactomic approach. We find that CTCF has 52 direct interaction partners while CTCFL only has 19. Almost all interactors already existed before the emergence of CTCF and CTCFL. The unique secondary loss of CTCF from several nematodes is paralleled by a loss of two of its interactors, the polycomb repressive complex subunit SuZ12 and the multifunctional transcription factor TYY1. In contrast to earlier studies reporting the absence of BORIS from birds, we present evidence for a multigene synteny block containing CTCFL that is conserved in mammals, reptiles, and several species of birds, indicating that not the entire lineage of birds experienced a loss of CTCFL. Within this synteny block, BORIS and its genomic neighbors seem to be partitioned into two nested chromatin loops. The high expression of SPO11, RAE1, RBM38, and PMEPA1 in male tissues suggests a possible link between CTCFL, meiotic recombination, and fertility-associated phenotypes. Using the 65,700 exomes and the 1000 genomes data, we observed a higher number of intergenic, non-synonymous, and loss-of-function mutations in CTCFL than in CTCF, suggesting a reduced strength of purifying selection, perhaps due to less functional constraint. Full article

(This article belongs to the Special Issue Evolution and Origin of Genomes)

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10 pages, 3848 KiB

Open AccessArticle

Sustainability of a Compartmentalized Host-Parasite Replicator System under Periodic Washout-Mixing Cycles

by Taro Furubayashi and Norikazu Ichihashi

Life 2018, 8(1), 3; https://doi.org/10.3390/life8010003 - 26 Jan 2018

Cited by 10 | Viewed by 4553

Abstract

The emergence and dominance of parasitic replicators are among the major hurdles for the proliferation of primitive replicators. Compartmentalization of replicators is proposed to relieve the parasite dominance; however, it remains unclear under what conditions simple compartmentalization uncoupled with internal reaction secures the [...] Read more.

The emergence and dominance of parasitic replicators are among the major hurdles for the proliferation of primitive replicators. Compartmentalization of replicators is proposed to relieve the parasite dominance; however, it remains unclear under what conditions simple compartmentalization uncoupled with internal reaction secures the long-term survival of a population of primitive replicators against incessant parasite emergence. Here, we investigate the sustainability of a compartmentalized host-parasite replicator (CHPR) system undergoing periodic washout-mixing cycles, by constructing a mathematical model and performing extensive simulations. We describe sustainable landscapes of the CHPR system in the parameter space and elucidate the mechanism of phase transitions between sustainable and extinct regions. Our findings revealed that a large population size of compartments, a high mixing intensity, and a modest amount of nutrients are important factors for the robust survival of replicators. We also found two distinctive sustainable phases with different mixing intensities. These results suggest that a population of simple host–parasite replicators assumed before the origin of life can be sustained by a simple compartmentalization with periodic washout-mixing processes. Full article

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2 pages, 178 KiB

Open AccessEditorial

Acknowledgement to Reviewers of Life in 2017

by Life Editorial Office

Life 2018, 8(1), 2; https://doi.org/10.3390/life8010002 - 12 Jan 2018

Viewed by 3370

Abstract

Peer review is an essential part in the publication process, ensuring that Life maintains high quality standards for its published papers. In 2017, a total of 51 papers were published in the journal.[...] Full article

22 pages, 1009 KiB

Open AccessArticle

Hydrogen Bonds and Life in the Universe

by Giovanni Vladilo and Ali Hassanali

Life 2018, 8(1), 1; https://doi.org/10.3390/life8010001 - 3 Jan 2018

Cited by 47 | Viewed by 10988

Abstract

The scientific community is allocating more and more resources to space missions and astronomical observations dedicated to the search for life beyond Earth. This experimental endeavor needs to be backed by a theoretical framework aimed at defining universal criteria for the existence of [...] Read more.

The scientific community is allocating more and more resources to space missions and astronomical observations dedicated to the search for life beyond Earth. This experimental endeavor needs to be backed by a theoretical framework aimed at defining universal criteria for the existence of life. With this aim in mind, we have explored which chemical and physical properties should be expected for life possibly different from the terrestrial one, but similarly sustained by genetic and catalytic molecules. We show that functional molecules performing genetic and catalytic tasks must feature a hierarchy of chemical interactions operating in distinct energy bands. Of all known chemical bonds and forces, only hydrogen bonds are able to mediate the directional interactions of lower energy that are needed for the operation of genetic and catalytic tasks. For this reason and because of the unique quantum properties of hydrogen bonding, the functional molecules involved in life processes are predicted to have extensive hydrogen-bonding capabilities. A molecular medium generating a hydrogen-bond network is probably essential to support the activity of the functional molecules. These hydrogen-bond requirements constrain the viability of hypothetical biochemistries alternative to the terrestrial one, provide thermal limits to life molecular processes, and offer a conceptual framework to define a transition from a “covalent-bond stage” to a “hydrogen-bond stage” in prebiotic chemistry. Full article

(This article belongs to the Section Astrobiology)

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Life, Volume 8, Issue 1 (March 2018) – 8 articles

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