Life | March 2017 - Browse Articles

2872 KiB

Open AccessReview

Efforts and Challenges in Engineering the Genetic Code

by Xiao Lin, Allen Chi Shing Yu and Ting Fung Chan

Life 2017, 7(1), 12; https://doi.org/10.3390/life7010012 - 14 Mar 2017

Cited by 13 | Viewed by 6798

This year marks the 48th anniversary of Francis Crick’s seminal work on the origin of the genetic code, in which he first proposed the “frozen accident” hypothesis to describe evolutionary selection against changes to the genetic code that cause devastating global proteome modification. [...] Read more.

This year marks the 48th anniversary of Francis Crick’s seminal work on the origin of the genetic code, in which he first proposed the “frozen accident” hypothesis to describe evolutionary selection against changes to the genetic code that cause devastating global proteome modification. However, numerous efforts have demonstrated the viability of both natural and artificial genetic code variations. Recent advances in genetic engineering allow the creation of synthetic organisms that incorporate noncanonical, or even unnatural, amino acids into the proteome. Currently, successful genetic code engineering is mainly achieved by creating orthogonal aminoacyl-tRNA/synthetase pairs to repurpose stop and rare codons or to induce quadruplet codons. In this review, we summarize the current progress in genetic code engineering and discuss the challenges, current understanding, and future perspectives regarding genetic code modification. 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)

► Show Figures

Figure 1

3700 KiB

Open AccessArticle

Micrometer-Scale Membrane Transition of Supported Lipid Bilayer Membrane Reconstituted with Cytosol of Dictyostelium discoideum

by Kei Takahashi and Taro Toyota

Life 2017, 7(1), 11; https://doi.org/10.3390/life7010011 - 07 Mar 2017

Cited by 1 | Viewed by 5460

Abstract

Background: The transformation of the supported lipid bilayer (SLB) membrane by extracted cytosol from living resources, has recently drawn much attention. It enables us to address the question of whether the purified phospholipid SLB membrane, including lipids related to amoeba locomotion, which was [...] Read more.

Background: The transformation of the supported lipid bilayer (SLB) membrane by extracted cytosol from living resources, has recently drawn much attention. It enables us to address the question of whether the purified phospholipid SLB membrane, including lipids related to amoeba locomotion, which was discussed in many previous studies, exhibits membrane deformation in the presence of cytosol extracted from amoeba; Methods: In this report, a method for reconstituting a supported lipid bilayer (SLB) membrane, composed of purified phospholipids and cytosol extracted from Dictyostelium discoideum, is described. This technique is a new reconstitution method combining the artificial constitution of membranes with the reconstitution using animate cytosol (without precise purification at a molecular level), contributing to membrane deformation analysis; Results: The morphology transition of a SLB membrane composed of phosphatidylcholines, after the addition of cytosolic extract, was traced using a confocal laser scanning fluorescence microscope. As a result, pore formation in the SLB membrane was observed and phosphatidylinositides incorporated into the SLB membrane tended to suppress pore formation and expansion; Conclusions: The current findings imply that phosphatidylinositides have the potential to control cytoplasm activity and bind to a phosphoinositide-containing SLB membrane. Full article

(This article belongs to the Section Cell Biology and Tissue Engineering)

► Show Figures

Figure 1

772 KiB

Open AccessReview

Future of the Genetic Code

by Hong Xue and J. Tze-Fei Wong

Life 2017, 7(1), 10; https://doi.org/10.3390/life7010010 - 28 Feb 2017

Cited by 4 | Viewed by 5354

Abstract

The methods for establishing synthetic lifeforms with rewritten genetic codes comprising non-canonical amino acids (NCAA) in addition to canonical amino acids (CAA) include proteome-wide replacement of CAA, insertion through suppression of nonsense codon, and insertion via the pyrrolysine and selenocysteine pathways. Proteome-wide reassignments [...] Read more.

The methods for establishing synthetic lifeforms with rewritten genetic codes comprising non-canonical amino acids (NCAA) in addition to canonical amino acids (CAA) include proteome-wide replacement of CAA, insertion through suppression of nonsense codon, and insertion via the pyrrolysine and selenocysteine pathways. Proteome-wide reassignments of nonsense codons and sense codons are also under development. These methods enable the application of NCAAs to enrich both fundamental and applied aspects of protein chemistry and biology. Sense codon reassignment to NCAA could incur problems arising from the usage of anticodons as identity elements on tRNA, and possible misreading of NNY codons by UNN anticodons. Evidence suggests that the problem of anticodons as identity elements can be diminished or resolved through removal from the tRNA of all identity elements besides the anticodon, and the problem of misreading of NNY codons by UNN anticodon can be resolved by the retirement of both the UNN anticodon and its complementary NNA codon from the proteome in the event that a restrictive post-transcriptional modification of the UNN anticodon by host enzymes to prevent the misreading cannot be obtained. 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)

► Show Figures

Figure 1

1260 KiB

Open AccessArticle

Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates

by Roman A. Gershgorin, Konstantin Yu. Gorbunov, Oleg A. Zverkov, Lev I. Rubanov, Alexandr V. Seliverstov and Vassily A. Lyubetsky

Life 2017, 7(1), 9; https://doi.org/10.3390/life7010009 - 27 Feb 2017

Cited by 5 | Viewed by 4791

Abstract

Recent phylogenetic analyses are incorporating ultraconserved elements (UCEs) and highly conserved elements (HCEs). Models of evolution of the genome structure and HCEs initially faced considerable algorithmic challenges, which gave rise to (often unnatural) constraints on these models, even for conceptually simple tasks such [...] Read more.

Recent phylogenetic analyses are incorporating ultraconserved elements (UCEs) and highly conserved elements (HCEs). Models of evolution of the genome structure and HCEs initially faced considerable algorithmic challenges, which gave rise to (often unnatural) constraints on these models, even for conceptually simple tasks such as the calculation of distance between two structures or the identification of UCEs. In our recent works, these constraints have been addressed with fast and efficient solutions with no constraints on the underlying models. These approaches have led us to an unexpected result: for some organelles and taxa, the genome structure and HCE set, despite themselves containing relatively little information, still adequately resolve the evolution of species. We also used the HCE identification to search for promoters and regulatory elements that characterize the functional evolution of the genome. Full article

(This article belongs to the Section Genetics and Genomics)

► Show Figures

Figure 1

2238 KiB

Open AccessArticle

Bioinformatic Analysis Reveals Archaeal tRNA^Tyr and tRNA^Trp Identities in Bacteria

by Takahito Mukai, Noah M. Reynolds, Ana Crnković and Dieter Söll

Life 2017, 7(1), 8; https://doi.org/10.3390/life7010008 - 21 Feb 2017

Cited by 15 | Viewed by 7945

Abstract

The tRNA identity elements for some amino acids are distinct between the bacterial and archaeal domains. Searching in recent genomic and metagenomic sequence data, we found some candidate phyla radiation (CPR) bacteria with archaeal tRNA identity for Tyr-tRNA and Trp-tRNA synthesis. These bacteria [...] Read more.

The tRNA identity elements for some amino acids are distinct between the bacterial and archaeal domains. Searching in recent genomic and metagenomic sequence data, we found some candidate phyla radiation (CPR) bacteria with archaeal tRNA identity for Tyr-tRNA and Trp-tRNA synthesis. These bacteria possess genes for tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase (TrpRS) predicted to be derived from DPANN superphylum archaea, while the cognate tRNA^Tyr and tRNA^Trp genes reveal bacterial or archaeal origins. We identified a trace of domain fusion and swapping in the archaeal-type TyrRS gene of a bacterial lineage, suggesting that CPR bacteria may have used this mechanism to create diverse proteins. Archaeal-type TrpRS of bacteria and a few TrpRS species of DPANN archaea represent a new phylogenetic clade (named TrpRS-A). The TrpRS-A open reading frames (ORFs) are always associated with another ORF (named ORF1) encoding an unknown protein without global sequence identity to any known protein. However, our protein structure prediction identified a putative HIGH-motif and KMSKS-motif as well as many α-helices that are characteristic of class I aminoacyl-tRNA synthetase (aaRS) homologs. These results provide another example of the diversity of molecular components that implement the genetic code and provide a clue to the early evolution of life and the genetic code. 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)

► Show Figures

Figure 1

621 KiB

Open AccessArticle

On the Uniqueness of the Standard Genetic Code

by Gabriel S. Zamudio and Marco V. José

Life 2017, 7(1), 7; https://doi.org/10.3390/life7010007 - 13 Feb 2017

Cited by 11 | Viewed by 5146

Abstract

In this work, we determine the biological and mathematical properties that are sufficient and necessary to uniquely determine both the primeval RNY (purine-any base-pyrimidine) code and the standard genetic code (SGC). These properties are: the evolution of the SGC from the RNY code; [...] Read more.

In this work, we determine the biological and mathematical properties that are sufficient and necessary to uniquely determine both the primeval RNY (purine-any base-pyrimidine) code and the standard genetic code (SGC). These properties are: the evolution of the SGC from the RNY code; the degeneracy of both codes, and the non-degeneracy of the assignments of aminoacyl-tRNA synthetases (aaRSs) to amino acids; the wobbling property; the consideration that glycine was the first amino acid; the topological and symmetrical properties of both codes. 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)

► Show Figures

Figure 1

7232 KiB

Open AccessReview

Homocysteine Editing, Thioester Chemistry, Coenzyme A, and the Origin of Coded Peptide Synthesis †

by Hieronim Jakubowski

Life 2017, 7(1), 6; https://doi.org/10.3390/life7010006 - 09 Feb 2017

Cited by 27 | Viewed by 8220

Abstract

Aminoacyl-tRNA synthetases (AARSs) have evolved “quality control” mechanisms which prevent tRNA aminoacylation with non-protein amino acids, such as homocysteine, homoserine, and ornithine, and thus their access to the Genetic Code. Of the ten AARSs that possess editing function, five edit homocysteine: Class I [...] Read more.

Aminoacyl-tRNA synthetases (AARSs) have evolved “quality control” mechanisms which prevent tRNA aminoacylation with non-protein amino acids, such as homocysteine, homoserine, and ornithine, and thus their access to the Genetic Code. Of the ten AARSs that possess editing function, five edit homocysteine: Class I MetRS, ValRS, IleRS, LeuRS, and Class II LysRS. Studies of their editing function reveal that catalytic modules of these AARSs have a thiol-binding site that confers the ability to catalyze the aminoacylation of coenzyme A, pantetheine, and other thiols. Other AARSs also catalyze aminoacyl-thioester synthesis. Amino acid selectivity of AARSs in the aminoacyl thioesters formation reaction is relaxed, characteristic of primitive amino acid activation systems that may have originated in the Thioester World. With homocysteine and cysteine as thiol substrates, AARSs support peptide bond synthesis. Evolutionary origin of these activities is revealed by genomic comparisons, which show that AARSs are structurally related to proteins involved in coenzyme A/sulfur metabolism and non-coded peptide bond synthesis. These findings suggest that the extant AARSs descended from ancestral forms that were involved in non-coded Thioester-dependent peptide synthesis, functionally similar to the present-day non-ribosomal peptide synthetases. 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)

► Show Figures

Figure 1

11493 KiB

Open AccessReview

The Role of Lipid Membranes in Life’s Origin

by David Deamer

Life 2017, 7(1), 5; https://doi.org/10.3390/life7010005 - 17 Jan 2017

Cited by 146 | Viewed by 13061

Abstract

At some point in early evolution, life became cellular. Assuming that this step was required for the origin of life, there would necessarily be a pre-existing source of amphihilic compounds capable of assembling into membranous compartments. It is possible to make informed guesses [...] Read more.

At some point in early evolution, life became cellular. Assuming that this step was required for the origin of life, there would necessarily be a pre-existing source of amphihilic compounds capable of assembling into membranous compartments. It is possible to make informed guesses about the properties of such compounds and the conditions most conducive to their self-assembly into boundary structures. The membranes were likely to incorporate mixtures of hydrocarbon derivatives between 10 and 20 carbons in length with carboxylate or hydroxyl head groups. Such compounds can be synthesized by chemical reactions and small amounts were almost certainly present in the prebiotic environment. Membrane assembly occurs most readily in low ionic strength solutions with minimal content of salt and divalent cations, which suggests that cellular life began in fresh water pools associated with volcanic islands rather than submarine hydrothermal vents. Full article

(This article belongs to the Special Issue The Emergence of Life: From Chemical Origins to Synthetic Biology)

► Show Figures

Figure 1

252 KiB

Open AccessEditorial

Acknowledgement to Reviewers of Life in 2016

by Life Editorial Office

Life 2017, 7(1), 4; https://doi.org/10.3390/life7010004 - 10 Jan 2017

Viewed by 3125

Abstract

The editors of Life would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2016. Full article

1824 KiB

Open AccessArticle

Selection of Prebiotic Molecules in Amphiphilic Environments

by Christian Mayer, Ulrich Schreiber and María J. Dávila

Life 2017, 7(1), 3; https://doi.org/10.3390/life7010003 - 07 Jan 2017

Cited by 21 | Viewed by 11147

Abstract

A basic problem in all postulated pathways of prebiotic chemistry is the low concentration which generally is expected for interesting reactants in fluid environments. Even though compounds, like nucleobases, sugars or peptides, principally may form spontaneously under environmental conditions, they will always be [...] Read more.

A basic problem in all postulated pathways of prebiotic chemistry is the low concentration which generally is expected for interesting reactants in fluid environments. Even though compounds, like nucleobases, sugars or peptides, principally may form spontaneously under environmental conditions, they will always be rapidly diluted in an aqueous environment. In addition, any such reaction leads to side products which often exceed the desired compound and generally hamper the first steps of a subsequent molecular evolution. Therefore, a mechanism of selection and accumulation of relevant prebiotic compounds seems to be crucial for molecular evolution. A very efficient environment for selection and accumulation can be found in the fluid continuum circulating in tectonic fault zones. Vesicles which form spontaneously at a depth of approximately 1 km present a selective trap for amphiphilic molecules, especially for peptides composed of hydrophilic and hydrophobic amino acids in a suitable sequence. The accumulation effect is shown in a numeric simulation on a simplified model. Further, possible mechanisms of a molecular evolution in vesicle membranes are discussed. Altogether, the proposed scenario can be seen as an ideal environment for constant, undisturbed molecular evolution in and on cell-like compartments. Full article

(This article belongs to the Section Hypotheses in the Life Sciences)

► Show Figures

Figure 1

1114 KiB

Open AccessArticle

Mobility of a Mononucleotide within a Lipid Matrix: A Neutron Scattering Study

by Loreto Misuraca, Francesca Natali, Laura Da Silva, Judith Peters, Bruno Demé, Jacques Ollivier, Tilo Seydel, Valerie Laux-Lesourd, Michael Haertlein, Giuseppe Zaccai, David Deamer and Marie Christine Maurel

Life 2017, 7(1), 2; https://doi.org/10.3390/life7010002 - 04 Jan 2017

Cited by 8 | Viewed by 5767

Abstract

An essential question in studies on the origins of life is how nucleic acids were first synthesized and then incorporated into compartments about 4 billion years ago. A recent discovery is that guided polymerization within organizing matrices could promote a non-enzymatic condensation reaction [...] Read more.

An essential question in studies on the origins of life is how nucleic acids were first synthesized and then incorporated into compartments about 4 billion years ago. A recent discovery is that guided polymerization within organizing matrices could promote a non-enzymatic condensation reaction allowing the formation of RNA-like polymers, followed by encapsulation in lipid membranes. Here, we used neutron scattering and deuterium labelling to investigate 5′-adenosine monophosphate (AMP) molecules captured in a multilamellar phospholipid matrix. The aim of the research was to determine and compare how mononucleotides are captured and differently organized within matrices and multilamellar phospholipid structures and to explore the role of water in organizing the system to determine at which level the system becomes sufficiently anhydrous to lock the AMP molecules into an organized structure and initiate ester bond synthesis. Elastic incoherent neutron scattering experiments were thus employed to investigate the changes of the dynamic properties of AMP induced by embedding the molecules within the lipid matrix. The influence of AMP addition to the lipid membrane organization was determined through diffraction measurement, which also helped us to define the best working Q range for dynamical data analysis with respect to specific hydration. The use of different complementary instruments allowed coverage of a wide time-scale domain, from ns to ps, of atomic mean square fluctuations, providing evidence of a well-defined dependence of the AMP dynamics on the hydration level. Full article

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

► Show Figures

Figure 1

3093 KiB

Open AccessArticle

Arsenite as an Electron Donor for Anoxygenic Photosynthesis: Description of Three Strains of Ectothiorhodospira from Mono Lake, California and Big Soda Lake, Nevada

by Shelley Hoeft McCann, Alison Boren, Jaime Hernandez-Maldonado, Brendon Stoneburner, Chad W. Saltikov, John F. Stolz and Ronald S. Oremland

Life 2017, 7(1), 1; https://doi.org/10.3390/life7010001 - 26 Dec 2016

Cited by 25 | Viewed by 6914

Abstract

Three novel strains of photosynthetic bacteria from the family Ectothiorhodospiraceae were isolated from soda lakes of the Great Basin Desert, USA by employing arsenite (As(III)) as the sole electron donor in the enrichment/isolation process. Strain PHS-1 was previously isolated from a hot spring [...] Read more.

Three novel strains of photosynthetic bacteria from the family Ectothiorhodospiraceae were isolated from soda lakes of the Great Basin Desert, USA by employing arsenite (As(III)) as the sole electron donor in the enrichment/isolation process. Strain PHS-1 was previously isolated from a hot spring in Mono Lake, while strain MLW-1 was obtained from Mono Lake sediment, and strain BSL-9 was isolated from Big Soda Lake. Strains PHS-1, MLW-1, and BSL-9 were all capable of As(III)-dependent growth via anoxygenic photosynthesis and contained homologs of arxA, but displayed different phenotypes. Comparisons were made with three related species: Ectothiorhodospira shaposhnikovii DSM 2111, Ectothiorhodospira shaposhnikovii DSM 243^T, and Halorhodospira halophila DSM 244. All three type cultures oxidized arsenite to arsenate but did not grow with As(III) as the sole electron donor. DNA–DNA hybridization indicated that strain PHS-1 belongs to the same species as Ect. shaposhnikovii DSM 2111 (81.1% sequence similarity), distinct from Ect. shaposhnikovii DSM 243^T (58.1% sequence similarity). These results suggest that the capacity for light-driven As(III) oxidation is a common phenomenon among purple photosynthetic bacteria in soda lakes. However, the use of As(III) as a sole electron donor to sustain growth via anoxygenic photosynthesis is confined to novel isolates that were screened for by this selective cultivation criterion. Full article

(This article belongs to the Special Issue Proceedings from the 11th Conference on Halophilic Microorganisms Halophiles 2016)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Life, Volume 7, Issue 1 (March 2017) – 12 articles

Further Information

Guidelines

MDPI Initiatives

Follow MDPI