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Open AccessOpinion

Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks

by Derek Caetano-Anollés and Gustavo Caetano-Anollés

Life 2016, 6(4), 43; https://doi.org/10.3390/life6040043 - 2 Dec 2016

Cited by 27 | Viewed by 8669

The origin of biomolecular machinery likely centered around an ancient and central molecule capable of interacting with emergent macromolecular complexity. tRNA is the oldest and most central nucleic acid molecule of the cell. Its co-evolutionary interactions with aminoacyl-tRNA synthetase protein enzymes define the specificities of the genetic code and those with the ribosome their accurate biosynthetic interpretation. Phylogenetic approaches that focus on molecular structure allow reconstruction of evolutionary timelines that describe the history of RNA and protein structural domains. Here we review phylogenomic analyses that reconstruct the early history of the synthetase enzymes and the ribosome, their interactions with RNA, and the inception of amino acid charging and codon specificities in tRNA that are responsible for the genetic code. We also trace the age of domains and tRNA onto ancient tRNA homologies that were recently identified in rRNA. Our findings reveal a timeline of recruitment of tRNA building blocks for the formation of a functional ribosome, which holds both the biocatalytic functions of protein biosynthesis and the ability to store genetic memory in primordial RNA genomic templates. 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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1065 KiB

Open AccessReview

Cyanobacteria as Chassis for Industrial Biotechnology: Progress and Prospects

by Lamya Al-Haj, Yuen Tin Lui, Raeid M.M. Abed, Mohamed A. Gomaa and Saul Purton

Life 2016, 6(4), 42; https://doi.org/10.3390/life6040042 - 30 Nov 2016

Cited by 48 | Viewed by 10751

Abstract

Cyanobacteria hold significant potential as industrial biotechnology (IB) platforms for the production of a wide variety of bio-products ranging from biofuels such as hydrogen, alcohols and isoprenoids, to high-value bioactive and recombinant proteins. Underpinning this technology, are the recent advances in cyanobacterial “omics” research, the development of improved genetic engineering tools for key species, and the emerging field of cyanobacterial synthetic biology. These approaches enabled the development of elaborate metabolic engineering programs aimed at creating designer strains tailored for different IB applications. In this review, we provide an overview of the current status of the fields of cyanobacterial omics and genetic engineering with specific focus on the current molecular tools and technologies that have been developed in the past five years. The paper concludes by giving insights on future commercial applications of cyanobacteria and highlights the challenges that need to be addressed in order to make cyanobacterial industrial biotechnology more feasible in the near future. Full article

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3372 KiB

Open AccessArticle

Screening of a Haloferax volcanii Transposon Library Reveals Novel Motility and Adhesion Mutants

by Georgio Legerme, Evan Yang, Rianne N. Esquivel, Saija Kiljunen, Harri Savilahti and Mechthild Pohlschroder

Life 2016, 6(4), 41; https://doi.org/10.3390/life6040041 - 26 Nov 2016

Cited by 18 | Viewed by 7338

Abstract

Archaea, like bacteria, use type IV pili to facilitate surface adhesion. Moreover, archaeal flagella—structures required for motility—share a common ancestry with type IV pili. While the characterization of archaeal homologs of bacterial type IV pilus biosynthesis components has revealed important aspects of flagellum and pilus biosynthesis and the mechanisms regulating motility and adhesion in archaea, many questions remain. Therefore, we screened a Haloferax volcanii transposon insertion library for motility mutants using motility plates and adhesion mutants, using an adapted air–liquid interface assay. Here, we identify 20 genes, previously unknown to affect motility or adhesion. These genes include potential novel regulatory genes that will help to unravel the mechanisms underpinning these processes. Both screens also identified distinct insertions within the genomic region lying between two chemotaxis genes, suggesting that chemotaxis not only plays a role in archaeal motility, but also in adhesion. Studying these genes, as well as hypothetical genes hvo_2512 and hvo_2876—also critical for both motility and adhesion—will likely elucidate how these two systems interact. Furthermore, this study underscores the usefulness of the transposon library to screen other archaeal cellular processes for specific phenotypic defects. Full article

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

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874 KiB

Open AccessReview

Taming Prebiotic Chemistry: The Role of Heterogeneous and Interfacial Catalysis in the Emergence of a Prebiotic Catalytic/Information Polymer System

by Pierre-Alain Monnard

Life 2016, 6(4), 40; https://doi.org/10.3390/life6040040 - 4 Nov 2016

Cited by 15 | Viewed by 7625

Abstract

Cellular life is based on interacting polymer networks that serve as catalysts, genetic information and structural molecules. The complexity of the DNA, RNA and protein biochemistry suggests that it must have been preceded by simpler systems. The RNA world hypothesis proposes RNA as the prime candidate for such a primal system. Even though this proposition has gained currency, its investigations have highlighted several challenges with respect to bulk aqueous media: (1) the synthesis of RNA monomers is difficult; (2) efficient pathways for monomer polymerization into functional RNAs and their subsequent, sequence-specific replication remain elusive; and (3) the evolution of the RNA function towards cellular metabolism in isolation is questionable in view of the chemical mixtures expected on the early Earth. This review will address the question of the possible roles of heterogeneous media and catalysis as drivers for the emergence of RNA-based polymer networks. We will show that this approach to non-enzymatic polymerizations of RNA from monomers and RNA evolution cannot only solve some issues encountered during reactions in bulk aqueous solutions, but may also explain the co-emergence of the various polymers indispensable for life in complex mixtures and their organization into primitive networks. Full article

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

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Life, Volume 6, Issue 4 (December 2016) – 4 articles

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