Special Issue "The Origins and Early Evolution of RNA"

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A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Chemistry".

Deadline for manuscript submissions: closed (30 September 2014)

Special Issue Editor

Guest Editor
Prof. Dr. Niles Lehman
Department of Chemistry, Portland State University, PO Box 751, Portland, OR 97207, USA
Website: http://www.pdx.edu/clas/profile/dr-niles-lehman
E-Mail: niles@pdx.edu
Phone: +1-503-725-8769
Interests: origins of life; RNA; ribozymes; recombination; prebiotic chemistry; systems chemistry, cooperation; in vitro evolution

Special Issue Information

Dear Colleagues,

The notion that molecular systems such as RNA can display a wide range of evolutionary processes in the absence of fully formed cellular life continues to gain support. Understanding how RNA can behave in an abiotic context is a key piece of our picture of how life developed and expanded on the Earth, and by proxy, elsewhere. We can study how RNA behaves in this regard through a combination of in vivo work (with small regulatory RNAs and larger catalytic RNAs alike), experimental work in the laboratory, and through powerful analytical and simulation studies. These efforts will not only grant us a better sense of the early stages of life on this planet but also of how RNA evolved to play a central role in contemporary metabolism. Many key ideas of primitive RNA functionality were developed in the 1970s and 1980s before we had either the experimental systems in place to fully explore these concepts or the appreciation of the extent to which RNAs were important to the cell. In this special issue, some of the recent discoveries and advances in RNA biology, biochemistry, and evolutionary biology are presented.

Prof. Dr. Niles Lehman
Guest Editor

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 300 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Keywords

  • RNA
  • primitive genotypes
  • genetic networks
  • fitness landscapes
  • genetic takeover
  • early evolutionary processes
  • evolvability
  • robustness
  • error threshold
  • quasispecies
  • small RNA-directed gene regulation

Published Papers (16 papers)

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Displaying article 1-16
p. 604-636
by , ,  and
Life 2015, 5(1), 604-636; doi:10.3390/life5010604
Received: 15 January 2015 / Revised: 4 February 2015 / Accepted: 6 February 2015 / Published: 27 February 2015
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(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
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p. 637-650
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Life 2015, 5(1), 637-650; doi:10.3390/life5010637
Received: 29 September 2014 / Revised: 9 February 2015 / Accepted: 12 February 2015 / Published: 27 February 2015
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(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
p. 372-384
by , , ,  and
Life 2015, 5(1), 372-384; doi:10.3390/life5010372
Received: 30 September 2014 / Revised: 20 January 2015 / Accepted: 22 January 2015 / Published: 30 January 2015
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(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
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p. 321-331
by
Life 2015, 5(1), 321-331; doi:10.3390/life5010321
Received: 12 November 2014 / Revised: 14 January 2015 / Accepted: 21 January 2015 / Published: 26 January 2015
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(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
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p. 294-320
by Jr.
Life 2015, 5(1), 294-320; doi:10.3390/life5010294
Received: 24 November 2014 / Accepted: 12 January 2015 / Published: 23 January 2015
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(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
p. 247-268
by ,  and
Life 2015, 5(1), 247-268; doi:10.3390/life5010247
Received: 2 October 2014 / Revised: 22 December 2014 / Accepted: 13 January 2015 / Published: 20 January 2015
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(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
p. 230-246
by  and
Life 2015, 5(1), 230-246; doi:10.3390/life5010230
Received: 30 November 2014 / Revised: 16 December 2014 / Accepted: 14 January 2015 / Published: 19 January 2015
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(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
p. 65-84
by  and
Life 2015, 5(1), 65-84; doi:10.3390/life5010065
Received: 16 October 2014 / Accepted: 23 December 2014 / Published: 5 January 2015
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(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
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p. 1050-1091
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Life 2014, 4(4), 1050-1091; doi:10.3390/life4041050
Received: 24 October 2014 / Revised: 2 December 2014 / Accepted: 9 December 2014 / Published: 19 December 2014
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(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
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p. 1013-1025
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Life 2014, 4(4), 1013-1025; doi:10.3390/life4041013
Received: 23 October 2014 / Revised: 27 November 2014 / Accepted: 11 December 2014 / Published: 16 December 2014
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(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
p. 887-902
by , ,  and
Life 2014, 4(4), 887-902; doi:10.3390/life4040887
Received: 12 October 2014 / Revised: 1 December 2014 / Accepted: 2 December 2014 / Published: 11 December 2014
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(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
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p. 800-818
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Life 2014, 4(4), 800-818; doi:10.3390/life4040800
Received: 7 October 2014 / Revised: 11 November 2014 / Accepted: 12 November 2014 / Published: 24 November 2014
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(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
p. 788-799
by ,  and
Life 2014, 4(4), 788-799; doi:10.3390/life4040788
Received: 30 September 2014 / Revised: 12 November 2014 / Accepted: 17 November 2014 / Published: 21 November 2014
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(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
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p. 341-373
by , , , , ,  and
Life 2014, 4(3), 341-373; doi:10.3390/life4030341
Received: 29 April 2014 / Revised: 23 July 2014 / Accepted: 25 July 2014 / Published: 11 August 2014
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(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
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p. 227-249
by  and
Life 2014, 4(2), 227-249; doi:10.3390/life4020227
Received: 30 January 2014 / Revised: 23 April 2014 / Accepted: 25 April 2014 / Published: 20 May 2014
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(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
p. 131-141
by , , ,  and
Life 2014, 4(2), 131-141; doi:10.3390/life4020131
Received: 27 February 2014 / Revised: 28 March 2014 / Accepted: 31 March 2014 / Published: 10 April 2014
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(This article belongs to the Special Issue The Origins and Early Evolution of RNA)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Acytota: Neglected Kingdom of Life
Authors:
Edward N. Trifonov 1 and Eduard Kejnovsky 2
Affiliation:
1 Genome Diversity Center, Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel
2
Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Kralovopolska 135, 61265 Brno, Czech Republic
Abstract:
There is a huge variety of RNA- and DNA-containing entities which multiply within and propagate between cells of all kingdoms of life, having no cells of their own. Apart of cellular organisms these entities (viroids, plasmids, mobile elements, viruses and others) are the only ones which have their distinct genetic identities, but not included in any kingdom of life, since all the traditional kingdoms are cellular. We suggest to introduce the distinct category of the acellular organisms, Acytota, as an additional, undeservedly ignored kingdom of life. Acytota are indispensable for cellular life and its evolution. Six traditional kingdoms (Cytota) together with Acytota complete the classification of biological world (Biota), leaving nothing life-like beyond.

Title: The Origin and Evolution of Ribonucleotide Reduction—A Repeated History of Reciprocal Dependencies
Authors:
Daniel Lundin 1, Gustav Berggren 1, David Nord 1, Derek Logan 2 and Britt-Marie Sjöberg 1
Affiliations:
1 Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, SE-106 91 Stockholm, Sweden
2
Department of Biochemistry and Structural Biology, Lund University, Box 124, SE-221 00 Lund, Sweden
Abstract
: Ribonucleotide reduction is the only pathway for de novo synthesisof deoxyribonucleotides in extant organisms. Ribonucleotide reductase (RNR) catalyses the reaction, which is chemically demanding and involves a carbon-based radical. The mechanism has been deemed unlikely to be catalysed by a ribozyme, creating an enigma regarding how the building blocks for DNA were synthesised at the transition from RNA to DNA encoded genomes. While it is entirely possible that a different pathway was used, later to be replaced with the extant mechanism, here we explore the evolutionary and biochemical limits for an origin of the mechanism in the RNA+protein world and suggest a model for a proto typical ribonucleotide reductase (protoRNR). From the protoRNR evolved the ancestor to extant RNRs, the urRNR, which diversified to the extant three classes characterised mainly by how the radical is initially generated. Subsequent to the origin of the three classes, RNRs have undergone further specialisations, and we describe a phylogenetic subclassification of the enzyme family. RNR genes are frequent hosts of selfish genetic elements—introns and inteins—and we observe an interesting organism distribution of classes and subclasses indicating both short and long-range horizontal transfer of RNR genes.

Last update: 25 February 2015

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