The progene hypothesis: the nucleoprotein world and how life began.

Abstract:

:In this article, I review the results of studies on the origin of life distinct from the popular RNA world hypothesis. The alternate scenario postulates the origin of the first bimolecular genetic system (a polynucleotide gene and a polypeptide processive polymerase) with simultaneous replication and translation and includes the following key features: 1. The bimolecular genetic system emerges not from mononucleotides and monoamino acids, but from progenes, namely, trinucleotides aminoacylated on 3'-end by a non-random amino acid (NpNpNp ~ pX ~ Aa, where N--deoxyribo- or ribonucleoside, p--phosphate, X--a bifunctional agent, for example ribose, Aa--amino acid, ~ macroerge bond). Progenes are used as substrates for simultaneous synthesis of a polynucleotide and a polypeptide. Growth of the system is controlled by the growing polypeptide, and the bimolecular genetic system emerges as an extremely rare event. The first living being (virus-like organism protoviroid, Protoviroidum primum) arises and reproduces in prebiotic liposome-like structures using progenes. A population of protoviroids possessing the genetic system evolves in accordance with the Darwinian principle. Early evolution from protoviroid world to protocell world is shortly described. 2. The progene forming mechanism (NpNp + Np ~ pX ~ Aa) makes it possible to explain the emergence of the prebiotic physicochemical group genetic code, as well as the selection of organic compounds for the future genetic system from the racemic environment. 3. The protoviroid is reproduced on a progene basis via replicative transcription-translation (RTT, the first molecular genetic process) that is similar to its modern counterparts. Nothing is required for the emergence and reproduction of the protoviroid except for progenes and conditions for their formation. 4. The general scheme of early evolution is as follows: prebiotic world → protoviroid (nucleoprotein) world → protocell (DNA-RNA-protein) world → LUCA (Last Universal Common Ancestor) → modern cell world. This scheme exclude the existence of an independent RNA world as predecessor of the cellular world.

journal_name

Biol Direct

journal_title

Biology direct

authors

Altstein AD

doi

10.1186/s13062-015-0096-z

subject

Has Abstract

pub_date

2015-11-26 00:00:00

pages

67

issn

1745-6150

pii

10.1186/s13062-015-0096-z

journal_volume

10

pub_type

杂志文章,评审
  • Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park.

    abstract:BACKGROUND:A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. RESULTS:The first terrestrial hyperthermophilic member of the Nanoarchaeota was collected from Obsidian Pool, a ...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-8-9

    authors: Podar M,Makarova KS,Graham DE,Wolf YI,Koonin EV,Reysenbach AL

    更新日期:2013-04-22 00:00:00

  • A novel superfamily containing the beta-grasp fold involved in binding diverse soluble ligands.

    abstract:BACKGROUND:Domains containing the beta-grasp fold are utilized in a great diversity of physiological functions but their role, if any, in soluble or small molecule ligand recognition is poorly studied. RESULTS:Using sensitive sequence and structure similarity searches we identify a novel superfamily containing the bet...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-2-4

    authors: Burroughs AM,Balaji S,Iyer LM,Aravind L

    更新日期:2007-01-24 00:00:00

  • Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements.

    abstract:BACKGROUND:In eukaryotes, RNA interference (RNAi) is a major mechanism of defense against viruses and transposable elements as well of regulating translation of endogenous mRNAs. The RNAi systems recognize the target RNA molecules via small guide RNAs that are completely or partially complementary to a region of the ta...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-4-29

    authors: Makarova KS,Wolf YI,van der Oost J,Koonin EV

    更新日期:2009-08-25 00:00:00

  • Rotational restriction of nascent peptides as an essential element of co-translational protein folding: possible molecular players and structural consequences.

    abstract:BACKGROUND:A basic tenet of protein science is that all information about the spatial structure of proteins is present in their sequences. Nonetheless, many proteins fail to attain native structure upon experimental denaturation and refolding in vitro, raising the question of the specific role of cellular machinery in ...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-017-0186-1

    authors: Sorokina I,Mushegian A

    更新日期:2017-05-31 00:00:00

  • Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.

    abstract:BACKGROUND:An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on suc...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-2-33

    authors: Makarova KS,Sorokin AV,Novichkov PS,Wolf YI,Koonin EV

    更新日期:2007-11-27 00:00:00

  • Impairment of translation in neurons as a putative causative factor for autism.

    abstract:BACKGROUND:A dramatic increase in the prevalence of autism and Autistic Spectrum Disorders (ASD) has been observed over the last two decades in USA, Europe and Asia. Given the accumulating data on the possible role of translation in the etiology of ASD, we analyzed potential effects of rare synonymous substitutions ass...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-9-16

    authors: Poliakov E,Koonin EV,Rogozin IB

    更新日期:2014-07-10 00:00:00

  • Why eukaryotic cells use introns to enhance gene expression: splicing reduces transcription-associated mutagenesis by inhibiting topoisomerase I cutting activity.

    abstract:BACKGROUND:The costs and benefits of spliceosomal introns in eukaryotes have not been established. One recognized effect of intron splicing is its known enhancement of gene expression. However, the mechanism regulating such splicing-mediated expression enhancement has not been defined. Previous studies have shown that ...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-6-24

    authors: Niu DK,Yang YF

    更新日期:2011-05-18 00:00:00

  • The mechanistic and evolutionary aspects of the 2'- and 3'-OH paradigm in biosynthetic machinery.

    abstract:BACKGROUND:The translation machinery underlies a multitude of biological processes within the cell. The design and implementation of the modern translation apparatus on even the simplest course of action is extremely complex, and involves different RNA and protein factors. According to the "RNA world" idea, the critica...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-8-17

    authors: Safro M,Klipcan L

    更新日期:2013-07-08 00:00:00

  • Modeling the population dynamics of lemon sharks.

    abstract:BACKGROUND:Long-lived marine megavertebrates (e.g. sharks, turtles, mammals, and seabirds) are inherently vulnerable to anthropogenic mortality. Although some mathematical models have been applied successfully to manage these animals, more detailed treatments are often needed to assess potential drivers of population d...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-9-23

    authors: White ER,Nagy JD,Gruber SH

    更新日期:2014-11-18 00:00:00

  • Elusive data underlying debate at the prokaryote-eukaryote divide.

    abstract:BACKGROUND:The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenerge...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-018-0221-x

    authors: Gerlitz M,Knopp M,Kapust N,Xavier JC,Martin WF

    更新日期:2018-10-03 00:00:00

  • The UBR-box and its relationship to binuclear RING-like treble clef zinc fingers.

    abstract:BACKGROUND:The N-end rule pathway is a part of the ubiquitin-dependent proteolytic system wherein N-recognin proteins recognize the amino terminal degradation signals (N-degrons) of the substrate. The type 1 N-degron recognizing UBR-box domain of the eukaryotic Arg/N-end rule pathway is known to possess a novel three-z...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-015-0066-5

    authors: Kaur G,Subramanian S

    更新日期:2015-07-17 00:00:00

  • On origin of genetic code and tRNA before translation.

    abstract:BACKGROUND:Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids (aas). A major challenge to the understanding of the origins of this assignment is the archetypal "key-lock vs. frozen accident" dilemma. Here we re-examine this dilemma in light of 1) the fundamental ...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-6-14

    authors: Rodin AS,Szathmáry E,Rodin SN

    更新日期:2011-02-22 00:00:00

  • Interplay of recombination and selection in the genomes of Chlamydia trachomatis.

    abstract:BACKGROUND:Chlamydia trachomatis is an obligate intracellular bacterial parasite, which causes several severe and debilitating diseases in humans. This study uses comparative genomic analyses of 12 complete published C. trachomatis genomes to assess the contribution of recombination and selection in this pathogen and t...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-6-28

    authors: Joseph SJ,Didelot X,Gandhi K,Dean D,Read TD

    更新日期:2011-05-26 00:00:00

  • Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons.

    abstract:BACKGROUND:While all codons that specify amino acids are universally recognized by tRNA molecules, codons signaling termination of translation are recognized by proteins known as class-I release factors (RF). In most eukaryotes and archaea a single RF accomplishes termination at all three stop codons. In most bacteria,...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-1-28

    authors: Baranov PV,Vestergaard B,Hamelryck T,Gesteland RF,Nyborg J,Atkins JF

    更新日期:2006-09-13 00:00:00

  • A network-based approach to classify the three domains of life.

    abstract:BACKGROUND:Identifying group-specific characteristics in metabolic networks can provide better insight into evolutionary developments. Here, we present an approach to classify the three domains of life using topological information about the underlying metabolic networks. These networks have been shown to share domain-...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-6-53

    authors: Mueller LA,Kugler KG,Netzer M,Graber A,Dehmer M

    更新日期:2011-10-13 00:00:00

  • Evolution before genes.

    abstract:BACKGROUND:Our current understanding of evolution is so tightly linked to template-dependent replication of DNA and RNA molecules that the old idea from Oparin of a self-reproducing 'garbage bag' ('coacervate') of chemicals that predated fully-fledged cell-like entities seems to be farfetched to most scientists today. ...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-7-1

    authors: Vasas V,Fernando C,Santos M,Kauffman S,Szathmáry E

    更新日期:2012-01-05 00:00:00

  • Proteomic changes associated with deletion of the Magnaporthe oryzae conidial morphology-regulating gene COM1.

    abstract:BACKGROUND:The rice blast disease caused by Magnaporthe oryzae is a major constraint on world rice production. The conidia produced by this fungal pathogen are the main source of disease dissemination. The morphology of conidia may be a critical factor in the spore dispersal and virulence of M. oryzae in the field. Del...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-5-61

    authors: Bhadauria V,Wang LX,Peng YL

    更新日期:2010-11-02 00:00:00

  • Structural analysis of hubs in human NR-RTK network.

    abstract:BACKGROUND:Currently a huge amount of protein-protein interaction data is available therefore extracting meaningful ones are a challenging task. In a protein-protein interaction network, hubs are considered as key proteins maintaining function and stability of the network. Therefore, studying protein-protein complexes ...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-6-49

    authors: Choura M,Rebaï A

    更新日期:2011-10-05 00:00:00

  • A highly conserved family of inactivated archaeal B family DNA polymerases.

    abstract::A widespread and highly conserved family of apparently inactivated derivatives of archaeal B-family DNA polymerases is described. Phylogenetic analysis shows that the inactivated forms comprise a distinct clade among archaeal B-family polymerases and that, within this clade, Euryarchaea and Crenarchaea are clearly sep...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-3-32

    authors: Rogozin IB,Makarova KS,Pavlov YI,Koonin EV

    更新日期:2008-08-06 00:00:00

  • Biased gene transfer and its implications for the concept of lineage.

    abstract:BACKGROUND:In the presence of horizontal gene transfer (HGT), the concepts of lineage and genealogy in the microbial world become more ambiguous because chimeric genomes trace their ancestry from a myriad of sources, both living and extinct. RESULTS:We present the evolutionary histories of three aminoacyl-tRNA synthet...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-6-47

    authors: Andam CP,Gogarten JP

    更新日期:2011-09-23 00:00:00

  • Orphan SelD proteins and selenium-dependent molybdenum hydroxylases.

    abstract::Bacterial and Archaeal cells use selenium structurally in selenouridine-modified tRNAs, in proteins translated with selenocysteine, and in the selenium-dependent molybdenum hydroxylases (SDMH). The first two uses both require the selenophosphate synthetase gene, selD. Examining over 500 complete prokaryotic genomes fi...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-3-4

    authors: Haft DH,Self WT

    更新日期:2008-02-20 00:00:00

  • Once upon a time the cell membranes: 175 years of cell boundary research.

    abstract::All modern cells are bounded by cell membranes best described by the fluid mosaic model. This statement is so widely accepted by biologists that little attention is generally given to the theoretical importance of cell membranes in describing the cell. This has not always been the case. When the Cell Theory was first ...

    journal_title:Biology direct

    pub_type: 历史文章,杂志文章,评审

    doi:10.1186/s13062-014-0032-7

    authors: Lombard J

    更新日期:2014-12-19 00:00:00

  • Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes.

    abstract:BACKGROUND:The prokaryotic toxin-antitoxin systems (TAS, also referred to as TA loci) are widespread, mobile two-gene modules that can be viewed as selfish genetic elements because they evolved mechanisms to become addictive for replicons and cells in which they reside, but also possess "normal" cellular functions in v...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-4-19

    authors: Makarova KS,Wolf YI,Koonin EV

    更新日期:2009-06-03 00:00:00

  • Activating and inhibiting connections in biological network dynamics.

    abstract:BACKGROUND:Many studies of biochemical networks have analyzed network topology. Such work has suggested that specific types of network wiring may increase network robustness and therefore confer a selective advantage. However, knowledge of network topology does not allow one to predict network dynamical behavior--for e...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-3-49

    authors: McDonald D,Waterbury L,Knight R,Betterton MD

    更新日期:2008-12-04 00:00:00

  • Domain enhanced lookup time accelerated BLAST.

    abstract:BACKGROUND:BLAST is a commonly-used software package for comparing a query sequence to a database of known sequences; in this study, we focus on protein sequences. Position-specific-iterated BLAST (PSI-BLAST) iteratively searches a protein sequence database, using the matches in round i to construct a position-specific...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-7-12

    authors: Boratyn GM,Schäffer AA,Agarwala R,Altschul SF,Lipman DJ,Madden TL

    更新日期:2012-04-17 00:00:00

  • Use of designed sequences in protein structure recognition.

    abstract:BACKGROUND:Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. In the Pfam database, structure description is ...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-018-0209-6

    authors: Kumar G,Mudgal R,Srinivasan N,Sandhya S

    更新日期:2018-05-09 00:00:00

  • Pathophysiology of Crohn's disease inflammation and recurrence.

    abstract::Chron's Disease is a chronic inflammatory intestinal disease, first described at the beginning of the last century. The disease is characterized by the alternation of periods of flares and remissions influenced by a complex pathogenesis in which inflammation plays a key role. Crohn's disease evolution is mediated by a...

    journal_title:Biology direct

    pub_type: 杂志文章,评审

    doi:10.1186/s13062-020-00280-5

    authors: Petagna L,Antonelli A,Ganini C,Bellato V,Campanelli M,Divizia A,Efrati C,Franceschilli M,Guida AM,Ingallinella S,Montagnese F,Sensi B,Siragusa L,Sica GS

    更新日期:2020-11-07 00:00:00

  • PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues.

    abstract:BACKGROUND:In the past, many methods have been developed for peptide tertiary structure prediction but they are limited to peptides having natural amino acids. This study describes a method PEPstrMOD, which is an updated version of PEPstr, developed specifically for predicting the structure of peptides containing natur...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-015-0103-4

    authors: Singh S,Singh H,Tuknait A,Chaudhary K,Singh B,Kumaran S,Raghava GP

    更新日期:2015-12-21 00:00:00

  • A computational approach to candidate gene prioritization for X-linked mental retardation using annotation-based binary filtering and motif-based linear discriminatory analysis.

    abstract:BACKGROUND:Several computational candidate gene selection and prioritization methods have recently been developed. These in silico selection and prioritization techniques are usually based on two central approaches--the examination of similarities to known disease genes and/or the evaluation of functional annotation of...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-6-30

    authors: Lombard Z,Park C,Makova KD,Ramsay M

    更新日期:2011-06-13 00:00:00

  • Predictability of drug-induced liver injury by machine learning.

    abstract:BACKGROUND:Drug-induced liver injury (DILI) is a major concern in drug development, as hepatotoxicity may not be apparent at early stages but can lead to life threatening consequences. The ability to predict DILI from in vitro data would be a crucial advantage. In 2018, the Critical Assessment Massive Data Analysis gro...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-020-0259-4

    authors: Chierici M,Francescatto M,Bussola N,Jurman G,Furlanello C

    更新日期:2020-02-13 00:00:00