MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases.

Abstract:

:The provenance and biochemical roles of eukaryotic MORC proteins have remained poorly understood since the discovery of their prototype MORC1, which is required for meiotic nuclear division in animals. The MORC family contains a combination of a gyrase, histidine kinase, and MutL (GHKL) and S5 domains that together constitute a catalytically active ATPase module. We identify the prokaryotic MORCs and establish that the MORC family belongs to a larger radiation of several families of GHKL proteins (paraMORCs) in prokaryotes. Using contextual information from conserved gene neighborhoods we show that these proteins primarily function in restriction-modification systems, in conjunction with diverse superfamily II DNA helicases and endonucleases. The common ancestor of these GHKL proteins, MutL and topoisomerase ATPase modules appears to have catalyzed structural reorganization of protein complexes and concomitant DNA-superstructure manipulations along with fused or standalone nuclease domains. Furthermore, contextual associations of the prokaryotic MORCs and their relatives suggest that their eukaryotic counterparts are likely to carry out chromatin remodeling by DNA superstructure manipulation in response to epigenetic signals such as histone and DNA methylation.

journal_name

Biol Direct

journal_title

Biology direct

authors

Iyer LM,Abhiman S,Aravind L

doi

10.1186/1745-6150-3-8

subject

Has Abstract

pub_date

2008-03-17 00:00:00

pages

8

issn

1745-6150

pii

1745-6150-3-8

journal_volume

3

pub_type

杂志文章
  • IPC - Isoelectric Point Calculator.

    abstract:BACKGROUND:Accurate estimation of the isoelectric point (pI) based on the amino acid sequence is useful for many analytical biochemistry and proteomics techniques such as 2-D polyacrylamide gel electrophoresis, or capillary isoelectric focusing used in combination with high-throughput mass spectrometry. Additionally, p...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-016-0159-9

    authors: Kozlowski LP

    更新日期:2016-10-21 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

  • Why call it developmental bias when it is just development?

    abstract::The concept of developmental constraints has been central to understand the role of development in morphological evolution. Developmental constraints are classically defined as biases imposed by development on the distribution of morphological variation.This opinion article argues that the concepts of developmental co...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-020-00289-w

    authors: Salazar-Ciudad I

    更新日期:2021-01-09 00:00:00

  • Putative adaptive inter-slope divergence of transposon frequency in fruit flies (Drosophila melanogaster) at "Evolution Canyon", Mount Carmel, Israel.

    abstract:BACKGROUND:The current analysis of transposon elements (TE) in Drosophila melanogaster at Evolution Canyon, (EC), Israel, is based on data and analysis done by our collaborators (Drs. J. Gonzalez, J. Martinez and W. Makalowski, this issue). They estimated the frequencies of 28 TEs (transposon elements) in fruit flies (...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-015-0074-5

    authors: Beiles A,Raz S,Ben-Abu Y,Nevo E

    更新日期:2015-10-14 00:00:00

  • 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 i...

    journal_title:Biology direct

    pub_type: 杂志文章,评审

    doi:10.1186/s13062-015-0096-z

    authors: Altstein AD

    更新日期:2015-11-26 00:00:00

  • 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

  • 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

  • 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

  • The common ancestry of life.

    abstract:BACKGROUND:It is common belief that all cellular life forms on earth have a common origin. This view is supported by the universality of the genetic code and the universal conservation of multiple genes, particularly those that encode key components of the translation system. A remarkable recent study claims to provide...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-5-64

    authors: Koonin EV,Wolf YI

    更新日期:2010-11-18 00:00:00

  • The multiple personalities of Watson and Crick strands.

    abstract:BACKGROUND:In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two terms, and the many usages contradict one another as well as the original definition. Here, we review t...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-6-7

    authors: Cartwright RA,Graur D

    更新日期:2011-02-08 00:00:00

  • Pseudo-chaotic oscillations in CRISPR-virus coevolution predicted by bifurcation analysis.

    abstract:BACKGROUND:The CRISPR-Cas systems of adaptive antivirus immunity are present in most archaea and many bacteria, and provide resistance to specific viruses or plasmids by inserting fragments of foreign DNA into the host genome and then utilizing transcripts of these spacers to inactivate the cognate foreign genome. The ...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-9-13

    authors: Berezovskaya FS,Wolf YI,Koonin EV,Karev GP

    更新日期:2014-07-02 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

  • Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions.

    abstract:BACKGROUND:H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are essential for understanding the infection mechanism of the formidable pathogen M. tuberculosis H37Rv. Computational prediction is an important strategy to fill the gap in experimental H. sapiens-M. tuberculosis H37Rv PPI data. Homolo...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-9-5

    authors: Zhou H,Gao S,Nguyen NN,Fan M,Jin J,Liu B,Zhao L,Xiong G,Tan M,Li S,Wong L

    更新日期:2014-04-08 00:00:00

  • A web server for analysis, comparison and prediction of protein ligand binding sites.

    abstract:BACKGROUND:One of the major challenges in the field of system biology is to understand the interaction between a wide range of proteins and ligands. In the past, methods have been developed for predicting binding sites in a protein for a limited number of ligands. RESULTS:In order to address this problem, we developed...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-016-0118-5

    authors: Singh H,Srivastava HK,Raghava GP

    更新日期:2016-03-25 00:00:00

  • Systematic evaluation of supervised machine learning for sample origin prediction using metagenomic sequencing data.

    abstract:BACKGROUND:The advent of metagenomic sequencing provides microbial abundance patterns that can be leveraged for sample origin prediction. Supervised machine learning classification approaches have been reported to predict sample origin accurately when the origin has been previously sampled. Using metagenomic datasets p...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-020-00287-y

    authors: Chen JC,Tyler AD

    更新日期:2020-12-10 00:00:00

  • Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage.

    abstract:BACKGROUND:The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with function by genetic or biochemical approaches, a lengthy process that often took years. Phylogenetic distr...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-7-32

    authors: de Crécy-Lagard V,Forouhar F,Brochier-Armanet C,Tong L,Hunt JF

    更新日期:2012-09-26 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

  • LINEs of evidence: noncanonical DNA replication as an epigenetic determinant.

    abstract::LINE-1 (L1) retrotransposons are repetitive elements in mammalian genomes. They are capable of synthesizing DNA on their own RNA templates by harnessing reverse transcriptase (RT) that they encode. Abundantly expressed full-length L1s and their RT are found to globally influence gene expression profiles, differentiati...

    journal_title:Biology direct

    pub_type: 杂志文章,评审

    doi:10.1186/1745-6150-8-22

    authors: Belan E

    更新日期:2013-09-13 00:00:00

  • From tumors to species: a SCANDAL hypothesis.

    abstract::ᅟ: Some tumor cells can evolve into transmissible parasites. Notable examples include the Tasmanian devil facial tumor disease, the canine transmissible venereal tumor and transmissible cancers of mollusks. We present a hypothesis that such transmissible tumors existed in the past and that some modern animal taxa are ...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-019-0233-1

    authors: Panchin AY,Aleoshin VV,Panchin YV

    更新日期:2019-01-23 00:00:00

  • Trees and networks before and after Darwin.

    abstract::It is well-known that Charles Darwin sketched abstract trees of relationship in his 1837 notebook, and depicted a tree in the Origin of Species (1859). Here I attempt to place Darwin's trees in historical context. By the mid-Eighteenth century the Great Chain of Being was increasingly seen to be an inadequate descript...

    journal_title:Biology direct

    pub_type: 历史文章,杂志文章,评审

    doi:10.1186/1745-6150-4-43

    authors: Ragan MA

    更新日期:2009-11-16 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

  • 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

  • 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

  • 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

  • Evidence-based gene models for structural and functional annotations of the oil palm genome.

    abstract:BACKGROUND:Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-017-0191-4

    authors: Chan KL,Tatarinova TV,Rosli R,Amiruddin N,Azizi N,Halim MAA,Sanusi NSNM,Jayanthi N,Ponomarenko P,Triska M,Solovyev V,Firdaus-Raih M,Sambanthamurthi R,Murphy D,Low EL

    更新日期:2017-09-08 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

  • 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

  • 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

  • Infinitely long branches and an informal test of common ancestry.

    abstract:BACKGROUND:The evidence for universal common ancestry (UCA) is vast and persuasive. A phylogenetic test has been proposed for quantifying its odds against independently originated sequences based on the comparison between one versus several trees. This test was successfully applied to a well-supported homologous sequen...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-016-0120-y

    authors: de Oliveira Martins L,Posada D

    更新日期:2016-04-07 00:00:00

  • Outer membrane protein genes and their small non-coding RNA regulator genes in Photorhabdus luminescens.

    abstract:INTRODUCTION:Three major outer membrane protein genes of Escherichia coli, ompF, ompC, and ompA respond to stress factors. Transcripts from these genes are regulated by the small non-coding RNAs micF, micC, and micA, respectively. Here we examine Photorhabdus luminescens, an organism that has a different habitat from E...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-1-12

    authors: Papamichail D,Delihas N

    更新日期:2006-05-22 00:00:00