Ancestral zinc-finger bearing protein MucR in alpha-proteobacteria: A novel xenogeneic silencer?

Abstract:

:The MucR/Ros family protein is conserved in alpha-proteobacteria and characterized by its zinc-finger motif that has been proposed as the ancestral domain from which the eukaryotic C2H2 zinc-finger structure evolved. In the past decades, accumulated evidences have revealed MucR as a pleiotropic transcriptional regulator that integrating multiple functions such as virulence, symbiosis, cell cycle and various physiological processes. Scattered reports indicate that MucR mainly acts as a repressor, through oligomerization and binding to multiple sites of AT-rich target promoters. The N-terminal region and zinc-finger bearing C-terminal region of MucR mediate oligomerization and DNA-binding, respectively. These features are convergent to those of xenogeneic silencers such as H-NS, MvaT, Lsr2 and Rok, which are mainly found in other lineages. Phylogenetic analysis of MucR homologs suggests an ancestral origin of MucR in alpha- and delta-proteobacteria. Multiple independent duplication and lateral gene transfer events contribute to the diversity and phyletic distribution of MucR. Finally, we posed questions which remain unexplored regarding the putative roles of MucR as a xenogeneic silencer and a general manager in balancing adaptation and regulatory integration in the pangenome context.

authors

Jiao J,Tian CF

doi

10.1016/j.csbj.2020.11.028

subject

Has Abstract

pub_date

2020-11-19 00:00:00

pages

3623-3631

issn

2001-0370

pii

S2001-0370(20)30495-5

journal_volume

18

pub_type

杂志文章,评审
  • The era of big data: Genome-scale modelling meets machine learning.

    abstract::With omics data being generated at an unprecedented rate, genome-scale modelling has become pivotal in its organisation and analysis. However, machine learning methods have been gaining ground in cases where knowledge is insufficient to represent the mechanisms underlying such data or as a means for data curation prio...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1016/j.csbj.2020.10.011

    authors: Antonakoudis A,Barbosa R,Kotidis P,Kontoravdi C

    更新日期:2020-10-16 00:00:00

  • Catch me if you can: Leukemia Escape after CD19-Directed T Cell Immunotherapies.

    abstract::Immunotherapy is the revolution in cancer treatment of this last decade. Among multiple approaches able to harness the power of the immune system against cancer, T cell based immunotherapies represent one of the most successful examples. In particular, biotechnological engineering of protein structures, like the T cel...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1016/j.csbj.2016.09.003

    authors: Ruella M,Maus MV

    更新日期:2016-09-28 00:00:00

  • Transcriptome and proteome analyses reveal the regulatory networks and metabolite biosynthesis pathways during the development of Tolypocladium guangdongense.

    abstract::Tolypocladium guangdongense has a similar metabolite profile to Ophiocordyceps sinensis, a highly regarded fungus used for traditional Chinese medicine with high nutritional and medicinal value. Although the genome sequence of T. guangdongense has been reported, relatively little is known about the regulatory networks...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章

    doi:10.1016/j.csbj.2020.07.014

    authors: Wang G,Li M,Zhang C,Cheng H,Gao Y,Deng W,Li T

    更新日期:2020-07-25 00:00:00

  • Constructing knowledge graphs and their biomedical applications.

    abstract::Knowledge graphs can support many biomedical applications. These graphs represent biomedical concepts and relationships in the form of nodes and edges. In this review, we discuss how these graphs are constructed and applied with a particular focus on how machine learning approaches are changing these processes. Biomed...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1016/j.csbj.2020.05.017

    authors: Nicholson DN,Greene CS

    更新日期:2020-06-02 00:00:00

  • A molecular device: A DNA molecular lock driven by the nicking enzymes.

    abstract::As people are placing more and more importance on information security, how to realize the protection of information has become a hotspot of current research. As a security device, DNA molecular locks have great potential to realize information protection at the molecular level. However, building a highly secure molec...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章

    doi:10.1016/j.csbj.2020.08.004

    authors: Zhang X,Zhang Q,Liu Y,Wang B,Zhou S

    更新日期:2020-08-06 00:00:00

  • A metagenome-wide association study of gut microbiome and visceral fat accumulation.

    abstract:Purpose:Visceral fat is an independent risk factor for metabolic and cardiovascular disease. The study aimed to investigate the associations between gut microbiome and visceral fat. Methods:We recruited 32 obese adults and 30 healthy controls at baseline. Among the obese subjects, 14 subjects underwent laparoscopic sl...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章

    doi:10.1016/j.csbj.2020.09.026

    authors: Nie X,Chen J,Ma X,Ni Y,Shen Y,Yu H,Panagiotou G,Bao Y

    更新日期:2020-09-20 00:00:00

  • Allosteric inhibition explained through conformational ensembles sampling distinct "mixed" states.

    abstract::Allosteric modulation provides an effective avenue for selective and potent enzyme inhibition. Here, we summarize and critically discuss recent advances on the mechanisms of allosteric partial agonists for three representative signalling enzymes activated by cyclic nucleotides: the cAMP-dependent protein kinase (PKA),...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1016/j.csbj.2020.10.026

    authors: Byun JA,VanSchouwen B,Akimoto M,Melacini G

    更新日期:2020-11-11 00:00:00

  • Tribology of bio-inspired nanowrinkled films on ultrasoft substrates.

    abstract::Biomimetic design of new materials uses nature as antetype, learning from billions of years of evolution. This work emphasizes the mechanical and tribological properties of skin, combining both hardness and wear resistance of its surface (the stratum corneum) with high elasticity of the bulk (epidermis, dermis, hypode...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章

    doi:10.5936/csbj.201303002

    authors: Lackner JM,Waldhauser W,Major L,Teichert C,Hartmann P

    更新日期:2013-05-08 00:00:00

  • Mini-review: Strategies for Variation and Evolution of Bacterial Antigens.

    abstract::Across the eubacteria, antigenic variation has emerged as a strategy to evade host immunity. However, phenotypic variation in some of these antigens also allows the bacteria to exploit variable host niches as well. The specific mechanisms are not shared-derived characters although there is considerable convergent evol...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1016/j.csbj.2015.07.002

    authors: Foley J

    更新日期:2015-07-26 00:00:00

  • A Blockchain-Based Notarization Service for Biomedical Knowledge Retrieval.

    abstract::Biomedical research and clinical decision depend increasingly on scientific evidence realized by a number of authoritative databases, mostly public and continually enriched via peer scientific contributions. Given the dynamic nature of biomedical evidence data and their usage in the sensitive domain of biomedical scie...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章

    doi:10.1016/j.csbj.2018.08.002

    authors: Kleinaki AS,Mytis-Gkometh P,Drosatos G,Efraimidis PS,Kaldoudi E

    更新日期:2018-08-17 00:00:00

  • A structural overview of GH61 proteins - fungal cellulose degrading polysaccharide monooxygenases.

    abstract::Recent years have witnessed a spurt of activities in the elucidation of the molecular function of a class of proteins with great potential in biomass degradation. GH61 proteins are of fungal origin and were originally classified in family 61 of the glycoside hydrolases. From the beginning they were strongly suspected ...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.5936/csbj.201209019

    authors: Lo Leggio L,Welner D,De Maria L

    更新日期:2012-11-30 00:00:00

  • Developing a mobile application to better inform patients and enable effective consultation in implant dentistry.

    abstract::The field of dentistry lacks satisfactory tools to help visualize planned procedures and their potential results to patients. Dentists struggle to provide an effective image in their patient's mind of the end results of the planned treatment only through verbal explanations. Thus, verbal explanations alone often canno...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章

    doi:10.1016/j.csbj.2016.06.006

    authors: Canbazoglu E,Salman YB,Yildirim ME,Merdenyan B,Ince IF

    更新日期:2016-06-29 00:00:00

  • Recent progress in experimental and human disease-associated multi-species biofilms.

    abstract::Human bodies are colonized by trillions of microorganisms, which are often referred to as human microbiota and play important roles in human health. Next generation sequencing studies have established links between the genetic content of human microbiota and various human diseases. However, it remains largely unknown ...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1016/j.csbj.2019.09.010

    authors: Bai F,Cai Z,Yang L

    更新日期:2019-10-25 00:00:00

  • Discovery of a novel (R)-selective bacterial hydroxynitrile lyase from Acidobacterium capsulatum.

    abstract::Hydroxynitrile lyases (HNLs) are powerful carbon-carbon bond forming enzymes. The reverse of their natural reaction - the stereoselective addition of hydrogen cyanide (HCN) to carbonyls - yields chiral cyanohydrins, versatile building blocks for the pharmaceutical and chemical industry. Recently, bacterial HNLs have b...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章

    doi:10.1016/j.csbj.2014.07.002

    authors: Wiedner R,Gruber-Khadjawi M,Schwab H,Steiner K

    更新日期:2014-07-08 00:00:00

  • Both intra and inter-domain interactions define the intrinsic dynamics and allosteric mechanism in DNMT1s.

    abstract::DNA methyltransferase 1 (DNMT1), a large multidomain enzyme, is believed to be involved in the passive transmission of genomic methylation patterns via methylation maintenance. Yet, the molecular mechanism of interaction networks underlying DNMT1 structures, dynamics, and its biological significance has yet to be full...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章

    doi:10.1016/j.csbj.2020.03.016

    authors: Liang Z,Zhu Y,Long J,Ye F,Hu G

    更新日期:2020-03-23 00:00:00

  • Treatment According to Molecular Profiling in Relapsed/Refractory Cancer Patients: A Review Focusing on Latest Profiling Studies.

    abstract::In this review we aim to summarize studies investigating the impact of a molecular profiling (MP)-guided treatment approach in heavily pretreated cancer patients. In summary, many independent single- and multicenter studies showed a significant benefit of MP-guided treatment regarding response rates and survival. Howe...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1016/j.csbj.2019.03.012

    authors: Zimmer K,Kocher F,Spizzo G,Salem M,Gastl G,Seeber A

    更新日期:2019-03-26 00:00:00

  • Ethical issues related to research on genome editing in human embryos.

    abstract::Although the potential advantages of clinical germline genome editing (GGE) over currently available methods are limited, the implementation of GGE in the clinic has been proposed and discussed. Ethical issues related to such an application have been extensively debated, meanwhile, seemingly less attention has been pa...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1016/j.csbj.2020.03.014

    authors: Niemiec E,Howard HC

    更新日期:2020-03-21 00:00:00

  • Predicting the impacts of mutations on protein-ligand binding affinity based on molecular dynamics simulations and machine learning methods.

    abstract:Purpose:Mutation-induced variation of protein-ligand binding affinity is the key to many genetic diseases and the emergence of drug resistance, and therefore predicting such mutation impacts is of great importance. In this work, we aim to predict the mutation impacts on protein-ligand binding affinity using efficient s...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章

    doi:10.1016/j.csbj.2020.02.007

    authors: Wang DD,Ou-Yang L,Xie H,Zhu M,Yan H

    更新日期:2020-02-20 00:00:00

  • An Artificial Neural Network Integrated Pipeline for Biomarker Discovery Using Alzheimer's Disease as a Case Study.

    abstract::The field of machine learning has allowed researchers to generate and analyse vast amounts of data using a wide variety of methodologies. Artificial Neural Networks (ANN) are some of the most commonly used statistical models and have been successful in biomarker discovery studies in multiple disease types. This review...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1016/j.csbj.2018.02.001

    authors: Zafeiris D,Rutella S,Ball GR

    更新日期:2018-02-21 00:00:00

  • Asymmetric Spontaneous Intercalation of Lutein into a Phospholipid Bilayer, a Computational Study.

    abstract::Lutein, a hydroxylated carotenoid, is a pigment synthesised by plants and bacteria. Animals are unable to synthesise lutein, nevertheless, it is present in animal tissues, where its only source is dietary intake. Both in plants and animals, carotenoids are associated mainly with membranes where they carry out importan...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章

    doi:10.1016/j.csbj.2019.04.001

    authors: Makuch K,Markiewicz M,Pasenkiewicz-Gierula M

    更新日期:2019-04-06 00:00:00

  • Characterization of ENU-induced Mutations in Red Blood Cell Structural Proteins.

    abstract::Murine models with modified gene function as a result of N-ethyl-N-nitrosourea (ENU) mutagenesis have been used to study phenotypes resulting from genetic change. This study investigated genetic factors associated with red blood cell (RBC) physiology and structural integrity that may impact on blood component storage ...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章

    doi:10.5936/csbj.201303012

    authors: Kildey K,Flower RL,Tran TV,Tunningley R,Harris J,Dean MM

    更新日期:2013-09-23 00:00:00

  • Statistical methods for the analysis of high-throughput metabolomics data.

    abstract::Metabolomics is a relatively new high-throughput technology that aims at measuring all endogenous metabolites within a biological sample in an unbiased fashion. The resulting metabolic profiles may be regarded as functional signatures of the physiological state, and have been shown to comprise effects of genetic regul...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.5936/csbj.201301009

    authors: Bartel J,Krumsiek J,Theis FJ

    更新日期:2013-03-22 00:00:00

  • Computational Enzyme Design: Advances, hurdles and possible ways forward.

    abstract::This mini review addresses recent developments in computational enzyme design. Successful protocols as well as known issues and limitations are discussed from an energetic perspective. It will be argued that improved results can be obtained by including a dynamic treatment in the design protocol. Finally, a molecular ...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.5936/csbj.201209009

    authors: Linder M

    更新日期:2012-10-23 00:00:00

  • Quantitative comparison of ABC membrane protein type I exporter structures in a standardized way.

    abstract::An increasing number of ABC membrane protein structures are determined by cryo-electron microscopy and X-ray crystallography, consequently identifying differences between their conformations has become an arising issue. Therefore, we propose to define standardized measures for ABC Type I exporter structure characteriz...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章

    doi:10.1016/j.csbj.2018.10.008

    authors: Csizmadia G,Farkas B,Spagina Z,Tordai H,Hegedűs T

    更新日期:2018-10-18 00:00:00

  • Structural insights into the mechanism of RNA recognition by the N-terminal RNA-binding domain of the SARS-CoV-2 nucleocapsid phosphoprotein.

    abstract::The emergence of recent SARS-CoV-2 has become a global health issue. This single-stranded positive-sense RNA virus is continuously spreading with increasing morbidities and mortalities. The proteome of this virus contains four structural and sixteen nonstructural proteins that ensure the replication of the virus in th...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章

    doi:10.1016/j.csbj.2020.08.006

    authors: Khan A,Tahir Khan M,Saleem S,Junaid M,Ali A,Shujait Ali S,Khan M,Wei DQ

    更新日期:2020-01-01 00:00:00

  • Taxonomy and evolution of Aspergillus, Penicillium and Talaromyces in the omics era - Past, present and future.

    abstract::Aspergillus, Penicillium and Talaromyces are diverse, phenotypically polythetic genera encompassing species important to the environment, economy, biotechnology and medicine, causing significant social impacts. Taxonomic studies on these fungi are essential since they could provide invaluable information on their evol...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章,评审

    doi:10.1016/j.csbj.2018.05.003

    authors: Tsang CC,Tang JYM,Lau SKP,Woo PCY

    更新日期:2018-05-31 00:00:00

  • Combining Ramachandran plot and molecular dynamics simulation for structural-based variant classification: Using TP53 variants as model.

    abstract::The wide application of new DNA sequencing technologies is generating vast quantities of genetic variation data at unprecedented speed. Developing methodologies to decode the pathogenicity of the variants is imperatively demanding. We hypothesized that as deleterious variants may function through disturbing structural...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章

    doi:10.1016/j.csbj.2020.11.041

    authors: Tam B,Sinha S,Wang SM

    更新日期:2020-12-02 00:00:00

  • AUDACITY: A comprehensive approach for the detection and classification of Runs of Homozygosity in medical and population genomics.

    abstract::Runs of Homozygosity (RoHs) are popular among geneticists as the footprint of demographic processes, evolutionary forces and inbreeding in shaping our genome, and are known to confer risk of Mendelian and complex diseases. Notwithstanding growing interest in their study, there is unmet need for reliable and rapid meth...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章

    doi:10.1016/j.csbj.2020.07.003

    authors: Magi A,Giangregorio T,Semeraro R,Carangelo G,Palombo F,Romeo G,Seri M,Pippucci T

    更新日期:2020-07-14 00:00:00

  • A Graph Based Framework to Model Virus Integration Sites.

    abstract::With next generation sequencing thousands of virus and viral vector integration genome targets are now under investigation to uncover specific integration preferences and to define clusters of integration, termed common integration sites (CIS), that may allow to assess gene therapy safety or to detect disease related ...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章

    doi:10.1016/j.csbj.2015.10.006

    authors: Fronza R,Vasciaveo A,Benso A,Schmidt M

    更新日期:2015-11-30 00:00:00

  • The impact of Gag non-cleavage site mutations on HIV-1 viral fitness from integrative modelling and simulations.

    abstract::The high mutation rate in retroviruses is one of the leading causes of drug resistance. In human immunodeficiency virus type-1 (HIV-1), synergistic mutations in its protease and the protease substrate - the Group-specific antigen (Gag) polyprotein - work together to confer drug resistance against protease inhibitors a...

    journal_title:Computational and structural biotechnology journal

    pub_type: 杂志文章

    doi:10.1016/j.csbj.2020.12.022

    authors: Samsudin F,Gan SK,Bond PJ

    更新日期:2020-12-23 00:00:00