Uncultured Archaea in a hydrothermal microbial assemblage: phylogenetic diversity and characterization of a genome fragment from a euryarchaeote

The Ochrobactrum genus consists of an extensive repertoire of biotechnologically valuable bacterial strains but also opportunistic pathogens. In our previous study, a novel strain, Ochrobactrum sp. POC9, which enhances biogas production in wastewater treatment plants (WWTPs) was identified and thoroughly characterized. Despite an insightful analysis of that bacterium, its susceptibility to bacteriophages present in WWTPs has not been evaluated. Using raw sewage sample from WWTP and applying the enrichment method, two virulent phages, vB_OspM_OC and vB_OspP_OH, which infect the POC9 strain, were isolated. These are the first virulent phages infecting Ochrobactrum spp. identified so far. Both phages were subjected to thorough functional and genomic analyses, which allowed classification of the vB_OspM_OC virus as a novel jumbo phage, with a genome size of over 227 kb. This phage encodes DNA methyltransferase, which mimics the specificity of cell cycle regulated CcrM methylase, a component of the epigenetic regulatory circuits in Alphaproteobacteria. In this study, an analysis of the overall diversity of Ochrobactrum-specific (pro)phages retrieved from databases and extracted in silico from bacterial genomes was also performed. Complex genome mining allowed us to build similarity networks to compare 281 Ochrobactrum-specific viruses. Analyses of the obtained networks revealed a high diversity of Ochrobactrum phages and their dissimilarity to the viruses infecting other bacteria.

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Identification and characterization of Fep15, a new selenocysteine-containing member of the Sep15 protein family

Biochemical Journal ◽

10.1042/bj20051569 ◽

2006 ◽

Vol 394 (3) ◽

pp. 575-579 ◽

Cited By ~ 28

Author(s):

Sergey V. Novoselov ◽

Deame Hua ◽

Alexey V. Lobanov ◽

Vadim N. Gladyshev

Keyword(s):

Mammalian Cells ◽

Insertion Sequence ◽

Phylogenetic Analyses ◽

Dependent Manner ◽

Putative Active Site ◽

A Genome ◽

Sequence Elements ◽

Identification And Characterization ◽

Insertion Sequence Elements

Sec (selenocysteine) is a rare amino acid in proteins. It is co-translationally inserted into proteins at UGA codons with the help of SECIS (Sec insertion sequence) elements. A full set of selenoproteins within a genome, known as the selenoproteome, is highly variable in different organisms. However, most of the known eukaryotic selenoproteins are represented in the mammalian selenoproteome. In addition, many of these selenoproteins have cysteine orthologues. Here, we describe a new selenoprotein, designated Fep15, which is distantly related to members of the 15 kDa selenoprotein (Sep15) family. Fep15 is absent in mammals, can be detected only in fish and is present in these organisms only in the selenoprotein form. In contrast with other members of the Sep15 family, which contain a putative active site composed of Sec and cysteine, Fep15 has only Sec. When transiently expressed in mammalian cells, Fep15 incorporated Sec in an SECIS- and SBP2 (SECIS-binding protein 2)-dependent manner and was targeted to the endoplasmic reticulum by its N-terminal signal peptide. Phylogenetic analyses of Sep15 family members suggest that Fep15 evolved by gene duplication.

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Chromatin architectural proteins regulate flowering time by precluding gene looping

Science Advances ◽

10.1126/sciadv.abg3097 ◽

2021 ◽

Vol 7 (24) ◽

pp. eabg3097

Author(s):

Bo Zhao ◽

Yanpeng Xi ◽

Junghyun Kim ◽

Sibum Sung

Keyword(s):

Chromatin Structure ◽

Cellular Processes ◽

Genome Wide ◽

A Genome ◽

Evolutionarily Conserved ◽

Architectural Proteins ◽

Floral Repressor ◽

Flanking Regions ◽

Genome Wide Study

Chromatin structure is critical for gene expression and many other cellular processes. In Arabidopsis thaliana, the floral repressor FLC adopts a self-loop chromatin structure via bridging of its flanking regions. This local gene loop is necessary for active FLC expression. However, the molecular mechanism underlying the formation of this class of gene loops is unknown. Here, we report the characterization of a group of linker histone-like proteins, named the GH1-HMGA family in Arabidopsis, which act as chromatin architecture modulators. We demonstrate that these family members redundantly promote the floral transition through the repression of FLC. A genome-wide study revealed that this family preferentially binds to the 5′ and 3′ ends of gene bodies. The loss of this binding increases FLC expression by stabilizing the FLC 5′ to 3′ gene looping. Our study provides mechanistic insights into how a family of evolutionarily conserved proteins regulates the formation of local gene loops.

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Epigenomic changes after acupuncture treatment in patients suffering from burnout

Complementary Medicine Research ◽

10.1159/000521347 ◽

2021 ◽

Author(s):

Marc Petitpierre ◽

Ludwig Stenz ◽

Ariane Paoloni-Giacobino

Keyword(s):

Acupuncture Treatment ◽

Maslach Burnout Inventory ◽

Personal Accomplishment ◽

Steroid Synthesis ◽

Genome Wide ◽

A Genome ◽

Before And After ◽

High Level ◽

The Brain

Introduction: The effects of acupuncture treatment in patients suffering from burnout may imply an epigenetic control mediated by DNA methylation changes. In this observational study, a genome-wide characterization of epigenetic changes in blood DNA, before and after acupuncture treatment, was performed in a cohort of 11 patients suffering from burnout. Methods: Burnout was assessed using the Maslach Burnout Inventory (MBI) and DNA was extracted from blood samples and analyzed by Illumina EPIC BeadChip. Results: Before acupuncture, all patients suffered of emotional exhaustion (EE) (MBI-EE score, 44±6), 81% suffered of depersonalization (DP) (MBI-DP score, 16±6), and 72% of low feelings of personal accomplishment (PA) (MBI-PA score, 29±9). After acupuncture, all MBI dimensions improved significantly (EE, 16±11 [p=1.5*10-4]; DP, 4±5 [p=5.3*10-4]; and PA, 40±6 [p=4.1*10-3]). For each patient, both methylomes obtained before and after acupuncture co-clustered in the multidimensional scaling plot, indicating a high level of similarity. Genes corresponding to the 10 most differentially methylated CpGs showed enrichment in the brain dopaminergic signalling, steroid synthesis and in the insulin sensitivity pathways. Conclusion: Acupuncture treatment was found to be highly effective on all burnout dimensions and the epigenetic targets identified were involved in some major disturbances of this syndrome.

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Genome-Wide Identification and Analysis of VQ Motif-containing Gene Family in Brassica napus and Functional Characterization of BnMKS1 in Response to Leptosphaeria maculans

Phytopathology ◽

10.1094/phyto-04-20-0134-r ◽

2020 ◽

Cited By ~ 1

Author(s):

Zhongwei Zou ◽

Fei Liu ◽

Shuanglong Huang ◽

DILANTHA GERARD FERNANDO

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Functional Characterization ◽

Leptosphaeria Maculans ◽

Defense Responses ◽

Marker Genes ◽

Blackleg Disease ◽

Genome Wide ◽

A Genome

Proteins containing Valine-glutamine (VQ) motifs play important roles in plant growth and development, as well as in defense responses to both abiotic and biotic stresses. Blackleg disease, which is caused by Leptosphaeria maculans, is the most important disease in canola (Brassica napus L.) worldwide. H; however, the identification of B. napus VQs and their functions in response to blackleg disease have not yet been reported. In this study, we conducted a genome genome-wide identification and characterization of the VQ gene family in B. napus, including chromosome location, phylogenetic relations, gene structure, motif domain, synteny analysis, and cis-elements categorization of their promoter regions. To understand B. napus VQ gene function in response to blackleg disease, we overexpressed BnVQ7 (BnaA01g36880D, also known as the mitogen-activated protein kinase4 substrate1 (MKS1) gene) in a blackleg-susceptible canola variety Westar. Overexpression The overexpression of BnMKS1 in canola did not improve its resistance to blackleg disease at the seedling stage. H; however, transgenic canola plants overexpressing BnMKS1 displayed an enhanced resistance to L. maculans infection at the adult plant stage. Expression levels of downstream and defense marker genes in cotyledons increased significantly at the necrotrophic stage of L. maculans infection in the overexpression line of BnMKS1, suggesting that the SA salicylic acid (SA)- and jasmonic acid (JA )-mediated signaling pathways were both involved in the defense responses. Together, these results suggest that BnMKS1 might play an important role in the defense against L. maculans.

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ABC Transporter Genes Show Upregulated Expression in Drug-Resistant Clinical Isolates of Candida auris: A Genome-Wide Characterization of ATP-Binding Cassette (ABC) Transporter Genes

Frontiers in Microbiology ◽

10.3389/fmicb.2019.01445 ◽

2019 ◽

Vol 10 ◽

Cited By ~ 14

Author(s):

Mohd Wasi ◽

Nitesh Kumar Khandelwal ◽

Alexander J. Moorhouse ◽

Remya Nair ◽

Poonam Vishwakarma ◽

...

Keyword(s):

Abc Transporter ◽

Clinical Isolates ◽

Atp Binding ◽

Drug Resistant ◽

Candida Auris ◽

Genome Wide ◽

A Genome ◽

Abc Transporter Genes ◽

Atp Binding Cassette

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Genome-wide identification, phylogenetic and expression pattern analysis of GATA family genes in Brassica napus

BMC Plant Biology ◽

10.1186/s12870-020-02752-2 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Weizhuo Zhu ◽

Yiyi Guo ◽

Yeke Chen ◽

Dezhi Wu ◽

Lixi Jiang

Keyword(s):

Brassica Napus ◽

Stress Condition ◽

Expression Patterns ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Good Opportunity ◽

Domain Structures ◽

Genome Wide ◽

A Genome

Abstract Background Transcription factors GATAs are involved in plant developmental processes and respond to environmental stresses through binding DNA regulatory regions to regulate their downstream genes. However, little information on the GATA genes in Brassica napus is available. The release of the reference genome of B. napus provides a good opportunity to perform a genome-wide characterization of GATA family genes in rapeseed. Results In this study, 96 GATA genes randomly distributing on 19 chromosomes were identified in B. napus, which were classified into four subfamilies based on phylogenetic analysis and their domain structures. The amino acids of BnGATAs were obvious divergence among four subfamilies in terms of their GATA domains, structures and motif compositions. Gene duplication and synteny between the genomes of B. napus and A. thaliana were also analyzed to provide insights into evolutionary characteristics. Moreover, BnGATAs showed different expression patterns in various tissues and under diverse abiotic stresses. Single nucleotide polymorphisms (SNPs) distributions of BnGATAs in a core collection germplasm are probably associated with functional disparity under environmental stress condition in different genotypes of B. napus. Conclusion The present study was investigated genomic structures, evolution features, expression patterns and SNP distributions of 96 BnGATAs. The results enrich our understanding of the GATA genes in rapeseed.

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Comparative Genomic Characterization of the Multimammate Mouse Mastomys coucha

Molecular Biology and Evolution ◽

10.1093/molbev/msz188 ◽

2019 ◽

Vol 36 (12) ◽

pp. 2805-2812

Author(s):

Aaron Hardin ◽

Kimberly A Nevonen ◽

Walter L Eckalbar ◽

Lucia Carbone ◽

Nadav Ahituv

Keyword(s):

Functional Characterization ◽

Mammary Glands ◽

Comparative Genomic ◽

Lassa Virus ◽

Enhancer Activity ◽

A Genome ◽

Genomic Tool ◽

Mastomys Coucha ◽

Comparative Genomic Tool

Abstract Mastomys are the most widespread African rodent and carriers of various diseases such as the plague or Lassa virus. In addition, mastomys have rapidly gained a large number of mammary glands. Here, we generated a genome, variome, and transcriptomes for Mastomys coucha. As mastomys diverged at similar times from mouse and rat, we demonstrate their utility as a comparative genomic tool for these commonly used animal models. Furthermore, we identified over 500 mastomys accelerated regions, often residing near important mammary developmental genes or within their exons leading to protein sequence changes. Functional characterization of a noncoding mastomys accelerated region, located in the HoxD locus, showed enhancer activity in mouse developing mammary glands. Combined, our results provide genomic resources for mastomys and highlight their potential both as a comparative genomic tool and for the identification of mammary gland number determining factors.

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