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1. A Ralstonia solanacearum Type III Effector Directs the Production of the Plant Signal Metabolite Trehalose-6-Phosphate

Author:
Poueymiro, M.; Cazalé, A. C.; François, J. M.; Parrou, J. L.; Peeters, N.; Genin, S.
Source:
mBio 2014 v.5 no.6 pp. e02065-14
ISSN:
2150-7511
Subject:
Nicotiana tabacum; Ralstonia solanacearum; alpha,alpha-trehalose-phosphate synthase (UDP-forming); bacterial wilt; biochemical pathways; carbon; cells; enzyme activity; genes; heterologous gene expression; host plants; hypersensitive response; metabolism; metabolites; plant pathogenic bacteria; tobacco; trehalose; type III secretion system; virulence
Abstract:
... The plant pathogen Ralstonia solanacearum possesses two genes encoding a trehalose-6-phosphate synthase (TPS), an enzyme of the trehalose biosynthetic pathway. One of these genes, named ripTPS , was found to encode a protein with an additional N-terminal domain which directs its translocation into host plant cells through the type 3 secretion system. RipTPS is a conserved effector in the R. solana ...
DOI:
10.1128/mBio.02065-14
PubMed:
25538193
PubMed Central:
PMC4278537

2. BPIFB3 Regulates Autophagy and Coxsackievirus B Replication through a Noncanonical Pathway Independent of the Core Initiation Machinery

Author:
Delorme-Axford, Elizabeth; Morosky, Stefanie; Bomberger, Jennifer; Stolz, Donna B.; Jackson, William T.; Coyne, Carolyn B.
Source:
mBio 2014 v.5 no.6 pp. e02147-14
ISSN:
2150-7511
Subject:
Enterovirus B; RNA interference; autophagy; cardiomyopathy; endoplasmic reticulum; genes; heart; homeostasis; small interfering RNA; virus replication; viruses
Abstract:
... Enteroviruses require autophagy to facilitate the formation of autophagosome (AP)-like double-membrane vesicles that provide the scaffolding for RNA replication. Here, we identify bactericidal/permeability-increasing protein (BPI) fold-containing family B, member 3 (BPIFB3) as a gene whose silencing greatly enhances coxsackievirus B (CVB) replication and induces dramatic alterations in the morphol ...
DOI:
10.1128/mBio.02147-14
PubMed:
25491355
PubMed Central:
PMC4324245

3. Chromosomal Transfers in Mycoplasmas: When Minimal Genomes Go Mobile

Author:
Dordet-Frisoni, Emilie; Sagné, Eveline; Baranowski, Eric; Breton, Marc; Nouvel, Laurent Xavier; Blanchard, Alain; Marenda, Marc Serge; Tardy, Florence; Sirand-Pugnet, Pascal; Citti, Christine
Source:
mBio 2014 v.5 no.6 pp. e01958-14
ISSN:
2150-7511
Subject:
DNA; Mycoplasma agalactiae; animal pathogens; bacteria; chromosomes; evolution; genes; high-throughput nucleotide sequencing; homologous recombination; horizontal gene transfer; humans; ruminants
Abstract:
... Horizontal gene transfer (HGT) is a main driving force of bacterial evolution and innovation. This phenomenon was long thought to be marginal in mycoplasmas, a large group of self-replicating bacteria characterized by minute genomes as a result of successive gene losses during evolution. Recent comparative genomic analyses challenged this paradigm, but the occurrence of chromosomal exchanges had n ...
DOI:
10.1128/mBio.01958-14
PubMed:
25425234
PubMed Central:
PMC4251992

4. Comparative Analyses of Nonpathogenic, Opportunistic, and Totally Pathogenic Mycobacteria Reveal Genomic and Biochemical Variabilities and Highlight the Survival Attributes of Mycobacterium tuberculosis

Author:
Rahman, Syed Asad; Singh, Yadvir; Kohli, Sakshi; Ahmad, Javeed; Ehtesham, Nasreen Z.; Tyagi, Anil K.; Hasnain, Seyed E.
Source:
mBio 2014 v.5 no.6 pp. e02020-14
ISSN:
2150-7511
Subject:
Mycobacterium avium; Mycobacterium intracellulare; Mycobacterium tuberculosis; biochemical pathways; environmental factors; evolution; genes; host-pathogen relationships; humans; immunomodulators; leprosy; metabolism; pathogenesis; proteins; proteome; proteomics; sequence analysis; virulence
Abstract:
... Mycobacterial evolution involves various processes, such as genome reduction, gene cooption, and critical gene acquisition. Our comparative genome size analysis of 44 mycobacterial genomes revealed that the nonpathogenic (NP) genomes were bigger than those of opportunistic (OP) or totally pathogenic (TP) mycobacteria, with the TP genomes being smaller yet variable in size—their genomic plasticity ...
DOI:
10.1128/mBio.02020-14
PubMed:
25370496
PubMed Central:
PMC4222108

5. Comparative Genomics of Pneumocystis Species Suggests the Absence of Genes for myo-Inositol Synthesis and Reliance on Inositol Transport and Metabolism

Author:
Porollo, Aleksey; Sesterhenn, Thomas M.; Collins, Margaret S.; Welge, Jeffrey A.; Cushion, Melanie T.
Source:
mBio 2014 v.5 no.6 pp. e01834-14
ISSN:
2150-7511
Subject:
Candida albicans; Cryptococcus neoformans; Pneumocystis; Schizosaccharomyces pombe; amino acid metabolism; auxotrophs; biosynthesis; complementary DNA; fungi; genes; genomics; hosts; immune system; in vitro culture; lungs; myo-inositol; pathogenesis; phosphoinositide 5-phosphatase; phylogeny; reverse transcriptase polymerase chain reaction; rodents; transporters; viability; virulence
Abstract:
... In the context of deciphering the metabolic strategies of the obligate pathogenic fungi in the genus Pneumocystis , the genomes of three species ( P. carinii , P. murina , and P. jirovecii ) were compared among themselves and with the free-living, phylogenetically related fission yeast ( Schizosaccharomyces pombe ). The underrepresentation of amino acid metabolism pathways compared to those in S.  ...
DOI:
10.1128/mBio.01834-14
PubMed:
25370490
PubMed Central:
PMC4222102

6. Contemporary Avian Influenza A Virus Subtype H1, H6, H7, H10, and H15 Hemagglutinin Genes Encode a Mammalian Virulence Factor Similar to the 1918 Pandemic Virus H1 Hemagglutinin

Author:
Qi, Li; Pujanauski, Lindsey M.; Davis, A. Sally; Schwartzman, Louis M.; Chertow, Daniel S.; Baxter, David; Scherler, Kelsey; Hartshorn, Kevan L.; Slemons, Richard D.; Walters, Kathie-Anne; Kash, John C.; Taubenberger, Jeffery K.
Source:
mBio 2014 v.5 no.6 pp. e02116-14
ISSN:
2150-7511
Subject:
Influenza A virus; Rodent protoparvovirus 1; birds; chimerism; epithelial cells; genes; hemagglutinins; human diseases; humans; macrophages; mice; monitoring; neutrophils; pandemic; surface proteins; virulence; viruses
Abstract:
... Zoonotic avian influenza virus infections may lead to epidemics or pandemics. The 1918 pandemic influenza virus has an avian influenza virus-like genome, and its H1 hemagglutinin was identified as a key mammalian virulence factor. A chimeric 1918 virus expressing a contemporary avian H1 hemagglutinin, however, displayed murine pathogenicity indistinguishable from that of the 1918 virus. Here, isog ...
DOI:
10.1128/mBio.02116-14
PubMed:
25406382
PubMed Central:
PMC4251996

7. Contrasting patterns in the evolution of the Rab GTPase family in Archaeplastida

Author:
Petrželková, Romana; Eliáš, Marek
Source:
Acta Societatis Botanicorum Poloniae 2014 v.83 no.4 pp. 303-315
ISSN:
0001-6977
Subject:
Chlorophyta; Rhodophyta; algae; cell membranes; embryophytes; endocytosis; eukaryotic cells; genes; guanosinetriphosphatase; monophyly; physiological transport; proteins; transcriptome
Abstract:
... Rab GTPases are a vast group of proteins serving a role of master regulators in membrane trafficking in eukaryotes. Previous studies delineated some 23 Rab and Rab-like paralogs ancestral for eukaryotes and mapped their current phylogenetic distribution, but the analyses relied on a limited sampling of the eukaryotic diversity. Taking advantage of the recent growth of genome and transcriptome reso ...
DOI:
10.5586/asbp.2014.052

8. Deep Sequencing Identifies Noncanonical Editing of Ebola and Marburg Virus RNAs in Infected Cells

Author:
Shabman, Reed S.; Jabado, Omar J.; Mire, Chad E.; Stockwell, Timothy B.; Edwards, Megan; Mahajan, Milind; Geisbert, Thomas W.; Basler, Christopher F.
Source:
mBio 2014 v.5 no.6 pp. e02011-14
ISSN:
2150-7511
Subject:
Zaire Ebola virus; adenosine deaminase; messenger RNA; nucleoproteins; translation (genetics); Marburg marburgvirus; high-throughput nucleotide sequencing; gene expression; genes; glycoproteins
Abstract:
... Deep sequencing of RNAs produced by Zaire ebolavirus (EBOV) or the Angola strain of Marburgvirus (MARV-Ang) identified novel viral and cellular mechanisms that diversify the coding and noncoding sequences of viral mRNAs and genomic RNAs. We identified previously undescribed sites within the EBOV and MARV-Ang mRNAs where apparent cotranscriptional editing has resulted in the addition of non-templat ...
DOI:
10.1128/mBio.02011-14
PubMed:
25370495
PubMed Central:
PMC4222107

9. Effect of Copper Treatment on the Composition and Function of the Bacterial Community in the Sponge Haliclona cymaeformis

Author:
Tian, Ren-Mao; Wang, Yong; Bougouffa, Salim; Gao, Zhao-Ming; Cai, Lin; Zhang, Wei-Peng; Bajic, Vladimir; Qian, Pei-Yuan
Source:
mBio 2014 v.5 no.6 pp. e01980-14
ISSN:
2150-7511
Subject:
Cyanobacteria; Ectothiorhodospiraceae; Porifera; autotrophic bacteria; bacterial communities; bacterial motility; bacteriophages; chemotaxis; community structure; copper; environmental impact; genes; metagenomics; microsymbionts; pollution; polysaccharides; ribosomal RNA; virulence
Abstract:
... Marine sponges are the most primitive metazoan and host symbiotic microorganisms. They are crucial components of the marine ecological system and play an essential role in pelagic processes. Copper pollution is currently a widespread problem and poses a threat to marine organisms. Here, we examined the effects of copper treatment on the composition of the sponge-associated bacterial community and ...
DOI:
10.1128/mBio.01980-14
PubMed:
25370493
PubMed Central:
PMC4222105

10. Efficient Production of Isoflavonoids by Astragalus membranaceus Hairy Root Cultures and Evaluation of Antioxidant Activities of Extracts

Author:
Jiao, Jiao; Gai, Qing-Yan; Fu, Yu-Jie; Ma, Wei; Peng, Xiao; Tan, Sheng-Nan; Efferth, Thomas
Source:
Journal of agricultural and food chemistry 2014 v.62 no.52 pp. 12649-12658
ISSN:
0021-8561
Subject:
Astragalus membranaceus; antioxidant activity; antioxidants; functional foods; genes; inhibitory concentration 50; isoflavonoids; polymerase chain reaction; roots
Abstract:
... In this study, Astragalus membranaceus hairy root cultures (AMHRCs) were established as an attractive alternative source for the efficient production of isoflavonoids (IF). A. membranaceus hairy root line II was screened as the most efficient line and was confirmed by PCR amplification of rolB, rolC and aux1 genes. Culture parameters of AMHRCs were systematically optimized, and five main IF consti ...
DOI:
10.1021/jf503839m

11. Evolution of Invasion in a Diverse Set of Fusobacterium Species

Author:
Manson McGuire, Abigail; Cochrane, Kyla; Griggs, Allison D.; Haas, Brian J.; Abeel, Thomas; Zeng, Qiandong; Nice, Justin B.; MacDonald, Hanlon; Birren, Bruce W.; Berger, Bryan W.; Allen-Vercoe, Emma; Earl, Ashlee M.
Source:
mBio 2014 v.5 no.6 pp. e01864-14
ISSN:
2150-7511
Subject:
sequence analysis; complement; adaptive radiation; humans; adhesins; Crohn disease; Fusobacterium; models; microorganisms; premature birth; pathogenesis; genes; adhesion; colorectal neoplasms; colitis; mixed infection; periodontal diseases
Abstract:
... The diverse Fusobacterium genus contains species implicated in multiple clinical pathologies, including periodontal disease, preterm birth, and colorectal cancer. The lack of genetic tools for manipulating these organisms leaves us with little understanding of the genes responsible for adherence to and invasion of host cells. Actively invading Fusobacterium species can enter host cells independent ...
DOI:
10.1128/mBio.01864-14
PubMed:
25370491
PubMed Central:
PMC4222103

12. Flexibility and Symmetry of Prokaryotic Genome Rearrangement Reveal Lineage-Associated Core-Gene-Defined Genome Organizational Frameworks

Author:
Kang, Yu; Gu, Chaohao; Yuan, Lina; Wang, Yue; Zhu, Yanmin; Li, Xinna; Luo, Qibin; Xiao, Jingfa; Jiang, Daquan; Qian, Minping; Ahmed Khan, Aftab; Chen, Fei; Zhang, Zhang; Yu, Jun
Source:
mBio 2014 v.5 no.6 pp. e01867-14
ISSN:
2150-7511
Subject:
DNA; DNA-directed DNA polymerase; Gram-negative bacteria; genes; genome assembly; horizontal gene transfer
Abstract:
... The prokaryotic pangenome partitions genes into core and dispensable genes. The order of core genes, albeit assumed to be stable under selection in general, is frequently interrupted by horizontal gene transfer and rearrangement, but how a core-gene-defined genome maintains its stability or flexibility remains to be investigated. Based on data from 30 species, including 425 genomes from six phyla, ...
DOI:
10.1128/mBio.01867-14
PubMed:
25425232
PubMed Central:
PMC4251990

13. Genetic Basis for Geosmin Production by the Water Bloom-Forming Cyanobacterium, Anabaena ucrainica

Author:
Wang, Zhongjie; Shao, Jihai; Xu, Yao; Yan, Biao; Li, Renhui
Source:
Water 2014 v.7 no.1 pp. 175-187
ISSN:
2073-4441
Subject:
2-methylisoborneol; Anabaena; Cyanobacterium (genus); cyclic AMP; fumarates; genes; geosmin; horizontal gene transfer; lakes; nitrate reductase; odors; phylogeny; polymerase chain reaction; sesquiterpenoids; transcription (genetics); China
Abstract:
... Geosmin is a common, musty-smelling sesquiterpene, principally produced by cyanobacteria. Anabaena ucrainica (Schhorb.) Watanabe, a water bloom-forming cyanobacterium, is the geosmin producer responsible for odor problems in Dianchi and Erhai lakes in China. In this study, the geosmin synthase gene (geo) of A. ucrainica and its flanking regions were identified and cloned by polymerase chain reacti ...
DOI:
10.3390/w7010175

14. Genetic Manipulation of the Toxoplasma gondii Genome by Fosmid Recombineering

Author:
Vinayak, Sumiti; Brooks, Carrie F.; Naumov, Anatoli; Suvorova, Elena S.; White, Michael W.; Striepen, Boris
Source:
mBio 2014 v.5 no.6 pp. e02021-14
ISSN:
2150-7511
Subject:
DNA; Toxoplasma gondii; clones; gene targeting; genes; genetic engineering; homologous recombination; humans; models; mutagenesis; mutants; parasites; parasitism; pathogenesis; pathogens; sequence analysis; site-specific recombination
Abstract:
... Apicomplexa are obligate intracellular parasites that cause important diseases in humans and animals. Manipulating the pathogen genome is the most direct way to understand the functions of specific genes in parasite development and pathogenesis. In Toxoplasma gondii , nonhomologous recombination is typically highly favored over homologous recombination, a process required for precise gene targetin ...
DOI:
10.1128/mBio.02021-14
PubMed:
25467441
PubMed Central:
PMC4324243

15. Gut Microbiota as an Epigenetic Regulator: Pilot Study Based on Whole-Genome Methylation Analysis

Author:
Kumar, Himanshu; Lund, Riikka; Laiho, Asta; Lundelin, Krista; Ley, Ruth E.; Isolauri, Erika; Salminen, Seppo
Source:
mBio 2014 v.5 no.6 pp. e02113-14
ISSN:
2150-7511
Subject:
DNA methylation; Firmicutes; Proteobacteria; biochemical pathways; blood; cardiovascular diseases; comorbidity; digestive system; environmental factors; epigenetics; genes; high-throughput nucleotide sequencing; humans; inflammation; intestinal microorganisms; lipid metabolism; metabolites; nucleotide sequences; obesity; pregnant women
Abstract:
... The core human gut microbiota contributes to the developmental origin of diseases by modifying metabolic pathways. To evaluate the predominant microbiota as an epigenetic modifier, we classified 8 pregnant women into two groups based on their dominant microbiota, i.e., Bacteroidetes , Firmicutes , and Proteobacteria . Deep sequencing of DNA methylomes revealed a clear association between bacterial ...
DOI:
10.1128/mBio.02113-14
PubMed:
25516615
PubMed Central:
PMC4271550

16. Helicosporidia: a genomic snapshot of an early transition to parasitism

Author:
Sun, Yukun; Pombert, Jean-Francois
Source:
Acta Societatis Botanicorum Poloniae 2014 v.83 no.4 pp. 377-385
ISSN:
0001-6977
Subject:
Auxenochlorella; Prototheca; algae; digestive system; genes; genomics; insects; invertebrates; nuclear genome; parasites; parasitism; photosynthesis
Abstract:
... Helicosporidia are gut parasites of invertebrates. These achlorophyllous, non-photosynthetic green algae are the first reported to infect insects. Helicosporidia are members of the green algal class Trebouxiophyceae and are further related to the photosynthetic and non-photosynthetic genera Auxenochlorella and Prototheca, respectively, the latter of which can also turn to parasitism under opportun ...
DOI:
10.5586/asbp.2014.039

17. High-Resolution Transcriptomic Analysis of the Adaptive Response of Staphylococcus aureus during Acute and Chronic Phases of Osteomyelitis

Author:
Szafranska, Anna K.; Oxley, Andrew P. A.; Chaves-Moreno, Diego; Horst, Sarah A.; Roßlenbroich, Steffen; Peters, Georg; Goldmann, Oliver; Rohde, Manfred; Sinha, Bhanu; Pieper, Dietmar H.; Löffler, Bettina; Jauregui, Ruy; Wos-Oxley, Melissa L.; Medina, Eva
Source:
mBio 2014 v.5 no.6 pp. e01775-14
ISSN:
2150-7511
Subject:
RNA; Staphylococcus aureus; arginine deiminase; gene expression; gene expression regulation; genes; gluconeogenesis; immune evasion; immune response; mice; nutrient availability; nutrient deficiencies; osteomyelitis; pathogens; proteins; proteolysis; quantitative analysis; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; starvation; stress response; transcription (genetics); transcriptome; transcriptomics
Abstract:
... Osteomyelitis is a difficult-to-eradicate bone infection typically caused by Staphylococcus aureus . In this study, we investigated the in vivo transcriptional adaptation of S. aureus during bone infection. To this end, we determined the transcriptome of S. aureus during the acute (day 7) and chronic (day 28) phases of experimental murine osteomyelitis using RNA sequencing (RNA-Seq). We identified ...
DOI:
10.1128/mBio.01775-14
PubMed:
25538190
PubMed Central:
PMC4278534

18. Human Cytomegalovirus-Encoded pUL7 Is a Novel CEACAM1-Like Molecule Responsible for Promotion of Angiogenesis

Author:
MacManiman, Jason D.; Meuser, Andrew; Botto, Sara; Smith, Patricia P.; Liu, Fenyong; Jarvis, Michael A.; Nelson, Jay A.; Caposio, Patrizia
Source:
mBio 2014 v.5 no.6 pp. e02035-14
ISSN:
2150-7511
Subject:
tissue repair; atherosclerosis; bioactive properties; humans; angiogenesis; mitogen-activated protein kinase; secretion; interleukin-6; immunoglobulins; sclerosis; genes; phosphorylation; cell adhesion; Human betaherpesvirus 5
Abstract:
... Persistent human cytomegalovirus (HCMV) infection has been linked to several diseases, including atherosclerosis, transplant vascular sclerosis (TVS), restenosis, and glioblastoma. We have previously shown that factors secreted from HCMV-infected cells induce angiogenesis and that this process is due, at least in part, to increased secretion of interleukin-6 (IL-6). In order to identify the HCMV g ...
DOI:
10.1128/mBio.02035-14
PubMed:
25352622
PubMed Central:
PMC4217178

19. Improving Microbial Biogasoline Production in Escherichia coli Using Tolerance Engineering

Author:
Foo, Jee Loon; Jensen, Heather M.; Dahl, Robert H.; George, Kevin; Keasling, Jay D.; Lee, Taek Soon; Leong, Susanna; Mukhopadhyay, Aindrila
Source:
mBio 2014 v.5 no.6 pp. e01932-14
ISSN:
2150-7511
Subject:
ABC transporters; Escherichia coli; alcohols; biofuels; biosynthesis; biotechnology; biotransformation; gene expression regulation; gene overexpression; genes; genetic engineering; heat; hosts; methionine; oxidative stress; phenotype; stress response; toxicity; transcriptomics
Abstract:
... Engineering microbial hosts for the production of fungible fuels requires mitigation of limitations posed on the production capacity. One such limitation arises from the inherent toxicity of solvent-like biofuel compounds to production strains, such as Escherichia coli . Here we show the importance of host engineering for the production of short-chain alcohols by studying the overexpression of gen ...
DOI:
10.1128/mBio.01932-14
PubMed:
25370492
PubMed Central:
PMC4222104

20. Kaposi’s Sarcoma-Associated Herpesvirus Genome Programming during the Early Stages of Primary Infection of Peripheral Blood Mononuclear Cells

Author:
Jha, Hem C.; Lu, Jie; Verma, Subhash C.; Banerjee, Shuvomoy; Mehta, Devan; Robertson, Erle S.
Source:
mBio 2014 v.5 no.6 pp. e02261-14
ISSN:
2150-7511
Subject:
precipitin tests; genes; mononuclear leukocytes; epigenetics; histones; methylation; gene expression; patients; pathogenesis; gene expression regulation; Human gammaherpesvirus 8; temporal variation; human diseases; humans; monitoring; morbidity; pandemic; mortality; binding sites; acetylation; chromatin
Abstract:
... The early period of Kaposi’s sarcoma-associated herpesvirus (KSHV) infection involves the dynamic expression of viral genes, which are temporally and epigenetically regulated. KSHV can effectively infect and persist in endothelial as well as human B cells with different gene expression patterns. To understand the temporal epigenetic changes which occur when KSHV infects the lymphocytic compartment ...
DOI:
10.1128/mBio.02261-14
PubMed:
25516617
PubMed Central:
PMC4271552