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Bacteria new gene origin

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https://www.readbyqxmd.com/read/28405712/emergence-of-new-srnas-in-enteric-bacteria-is-associated-with-low-expression-and-rapid-evolution
#1
Fenil R Kacharia, Jess A Millar, Rahul Raghavan
Non-coding small RNAs (sRNAs) are critical to post-transcriptional gene regulation in bacteria. However, unlike for protein-coding genes, the evolutionary forces that shape sRNAs are not understood. We investigated sRNAs in enteric bacteria and discovered that recently emerged sRNAs evolve at significantly faster rates than older sRNAs. Concomitantly, younger sRNAs are expressed at significantly lower levels than older sRNAs. This process could potentially facilitate the integration of newly emerged sRNAs into bacterial regulatory networks...
April 12, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28353400/evolutionary-history-of-subtilases-in-land-plants-and-their-involvement-in-symbiotic-interactions
#2
Alexander Taylor, Yin-Long Qiu
Subtilases, a family of proteases involved in a variety of developmental processes in land plants, are also involved in both mutualistic symbiosis and host-pathogen interactions in different angiosperm lineages. We examined the evolutionary history of subtilase genes across land plants through a phylogenetic analysis integrating amino acid sequence data from full genomes, transcriptomes, and characterized subtilases of 341 species of diverse green algae and land plants, along with subtilases from 12 species of other eukaryotes, archaea and bacteria...
March 29, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/28344994/a-new-broad-range-plasmid-for-dna-delivery-in-eukaryotic-cells-using-lactic-acid-bacteria-in%C3%A2-vitro-and-in%C3%A2-vivo-assays
#3
Pamela Mancha-Agresti, Mariana Martins Drumond, Fillipe Luiz Rosa do Carmo, Monica Morais Santos, Janete Soares Coelho Dos Santos, Franco Venanzi, Jean-Marc Chatel, Sophie Yvette Leclercq, Vasco Azevedo
Lactococcus lactis is well documented as a promising candidate for development of novel oral live vaccines. It has been broadly engineered for heterologous expression, as well as for plasmid expression vector delivery, directly inside eukaryotic cells, for DNA vaccine, or as therapeutic vehicle. This work describes the characteristics of a new plasmid, pExu (extra chromosomal unit), for DNA delivery using L. lactis and evaluates its functionality both by in vitro and in vivo assays. This plasmid exhibits the following features: (1) a theta origin of replication and (2) an expression cassette containing a multiple cloning site and a eukaryotic promoter, the cytomegalovirus (pCMV)...
March 17, 2017: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/28337182/new-insights-into-the-anti-pathogenic-potential-of-lactococcus-garvieae-against-staphylococcus-aureus-based-on-rna-sequencing-profiling
#4
Pierre Delpech, Etienne Rifa, Graham Ball, Sabine Nidelet, Emeric Dubois, Geneviève Gagne, Marie-Christine Montel, Céline Delbès, Stéphanie Bornes
The bio-preservation potential of Lactococcus garvieae lies in its capacity to inhibit the growth of staphylococci, especially Staphylococcus aureus, in dairy products and in vitro. In vitro, inhibition is modulated by the level of aeration, owing to hydrogen peroxide (H2O2) production by L. garvieae under aeration. The S. aureus response to this inhibition has already been studied. However, the molecular mechanisms of L. garvieae underlying the antagonism against S. aureus have never been explored. This study provides evidence of the presence of another extracellular inhibition effector in vitro...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28275945/enrichment-culture-and-identification-of-endophytic-methanotrophs-isolated-from-peatland-plants
#5
Zofia Stępniewska, Weronika Goraj, Agnieszka Kuźniar, Natalia Łopacka, Magdalena Małysza
Aerobic methane-oxidizing bacteria (MOB) are an environmentally significant group of microorganisms due to their role in the global carbon cycle. Research conducted over the past few decades has increased the interest in discovering novel genera of methane-degrading bacteria, which efficiently utilize methane and decrease the global warming effect. Moreover, methanotrophs have more promising applications in environmental bioengineering, biotechnology, and pharmacy. The investigations were undertaken to recognize the variety of endophytic methanotrophic bacteria associated with Carex nigra, Vaccinium oxycoccus, and Eriophorum vaginatum originating from Moszne peatland (East Poland)...
March 9, 2017: Folia Microbiologica
https://www.readbyqxmd.com/read/28242668/plasmid-mediated-novel-blandm-17-gene-encoding-a-carbapenemase-with-enhanced-activity-in-a-st48-escherichia-coli-strain
#6
Zhihai Liu, Yang Wang, Timothy R Walsh, Dejun Liu, Zhangqi Shen, Rongmin Zhang, Wenjuan Yin, Hong Yao, Jiyun Li, Jianzhong Shen
Carbapenem-resistant Enterobacteriaceae (CRE) have spread worldwide, leaving very few treatment options available. New Delhi metallo-beta-lactamase (NDM) is the main carbapenemase mediating CRE resistance, and is of increasing concern. NDM-positive Enterobacteriaceae of human origin are frequently identified; however, the emergence of NDM, particularly novel variants, in bacteria of food animal origin has never been reported. Here, we characterize a novel NDM variant (assigned NDM-17) identified in a β-lactam-resistant sequence type 48 (ST48) Escherichia coli strain that was isolated from a chicken in China...
February 27, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28236853/in-pursuit-of-cancer-metastasis-therapy-by-bacteria-and-its-biofilms-history-or-future
#7
Mohd Adnan, Saif Khan, Eyad Al-Shammari, Mitesh Patel, Mohd Saeed, Sibte Hadi
The 20th century observation of increasing comprehensive load of cancer, advanced cancer prevention strategies, creative hypotheses and control procedures by research communities are being traversed and stimulated in multiple facets. Inference of genetically modified non-pathogenic and natural bacterial species as potential anti-tumor agents is one such original perspective. Live, genetically modified non-pathogenic or attenuated bacterial species are able to form biofilms by multiplying selectively or non-selectively on cancer cells, which will lead to metastasis disruption...
March 2017: Medical Hypotheses
https://www.readbyqxmd.com/read/28231283/rapid-evolution-of-distinct-helicobacter-pylori-subpopulations-in-the-americas
#8
Kaisa Thorell, Koji Yahara, Elvire Berthenet, Daniel J Lawson, Jane Mikhail, Ikuko Kato, Alfonso Mendez, Cosmeri Rizzato, María Mercedes Bravo, Rumiko Suzuki, Yoshio Yamaoka, Javier Torres, Samuel K Sheppard, Daniel Falush
For the last 500 years, the Americas have been a melting pot both for genetically diverse humans and for the pathogenic and commensal organisms associated with them. One such organism is the stomach-dwelling bacterium Helicobacter pylori, which is highly prevalent in Latin America where it is a major current public health challenge because of its strong association with gastric cancer. By analyzing the genome sequence of H. pylori isolated in North, Central and South America, we found evidence for admixture between H...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28230768/bioinformatic-analysis-reveals-archaeal-trna-tyr-and-trna-trp-identities-in-bacteria
#9
Takahito Mukai, Noah M Reynolds, Ana Crnković, Dieter Söll
The tRNA identity elements for some amino acids are distinct between the bacterial and archaeal domains. Searching in recent genomic and metagenomic sequence data, we found some candidate phyla radiation (CPR) bacteria with archaeal tRNA identity for Tyr-tRNA and Trp-tRNA synthesis. These bacteria possess genes for tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase (TrpRS) predicted to be derived from DPANN superphylum archaea, while the cognate tRNA(Tyr) and tRNA(Trp) genes reveal bacterial or archaeal origins...
February 21, 2017: Life
https://www.readbyqxmd.com/read/28174306/a-mobile-element-in-muts-drives-hypermutation-in-a-marine-vibrio
#10
Nathaniel D Chu, Sean A Clarke, Sonia Timberlake, Martin F Polz, Alan D Grossman, Eric J Alm
Bacteria face a trade-off between genetic fidelity, which reduces deleterious mistakes in the genome, and genetic innovation, which allows organisms to adapt. Evidence suggests that many bacteria balance this trade-off by modulating their mutation rates, but few mechanisms have been described for such modulation. Following experimental evolution and whole-genome resequencing of the marine bacterium Vibrio splendidus 12B01, we discovered one such mechanism, which allows this bacterium to switch to an elevated mutation rate...
February 7, 2017: MBio
https://www.readbyqxmd.com/read/28164795/comparative-genomic-analysis-of-the-genus-enterococcus
#11
Zhi Zhong, Wenyi Zhang, Yuqin Song, Wenjun Liu, Haiyan Xu, Xiaoxia Xi, Bilige Menghe, Heping Zhang, Zhihong Sun
As important lactic acid bacteria, Enterococcus species are widely used in the production of fermented food. However, as some strains of Enterococcus are opportunistic pathogens, their safety has not been generally accepted. In recent years, a large number of new species have been described and classified within the genus Enterococcus, so a better understanding of the genetic relationships and evolution of Enterococcus species is needed. In this study, the genomes of 29 type strains of Enterococcus species were sequenced...
March 2017: Microbiological Research
https://www.readbyqxmd.com/read/28127420/permanent-draft-genome-of-thiobacillus-thioparus-dsm-505-t-an-obligately-chemolithoautotrophic-member-of-the-betaproteobacteria
#12
Lee P Hutt, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, Tatiparthi Reddy, Chris Daum, Nicole Shapiro, Natalia Ivanova, Nikos Kyrpides, Tanja Woyke, Rich Boden
Thiobacillus thioparus DSM 505(T) is one of first two isolated strains of inorganic sulfur-oxidising Bacteria. The original strain of T. thioparus was lost almost 100 years ago and the working type strain is Culture C(T) (=DSM 505(T) = ATCC 8158(T)) isolated by Starkey in 1934 from agricultural soil at Rutgers University, New Jersey, USA. It is an obligate chemolithoautotroph that conserves energy from the oxidation of reduced inorganic sulfur compounds using the Kelly-Trudinger pathway and uses it to fix carbon dioxide It is not capable of heterotrophic or mixotrophic growth...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28088165/genomic-characterization-of-ensifer-aridi-a-proposed-new-species-of-nitrogen-fixing-rhizobium-recovered-from-asian-african-and-american-deserts
#13
Antoine Le Quéré, Nisha Tak, Hukam Singh Gehlot, Celine Lavire, Thibault Meyer, David Chapulliot, Sonam Rathi, Ilham Sakrouhi, Guadalupe Rocha, Marine Rohmer, Dany Severac, Abdelkarim Filali-Maltouf, Jose-Antonio Munive
BACKGROUND: Nitrogen fixing bacteria isolated from hot arid areas in Asia, Africa and America but from diverse leguminous plants have been recently identified as belonging to a possible new species of Ensifer (Sinorhizobium). In this study, 6 strains belonging to this new clade were compared with Ensifer species at the genome-wide level. Their capacities to utilize various carbon sources and to establish a symbiotic interaction with several leguminous plants were examined. RESULTS: Draft genomes of selected strains isolated from Morocco (Merzouga desert), Mexico (Baja California) as well as from India (Thar desert) were produced...
January 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28087696/genetic-and-biochemical-characterization-of-a-gene-operon-for-trans-aconitic-acid-a-novel-nematicide-from-bacillus-thuringiensis
#14
Cuiying Du, Shiyun Cao, Xiangyu Shi, Xiangtao Nie, Jinshui Zheng, Yun Deng, Lifang Ruan, Donghai Peng, Ming Sun
trans-Aconitic acid (TAA) is an isomer of cis-aconitic acid (CAA), an intermediate of the tricarboxylic acid cycle that is synthesized by aconitase. Although TAA production has been detected in bacteria and plants for many years and is known to be a potent inhibitor of aconitase, its biosynthetic origins and the physiological relevance of its activity have remained unclear. We have serendipitously uncovered key information relevant to both of these questions. Specifically, in a search for novel nematicidal factors from Bacillus thuringiensis, a significant nematode pathogen harboring many protein virulence factors, we discovered a high yielding component that showed activity against the plant-parasitic nematode Meloidogyne incognita and surprisingly identified it as TAA...
February 24, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28072419/an-acid-tolerant-ammonia-oxidizing-%C3%AE-proteobacterium-from-soil
#15
Masahito Hayatsu, Kanako Tago, Ikuo Uchiyama, Atsushi Toyoda, Yong Wang, Yumi Shimomura, Takashi Okubo, Futoshi Kurisu, Yuhei Hirono, Kunihiko Nonaka, Hiroko Akiyama, Takehiko Itoh, Hideto Takami
Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, occurs in a wide range of acidic soils. However, the ammonia-oxidizing bacteria (AOB) that have been isolated from soil to date are acid-sensitive. Here we report the isolation and characterization of an acid-adapted AOB from an acidic agricultural soil. The isolated AOB, strain TAO100, is classified within the Gammaproteobacteria based on phylogenetic characteristics. TAO100 can grow in the pH range of 5-7.5 and survive in highly acidic conditions until pH 2 by forming cell aggregates...
May 2017: ISME Journal
https://www.readbyqxmd.com/read/28025249/glucosylglycerate-metabolism-bioversatility-and-mycobacterial-survival
#16
Daniela Nunes-Costa, Ana Maranha, Mafalda Costa, Susana Alarico, Nuno Empadinhas
Despite the progressive decline in tuberculosis mortality, strains resistant to our dated antibiotics remain a global threat, as are the emerging nontuberculous mycobacteria, ubiquitous in natural and human environments. This pressing situation boosted by debilitated immune systems, chronic illness and the aged population calls for efficient strategies to fight these successful organisms, and identifying pathways critical for their survival is a crucial step towards this goal. In this context, the glycoside glucosylglycerate (GG) has been implicated in the adaptation of mycobacteria to nitrogen starvation and to thermal stress, and the key gene for GG synthesis has been considered essential for Mycobacterium tuberculosis growth...
March 4, 2017: Glycobiology
https://www.readbyqxmd.com/read/28018304/identification-of-electrode-respiring-hydrocarbonoclastic-bacterial-strain-stenotrophomonas-maltophilia-mk2-highlights-the-untapped-potential-for-environmental-bioremediation
#17
Krishnaveni Venkidusamy, Mallavarapu Megharaj
Electrode respiring bacteria (ERB) possess a great potential for many biotechnological applications such as microbial electrochemical remediation systems (MERS) because of their exoelectrogenic capabilities to degrade xenobiotic pollutants. Very few ERB have been isolated from MERS, those exhibited a bioremediation potential toward organic contaminants. Here we report once such bacterial strain, Stenotrophomonas maltophilia MK2, a facultative anaerobic bacterium isolated from a hydrocarbon fed MERS, showed a potent hydrocarbonoclastic behavior under aerobic and anaerobic environments...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27966343/biosynthetic-origin-of-the-ether-ring-in-platensimycin
#18
Jeffrey D Rudolf, Liao-Bin Dong, Karina Manoogian, Ben Shen
Platensimycin (PTM) and platencin (PTN) are highly functionalized bacterial diterpenoid natural products that target bacterial and mammalian fatty acid synthases. PTM and PTN feature varying diterpene-derived ketolides that are linked to the same 3-amino-2,4-dihydroxybenzoic acid moiety. As a result, PTM is a selective inhibitor for FabF/FabB, while PTN is a dual inhibitor of FabF/FabB and FabH. We previously determined that the PTM cassette, consisting of five genes found in the ptm, but not ptn, gene cluster, partitions the biosynthesis of the PTM and PTN diterpene-derived ketolides...
December 28, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27965627/bacteriophage-wo-can-mediate-horizontal-gene-transfer-in-endosymbiotic-wolbachia-genomes
#19
Guan H Wang, Bao F Sun, Tuan L Xiong, Yan K Wang, Kristen E Murfin, Jin H Xiao, Da W Huang
Phage-mediated horizontal gene transfer (HGT) is common in free-living bacteria, and many transferred genes can play a significant role in their new bacterial hosts. However, there are few reports concerning phage-mediated HGT in endosymbionts (obligate intracellular bacteria within animal or plant hosts), such as Wolbachia. The Wolbachia-infecting temperate phage WO can actively shift among Wolbachia genomes and has the potential to mediate HGT between Wolbachia strains. In the present study, we extend previous findings by validating that the phage WO can mediate transfer of non-phage genes...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27926825/mycobacterium-malmesburyense-sp-nov-a-novel-non-tuberculous-mycobacterium-species-revealed-by-multiple-gene-sequence-characterization
#20
Nomakorinte Gcebe, Victor Rutten, Nicolaas Gey van Pittius, Brendon Naicker, Anita Michel
Non-tuberculous mycobacteria (NTM) are ubiquitous in the environment and an increasing number of NTM species have been isolated and characterized from both humans and animals, highlighting the zoonotic potential of these bacteria. Host exposure to NTM may impact on cross-reactive immune responsiveness which may affect diagnosis of bovine tuberculosis and may also play a role in the variability of the efficacy of Mycobacterium bovis BCG vaccination against tuberculosis. In this study we characterized 10 NTM isolates originating from water, soil, nasal swabs of cattle and African buffalo as well as bovine tissue samples...
December 5, 2016: International Journal of Systematic and Evolutionary Microbiology
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