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Horizontal DNA transfer

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https://www.readbyqxmd.com/read/28720902/comparative-genomic-analysis-of-paenibacillus-sp-ssg-1-and-its-closely-related-strains-reveals-the-effect-of-glycometabolism-on-environmental-adaptation
#1
Hui Xu, Shishang Qin, Yanhong Lan, Mengjia Liu, Xiyue Cao, Dairong Qiao, Yu Cao, Yi Cao
The extensive environmental adaptability of the genus Paenibacillus is related to the enormous diversity of its gene repertoires. Paenibacillus sp. SSG-1 has previously been reported, and its agar-degradation trait has attracted our attention. Here, the genome sequence of Paenibacillus sp. SSG-1, together with 76 previously sequenced strains, was comparatively studied. The results show that the pan-genome of Paenibacillus is open and indicate that the current taxonomy of this genus is incorrect. The incessant flux of gene repertoires resulting from the processes of gain and loss largely contributed to the difference in genomic content and genome size in Paenibacillus...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28706512/comparative-genomics-reveals-high-genomic-diversity-in-the-genus-photobacterium
#2
Henrique Machado, Lone Gram
Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two misidentified strains...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28698278/on-the-origin-of-reverse-transcriptase-using-crispr-cas-systems-and-their-hyperdiverse-enigmatic-spacer-repertoires
#3
Sukrit Silas, Kira S Makarova, Sergey Shmakov, David Páez-Espino, Georg Mohr, Yi Liu, Michelle Davison, Simon Roux, Siddharth R Krishnamurthy, Becky Xu Hua Fu, Loren L Hansen, David Wang, Matthew B Sullivan, Andrew Millard, Martha R Clokie, Devaki Bhaya, Alan M Lambowitz, Nikos C Kyrpides, Eugene V Koonin, Andrew Z Fire
Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent) to a gene encoding a reverse transcriptase (RT) related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains...
July 11, 2017: MBio
https://www.readbyqxmd.com/read/28683561/ros-mediated-autophagy-defines-the-fate-of-cancer-stem-cells
#4
Matilde E Lleonart, Etna Abad, Dmitry Graifer, Alex Lyakhovich
SIGNIFICANCE: A fraction of tumorigenic cells, also known as tumor initiating or cancer stem cells, is thought to drive tumor growth, metastasis and chemoresistance. However, little is known regarding mechanisms that convey relevant pathways contributing to their self-renewal, proliferation and differentiation abilities. Recent Advances: Recent works on cancer stem cells provide evidence on the role of redox disruption and regulation of autophagic flux. This has been linked to increased DNA repair capacity and chemoresistance...
July 6, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28683122/the-nucleoid-occlusion-protein-slma-is-a-direct-transcriptional-activator-of-chitobiose-utilization-in-vibrio-cholerae
#5
Catherine A Klancher, Chelsea A Hayes, Ankur B Dalia
Chitin utilization by the cholera pathogen Vibrio cholerae is required for its persistence and evolution via horizontal gene transfer in the marine environment. Genes involved in the uptake and catabolism of the chitin disaccharide chitobiose are encoded by the chb operon. The orphan sensor kinase ChiS is critical for regulation of this locus, however, the mechanisms downstream of ChiS activation that result in expression of the chb operon are poorly understood. Using an unbiased transposon mutant screen, we uncover that the nucleoid occlusion protein SlmA is a regulator of the chb operon...
July 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28682556/-the-origin-of-hydrogen-peroxide-in-oral-cavity-and-its-role-in-oral-microecology-balance
#6
Zhang Keke, Zhou Xuedong, Xu Xin
Hydrogen peroxide, an important antimicrobial agent in oral cavity, plays a significant role in the balance of oral microecology. At the early stage of biofilm formation, about 80% of the detected initial colonizers belong to the genus Streptococcus. These oral streptococci use different oxidase to produce hydrogen peroxide. Recent studies showed that the produced hydrogen peroxide plays a critical role in modulating oral microecology. Hydrogen peroxide modulates biofilm development attributed to its growth inhibitory nature...
April 1, 2017: Hua Xi Kou Qiang Yi Xue za Zhi, Huaxi Kouqiang Yixue Zazhi, West China Journal of Stomatology
https://www.readbyqxmd.com/read/28676809/phylogenomic-analysis-and-dynamic-evolution-of-chloroplast-genomes-in-salicaceae
#7
Yuan Huang, Jun Wang, Yongping Yang, Chuanzhu Fan, Jiahui Chen
Chloroplast genomes of plants are highly conserved in both gene order and gene content. Analysis of the whole chloroplast genome is known to provide much more informative DNA sites and thus generates high resolution for plant phylogenies. Here, we report the complete chloroplast genomes of three Salix species in family Salicaceae. Phylogeny of Salicaceae inferred from complete chloroplast genomes is generally consistent with previous studies but resolved with higher statistical support. Incongruences of phylogeny, however, are observed in genus Populus, which most likely results from homoplasy...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28669811/evolutionary-persistence-of-tripartite-integrative-and-conjugative-elements
#8
REVIEW
Timothy L Haskett, Joshua P Ramsay, Amanuel A Bekuma, John T Sullivan, Graham W O'Hara, Jason J Terpolilli
Integrative and conjugative elements (ICEs) are generally regarded as regions of contiguous DNA integrated within a bacterial genome that are capable of excision and horizontal transfer via conjugation. We recently characterized a unique group of ICEs present in Mesorhizobium spp., which exist as three entirely separate but inextricably linked chromosomal regions termed α, β and γ. These regions occupy three different recombinase attachment (att) sites; however, they do not excise independently. Rather, they recombine the host chromosome to form a single contiguous region prior to excision and conjugative transfer...
June 29, 2017: Plasmid
https://www.readbyqxmd.com/read/28659339/structure-of-the-competence-pilus-major-pilin-comgc-in-streptococcus-pneumoniae
#9
Sandra Muschiol, Simon Erlendsson, Marie-Stephanie Aschtgen, Vitor Oliveira, Peter Schmieder, Casper de Lichtenberg, Kaare Teilum, Thomas Boesen, Umit Akbey, Birgitta Henriques-Normark
Type IV pili are important virulence factors on the surface of many pathogenic bacteria and have been implicated in a wide range of diverse functions including attachment, twitching motility, biofilm formation and horizontal gene transfer. The respiratory pathogen Streptococcus pneumoniae deploys type IV pili to take up DNA during transformation. These "competence pili" are composed of the major pilin protein ComGC and exclusively assembled during bacterial competence, but their biogenesis remains unclear. Here, we report the high resolution NMR structure of N-terminal truncated ComGC revealing a highly flexible and structurally divergent type IV pilin...
June 28, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28630398/hcf-1-encoded-by-baculovirus-acmnpv-is-required-for-productive-nucleopolyhedrovirus-infection-of-non-permissive-tn368-cells
#10
Ami Tachibana, Rina Hamajima, Moe Tomizaki, Takuya Kondo, Yoshie Nanba, Michihiro Kobayashi, Hayato Yamada, Motoko Ikeda
Baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) replicates in both Spodoptera frugiperda Sf21 and Trichoplusia ni Tn368 cells, whereas AcMNPV defective in hcf-1 (host cell-factor 1) gene productively infects only Sf21 cells, indicating that HCF-1 is indispensable for the AcMNPV productive infection of Tn368 cells. Here, we demonstrated that HCF-1 protein transiently expressed in Tn368 cells promotes the DNA synthesis of Hyphantria cunea MNPV (HycuMNPV), Orygia pseudotsugata MNPV and Bombyx mori NPV, which are normally unable to replicate in Tn368 cells...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28621762/the-landscape-of-the-emergence-of-life
#11
Sohan Jheeta
This paper reports on the various nuances of the origins of life on Earth and highlights the latest findings in that arena as reported at the Network of Researchers on Horizontal Gene Transfer and the Last Universal Common Ancestor (NoR HGT and LUCA) which was held from the 3-4th November 2016 at the Open University, UK. Although the answers to the question of the origin of life on Earth will not be fathomable anytime soon, a wide variety of subject matter was able to be covered, ranging from examining what constitutes a LUCA, looking at viral connections and "from RNA to DNA", i...
June 16, 2017: Life
https://www.readbyqxmd.com/read/28620358/the-transcriptional-regulators-of-the-crp-family-regulate-different-essential-bacterial-functions-and-can-be-inherited-vertically-and-horizontally
#12
REVIEW
Gloria Soberón-Chávez, Luis D Alcaraz, Estefanía Morales, Gabriel Y Ponce-Soto, Luis Servín-González
One of the best-studied transcriptional regulatory proteins in bacteria is the Escherichia coli catabolite repressor protein (CRP) that when complexed with 3'-5'-cyclic AMP (cAMP) changes its conformation and interacts with specific DNA-sequences. CRP DNA-binding can result in positive or negative regulation of gene expression depending on the position of its interaction with respect to RNA polymerase binding site. The aim of this work is to review the biological role and phylogenetic relations that some members of the CRP family of transcriptional regulators (also known as cAMP receptor protein family) have in different bacterial species...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28612702/genetic-variability-and-population-structure-of-the-new-world-begomovirus-euphorbia-yellow-mosaic-virus
#13
Talita Bernardon Mar, César Augusto Diniz Xavier, Alison Talis Martins Lima, Angélica Maria Nogueira, José Cleydson Ferreira Silva, Roberto Ramos-Sobrinho, Douglas Lau, F Murilo Zerbini
The emergence of begomoviruses (whitefly-transmitted viruses classified in the genus Begomovirus, family Geminiviridae) in Brazil probably occurred by horizontal transfer from non-cultivated plants after the introduction of Bemisia tabaci MEAM1. The centre of diversity of Euphorbia heterophylla (Euphorbiaceae) is located in Brazil and Paraguay, where it is an invasive species in soybean and other crops. Reports of possible begomovirus infection of E. heterophylla in Brazil date back to the 1950s. In 2011, Euphorbia yellow mosaic virus (EuYMV) was described in symptomatic plants collected in the Brazilian state of Goiás...
June 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28600959/beyond-the-canonical-strategies-of-horizontal-gene-transfer-in-prokaryotes
#14
REVIEW
Cristina García-Aljaro, Elisenda Ballesté, Maite Muniesa
Efforts to identify and characterize strategies for horizontal gene transfer (HGT) in prokaryotes could have overlooked some mechanisms that do not entirely fit in with the canonical ones most often described (conjugation of plasmids, phage transduction and transformation). The difficulty in distinguishing the different HGT strategies could have contributed to underestimate their real extent. Here we review non classical HGT strategies: some that require mobile genetic elements (MGEs) and others independent of MGE...
June 7, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28596758/a-functional-metagenomic-analysis-of-tetracycline-resistance-in-cheese-bacteria
#15
Ana B Flórez, Lucía Vázquez, Baltasar Mayo
Metagenomic techniques have been successfully used to monitor antibiotic resistance genes in environmental, animal and human ecosystems. However, despite the claim that the food chain plays a key role in the spread of antibiotic resistance, metagenomic analysis has scarcely been used to investigate food systems. The present work reports a functional metagenomic analysis of the prevalence and evolution of tetracycline resistance determinants in a raw-milk, blue-veined cheese during manufacturing and ripening...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28592722/release-and-constancy-of-an-antibiotic-resistance-gene-in-seawater-under-grazing-stress-by-ciliates-and-heterotrophic-nanoflagellates
#16
Thi Lan Thanh Bien, Ngo Vy Thao, Shin-Ichi Kitamura, Yumiko Obayashi, Satoru Suzuki
Extracellular DNA (exDNA) is released from bacterial cells through various processes. The antibiotic resistance genes (ARGs) coded on exDNA may be horizontally transferred among bacterial communities by natural transformation. We quantitated the released/leaked tetracycline resistance gene, tet(M) over time under grazing stress by ciliates and heterotrophic nanoflagellates (HNFs), and found that extracellular tet(M) (ex-tetM) increased with bacterial grazing. Separate microcosms containing tet(M)-possessing bacteria with ciliates or HNFs were prepared...
June 24, 2017: Microbes and Environments
https://www.readbyqxmd.com/read/28591314/complete-plasmid-sequence-carrying-type-iv-like-and-type-vii-secretion-systems-from-an-atypical-mycobacteria-strain
#17
Sergio Mascarenhas Morgado, Michel Abanto Marín, Fernanda S Freitas, Erica Lourenço Fonseca, Ana Carolina Paulo Vicente
The genus Mycobacterium is highly diverse and ubiquitous in nature, comprehending fast- and slow-growing species with distinct impact in public health. The plasmid-mediated horizontal gene transfer represents one of the major events in bacteria evolution. Here, we report the complete sequence of a 160,489 bp circular plasmid (pCBMA213_2) from an atypical and fast-growing environmental mycobacteria. This is a unique plasmid, in comparison with the characterised mycobacteria plasmids, harboring a type IV-like and ESX-P2 type VII secretion systems...
July 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/28567486/xenobiology-state-of-the-art-ethics-and-philosophy-of-new-to-nature-organisms
#18
Markus Schmidt, Lei Pei, Nediljko Budisa
The basic chemical constitution of all living organisms in the context of carbon-based chemistry consists of a limited number of small molecules and polymers. Until the twenty-first century, biology was mainly an analytical science and has now reached a point where it merges with engineering science, paving the way for synthetic biology. One of the objectives of synthetic biology is to try to change the chemical compositions of living cells, that is, to create an artificial biological diversity, which in turn fosters a new sub-field of synthetic biology, xenobiology...
June 1, 2017: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/28559293/a-conserved-metal-binding-motif-in-the-bacillus-subtilis-competence-protein-comfa-enhances-transformation
#19
Scott S Chilton, Tanya G Falbel, Susan Hromada, Briana M Burton
Genetic competence is a process in which cells are able to take up DNA from their environment, resulting in horizontal gene transfer, a major mechanism for generating diversity in bacteria. Many bacteria carry homologs of the central DNA uptake machinery that has been well characterized in Bacillus subtilis It has been postulated that the B. subtilis competence helicase ComFA belongs to the DEAD-box family of helicases/translocases. Here, we make a series of mutants to analyze conserved amino acid motifs in several regions of B...
May 30, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28550453/exchange-of-genetic-sequences-between-viruses-and-hosts
#20
Robin A Weiss
Although genetic transfer between viruses and vertebrate hosts occurs less frequently than gene flow between bacteriophages and prokaryotes, it is extensive and has affected the evolution of both parties. With retroviruses, the integration of proviral DNA into chromosomal DNA can result in the activation of adjacent host gene expression and in the transduction of host transcripts into retroviral genomes as oncogenes. Yet in contrast to lysogenic phage, there is little evidence that viral oncogenes persist in a chain of natural transmission or that retroviral transduction is a significant driver of the horizontal spread of host genes...
May 28, 2017: Current Topics in Microbiology and Immunology
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