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https://www.readbyqxmd.com/read/28100665/co-option-of-bacteriophage-lysozyme-genes-by-bivalve-genomes
#1
Qian Ren, Chunyang Wang, Min Jin, Jiangfeng Lan, Ting Ye, Kaimin Hui, Jingmin Tan, Zheng Wang, Gerald J Wyckoff, Wen Wang, Guan-Zhu Han
Eukaryotes have occasionally acquired genetic material through horizontal gene transfer (HGT). However, little is known about the evolutionary and functional significance of such acquisitions. Lysozymes are ubiquitous enzymes that degrade bacterial cell walls. Here, we provide evidence that two subclasses of bivalves (Heterodonta and Palaeoheterodonta) acquired a lysozyme gene via HGT, building on earlier findings. Phylogenetic analyses place the bivalve lysozyme genes within the clade of bacteriophage lysozyme genes, indicating that the bivalves acquired the phage-type lysozyme genes from bacteriophages, either directly or through intermediate hosts...
January 2017: Open Biology
https://www.readbyqxmd.com/read/28095778/the-pangenome-of-antarctic-pseudoalteromonas-bacteria-evolutionary-and-functional-insights
#2
Emanuele Bosi, Marco Fondi, Valerio Orlandini, Elena Perrin, Isabel Maida, Donatella de Pascale, Maria Luisa Tutino, Ermenegilda Parrilli, Angelina Lo Giudice, Alain Filloux, Renato Fani
BACKGROUND: Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production...
January 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28067311/supra-operonic-clusters-of-functionally-related-genes-socs-are-a-source-of-horizontal-gene-co-transfers
#3
Tin Yau Pang, Martin J Lercher
Adaptation of bacteria occurs predominantly via horizontal gene transfer (HGT). While it is widely recognized that horizontal acquisitions frequently encompass multiple genes, it is unclear what the size distribution of successfully transferred DNA segments looks like and what evolutionary forces shape this distribution. Here, we identified 1790 gene family pairs that were consistently co-gained on the same branches across a phylogeny of 53 E. coli strains. We estimated a lower limit of their genomic distances at the time they were transferred to their host genomes; this distribution shows a sharp upper bound at 30 kb...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28049420/horizontal-gene-transfer-drives-the-evolution-of-rh50-permeases-in-prokaryotes
#4
Giorgio Matassi
BACKGROUND: Rh50 proteins belong to the family of ammonia permeases together with their Amt/MEP homologs. Ammonia permeases increase the permeability of NH3/NH4(+) across cell membranes and are believed to be involved in excretion of toxic ammonia and in the maintenance of pH homeostasis. RH50 genes are widespread in eukaryotes but absent in land plants and fungi, and remarkably rare in prokaryotes. The evolutionary history of RH50 genes in prokaryotes is just beginning to be unveiled...
January 3, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28041851/acquisition-of-phage-sensitivity-by-bacteria-through-exchange-of-phage-receptors
#5
Elhanan Tzipilevich, Michal Habusha, Sigal Ben-Yehuda
Bacteriophages (phages) typically exhibit a narrow host range, yet they tremendously impact horizontal gene transfer (HGT). Here, we investigate phage dynamics in communities harboring phage-resistant (R) and sensitive (S) bacteria, a common scenario in nature. Using Bacillus subtilis and its lytic phage SPP1, we demonstrate that R cells, lacking SPP1 receptor, can be lysed by SPP1 when co-cultured with S cells. This unanticipated lysis was triggered in part by phage lytic enzymes released from nearby infected cells...
January 12, 2017: Cell
https://www.readbyqxmd.com/read/28029340/horizontal-gene-transfer-versus-biostimulation-a-strategy-for-bioremediation-in-goa
#6
Rajesh Pasumarthi, Srikanth Mutnuri
Bioaugmentation, Biostimulation and Horizontal gene transfer (HGT) of catabolic genes have been proven for their role in bioremediation of hydrocarbons. It also has been proved that selection of either biostimulation or bioremediation varies for every contaminated site. The reliability of HGT compared to biostimulation and bioremediation was not tested. The present study focuses on reliability of biostimulatiion, bioaugmentation and HGT during biodegradation of Diesel oil and Non aqueous phase liquids (NAPL)...
October 28, 2016: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/28018913/evolution-of-bopa-gene-in-burkholderia-a-case-of-convergent-evolution-as-a-mechanism-for-bacterial-autophagy-evasion
#7
Dong Yu, Zhiqiu Yin, Yuan Jin, Jing Zhou, Hongguang Ren, Mingda Hu, Beiping Li, Wei Zhou, Long Liang, Junjie Yue
Autophagy is an important defense mechanism targeting intracellular bacteria to restrict their survival and growth. On the other hand, several intracellular pathogens have developed an antiautophagy mechanism to facilitate their own replication or intracellular survival. Up to now, no information about the origin or evolution of the antiautophagic genes in bacteria is available. BopA is an effector protein secreted by Burkholderia pseudomallei via the type three secretion system, and it has been shown to play a pivotal role in their escape from autophagy...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27966630/arsenic-resistance-strategy-in-pantoea-sp-imh-organization-function-and-evolution-of-ars-genes
#8
Liying Wang, Xuliang Zhuang, Guoqiang Zhuang, Chuanyong Jing
Pantoea sp. IMH is the only bacterium found in genus Pantoea with a high As resistance capacity, but its molecular mechanism is unknown. Herein, the organization, function, and evolution of ars genes in IMH are studied starting with analysis of the whole genome. Two ars systems - ars1 (arsR1B1C1H1) and ars2 (arsR2B2C2H2) - with low sequence homology and two arsC-like genes, were found in the IMH genome. Both ars1 and ars2 are involved in the As resistance, where ars1 is the major contributor at 15 °C and ars2 at 30 °C...
December 14, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27965627/bacteriophage-wo-can-mediate-horizontal-gene-transfer-in-endosymbiotic-wolbachia-genomes
#9
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/27906133/the-plastid-genome-of-some-eustigmatophyte-algae-harbours-a-bacteria-derived-six-gene-cluster-for-biosynthesis-of-a-novel-secondary-metabolite
#10
Tatiana Yurchenko, Tereza Ševčíková, Hynek Strnad, Anzhelika Butenko, Marek Eliáš
Acquisition of genes by plastid genomes (plastomes) via horizontal gene transfer (HGT) seems to be a rare phenomenon. Here, we report an interesting case of HGT revealed by sequencing the plastomes of the eustigmatophyte algae Monodopsis sp. MarTras21 and Vischeria sp. CAUP Q 202. These plastomes proved to harbour a unique cluster of six genes, most probably acquired from a bacterium of the phylum Bacteroidetes, with homologues in various bacteria, typically organized in a conserved uncharacterized putative operon...
November 2016: Open Biology
https://www.readbyqxmd.com/read/27905863/associations-between-omega-3-fatty-acids-selenium-content-and-mercury-levels-in-wild-harvested-fish-from-the-dehcho-region-northwest-territories-canada
#11
Ellen S Reyes, Juan J Aristizabal Henao, Katherine M Kornobis, Rhona M Hanning, Shannon E Majowicz, Karsten Liber, Ken D Stark, George Low, Heidi K Swanson, Brian D Laird
To better understand the risks and benefits of eating wild-harvested fish from the Northwest Territories, Canada, levels of total mercury (HgT) and selenium (Se) and composition of omega-3 fatty acid (n-3 FA) were measured in muscle tissue of fish harvested from lakes in the Dehcho Region, Northwest Territories, Canada. Average HgT levels ranged from 0.057 mg/kg (cisco) to 0.551 mg/kg (northern pike), while average n-3 FA concentrations ranged from 101 mg/100 g (burbot) to 1,689 mg/100 g (lake trout). In contrast to HgT and n-3 FA, mean Se concentrations were relatively similar among species...
December 1, 2016: Journal of Toxicology and Environmental Health. Part A
https://www.readbyqxmd.com/read/27905116/unparalleled-replacement-of-native-mitochondrial-genes-by-foreign-homologs-in-a-holoparasitic-plant
#12
M Virginia Sanchez-Puerta, Laura E García, Josefina Wohlfeiler, Luis F Ceriotti
Horizontal gene transfer (HGT) among flowering plant mitochondria occurs frequently and, in most cases, leads to nonfunctional transgenes in the recipient genome. Parasitic plants are particularly prone to this phenomenon, but their mitochondrial genomes (mtDNA) have been largely unexplored. We undertook a large-scale mitochondrial genomic study of the holoparasitic plant Lophophytum mirabile (Balanophoraceae). Comprehensive phylogenetic analyses were performed to address the frequency, origin, and impact of HGT...
November 30, 2016: New Phytologist
https://www.readbyqxmd.com/read/27902194/flavobacterium-orientale-sp-nov-isolated-from-lake-water
#13
Ai-Hua Li, Hong-Can Liu, Yu-Guang Zhou
Two Gram-stain-negative, obligately aerobic, non-motile, rod-shaped bacterial strains, designated SP3T and SP38, were isolated from a cold-water lake, in the west of China. Polyphasic taxonomy was performed for the strains. Alignment of 16S rRNA gene sequences indicated that strains SP3T and SP38 were associated with the genus Flavobacterium and were most closely related to Flavobacterium lacus NP180T (96.4 % sequence similarity), Flavobacterium ponti GSW-R14T (95.6 %) and Flavobacterium yanchengense hgT (95...
October 17, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27896274/halo-gravity-traction-is-associated-with-reduced-bone-mineral-density-of-patients-with-severe-kyphoscoliosis
#14
Xiao Han, Weixiang Sun, Yong Qiu, Leilei Xu, Shifu Sha, Benlong Shi, Huang Yan, Zhen Liu, Zezhang Zhu
Background. Halo gravity traction (HGT) is one of the most commonly used perioperative techniques for the treatment of severe kyphoscoliosis. This study was to explore the influence of HGT on the BMD of these patients. Methods. Patients with severe kyphoscoliosis treated by preoperative HGT for at least 2 months were included. Patients' BMD were assessed by dual-energy X-ray absorptiometry at lumbar spine (LS, L2-L4) and femur neck (FN) of the nondominant side. The weight and duration of traction, as well as baseline characteristics, were recorded...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27895636/genomic-and-transcriptomic-evidence-for-carbohydrate-consumption-among-microorganisms-in-a-cold-seep-brine-pool
#15
Weipeng Zhang, Wei Ding, Bo Yang, Renmao Tian, Shuo Gu, Haiwei Luo, Pei-Yuan Qian
The detailed lifestyle of microorganisms in deep-sea brine environments remains largely unexplored. Using a carefully calibrated genome binning approach, we reconstructed partial to nearly-complete genomes of 51 microorganisms in biofilms from the Thuwal cold seep brine pool of the Red Sea. The recovered metagenome-assembled genomes (MAGs) belong to six different phyla: Actinobacteria, Proteobacteria, Candidatus Cloacimonetes, Candidatus Marinimicrobia, Bathyarchaeota, and Thaumarchaeota. By comparison with close relatives of these microorganisms, we identified a number of unique genes associated with organic carbon metabolism and energy generation...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27894995/short-branches-lead-to-systematic-artifacts-when-blast-searches-are-used-as-surrogate-for-phylogenetic-reconstruction
#16
Amanda A Dick, Timothy J Harlow, J Peter Gogarten
Long Branch Attraction (LBA) is a well-known artifact in phylogenetic reconstruction when dealing with branch length heterogeneity. Here we show another phenomenon, Short Branch Attraction (SBA), which occurs when BLAST searches, a phenetic analysis, are used as a surrogate method for phylogenetic analysis. This error also results from branch length heterogeneity, but this time it is the short branches that are attracting. The SBA artifact is reciprocal and can be returned 100% of the time when multiple branches differ in length by a factor of more than two...
November 26, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27885411/scopolamine-disrupts-place-navigation-in-rats-and-humans-a-translational-validation-of-the-hidden-goal-task-in-the-morris-water-maze-and-a-real-maze-for-humans
#17
Jan Laczó, Hana Markova, Veronika Lobellova, Ivana Gazova, Martina Parizkova, Jiri Cerman, Tereza Nekovarova, Karel Vales, Sylva Klovrzova, John Harrison, Manfred Windisch, Kamil Vlcek, Jan Svoboda, Jakub Hort, Ales Stuchlik
RATIONALE: Development of new drugs for treatment of Alzheimer's disease (AD) requires valid paradigms for testing their efficacy and sensitive tests validated in translational research. OBJECTIVES: We present validation of a place-navigation task, a Hidden Goal Task (HGT) based on the Morris water maze (MWM), in comparable animal and human protocols. METHODS: We used scopolamine to model cognitive dysfunction similar to that seen in AD and donepezil, a symptomatic medication for AD, to assess its potential reversible effect on this scopolamine-induced cognitive dysfunction...
November 24, 2016: Psychopharmacology
https://www.readbyqxmd.com/read/27881071/genome-wide-analyses-of-chitin-synthases-identify-horizontal-gene-transfers-towards-bacteria-and-allow-a-robust-and-unifying-classification-into-fungi
#18
Isabelle R Gonçalves, Sophie Brouillet, Marie-Christine Soulié, Simonetta Gribaldo, Catherine Sirven, Noémie Charron, Martine Boccara, Mathias Choquer
BACKGROUND: Chitin, the second most abundant biopolymer on earth after cellulose, is found in probably all fungi, many animals (mainly invertebrates), several protists and a few algae, playing an essential role in the development of many of them. This polysaccharide is produced by type 2 glycosyltransferases, called chitin synthases (CHS). There are several contradictory classifications of CHS isoenzymes and, as regards their evolutionary history, their origin and diversity is still a matter of debate...
November 24, 2016: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/27875306/family-wide-structural-characterization-and-genomic-comparisons-decode-the-diversity-oriented-biosynthesis-of-thalassospiramides-by-marine-proteobacteria
#19
Weipeng Zhang, Liang Lu, Qiliang Lai, Beika Zhu, Zhongrui Li, Ying Xu, Zongze Shao, Karl Herrup, Bradley S Moore, Avena C Ross, Pei-Yuan Qian
The thalassospiramide lipopeptides have great potential for therapeutic applications; however, their structural and functional diversity and biosynthesis are poorly understood. Here, by cultivating 130 Rhodospirillaceae strains sampled from oceans worldwide, we discovered 21 new thalassospiramide analogues and demonstrated their neuroprotective effects. To investigate the diversity of biosynthetic gene cluster (BGC) architectures, we sequenced the draft genomes of 28 Rhodospirillaceae strains. Our family-wide genomic analysis revealed three types of dysfunctional BGCs and four functional BGCs whose architectures correspond to four production patterns...
December 30, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27867010/quorum-sensing-controls-adaptive-immunity-through-the-regulation-of-multiple-crispr-cas-systems
#20
Adrian G Patterson, Simon A Jackson, Corinda Taylor, Gary B Evans, George P C Salmond, Rita Przybilski, Raymond H J Staals, Peter C Fineran
Bacteria commonly exist in high cell density populations, making them prone to viral predation and horizontal gene transfer (HGT) through transformation and conjugation. To combat these invaders, bacteria possess an arsenal of defenses, such as CRISPR-Cas adaptive immunity. Many bacterial populations coordinate their behavior as cell density increases, using quorum sensing (QS) signaling. In this study, we demonstrate that QS regulation results in increased expression of the type I-E, I-F, and III-A CRISPR-Cas systems in Serratia cells in high-density populations...
December 15, 2016: Molecular Cell
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