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Bacteria evolution

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https://www.readbyqxmd.com/read/28220205/global-properties-of-nested-network-model-with-application-to-multi-epitope-hiv-ctl-dynamics
#1
Cameron Browne
Mathematical modeling and analysis can provide insight on the dynamics of ecosystems which maintain biodiversity in the face of competitive and prey-predator interactions. Of primary interests are the underlying structure and features which stabilize diverse ecological networks. Recently Korytowski and Smith (Theor Ecol 8(1):111-120, 2015) proved that a perfectly nested infection network, along with appropriate life history trade-offs, leads to coexistence and persistence of bacteria-phage communities in a chemostat model...
February 20, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28217917/a-comprehensive-phylogenetic-analysis-of-copper-transporting-p1b-atpases-from-bacteria-of-the-rhizobiales-order-uncovers-multiplicity-diversity-and-novel-taxonomic-subtypes
#2
Ciro Cubillas, Fabiola Miranda-Sánchez, Antonio González-Sánchez, José Pedro Elizalde, Pablo Vinuesa, Susana Brom, Alejandro García-de Los Santos
The ubiquitous cytoplasmic membrane copper transporting P1B-1 and P1B-3 -type ATPases pump out Cu(+) and Cu(2+) , respectively, to prevent cytoplasmic accumulation and avoid toxicity. The presence of five copies of Cu-ATPases in the symbiotic nitrogen-fixing bacteria Sinorhizobium meliloti is remarkable; it is the largest number of Cu(+) -transporters in a bacterial genome reported to date. Since the prevalence of multiple Cu-ATPases in members of the Rhizobiales order is unknown, we performed an in silico analysis to understand the occurrence, diversity and evolution of Cu(+) -ATPases in members of the Rhizobiales order...
February 20, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28217741/transcriptome-level-signatures-in-gene-expression-and-gene-expression-variability-during-bacterial-adaptive-evolution
#3
Keesha E Erickson, Peter B Otoupal, Anushree Chatterjee
Antibiotic-resistant bacteria are an increasingly serious public health concern, as strains emerge that demonstrate resistance to almost all available treatments. One factor that contributes to the crisis is the adaptive ability of bacteria, which exhibit remarkable phenotypic and gene expression heterogeneity in order to gain a survival advantage in damaging environments. This high degree of variability in gene expression across biological populations makes it a challenging task to identify key regulators of bacterial adaptation...
January 2017: MSphere
https://www.readbyqxmd.com/read/28217442/whole-genome-sequencing-and-analysis-of-campylobacter-coli-yh502-from-retail-chicken-reveals-a-plasmid-borne-type-vi-secretion-system
#4
Sandeep Ghatak, Yiping He, Sue Reed, Terence Strobaugh, Peter Irwin
Campylobacter is a major cause of foodborne illnesses worldwide. Campylobacter infections, commonly caused by ingestion of undercooked poultry and meat products, can lead to gastroenteritis and chronic reactive arthritis in humans. Whole genome sequencing (WGS) is a powerful technology that provides comprehensive genetic information about bacteria and is increasingly being applied to study foodborne pathogens: e.g., evolution, epidemiology/outbreak investigation, and detection. Herein we report the complete genome sequence of Campylobacter coli strain YH502 isolated from retail chicken in the United States...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28217109/e-coli-group-1-capsular-polysaccharide-exportation-nanomachinary-as-a-plausible-antivirulence-target-in-the-perspective-of-emerging-antimicrobial-resistance
#5
REVIEW
Shivangi Sachdeva, Raghuvamsi V Palur, Karpagam U Sudhakar, Thenmalarchelvi Rathinavelan
Bacteria evolving resistance against the action of multiple drugs and its ability to disseminate the multidrug resistance trait(s) across various strains of the same bacteria or different bacterial species impose serious threat to public health. Evolution of such multidrug resistance is due to the fact that, most of the antibiotics target bacterial survival mechanisms which exert selective pressure on the bacteria and aids them to escape from the action of antibiotics. Nonetheless, targeting bacterial virulence strategies such as bacterial surface associated polysaccharides biosynthesis and their surface accumulation mechanisms may be an attractive strategy, as they impose less selective pressure on the bacteria...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28216008/computational-tools-for-exploring-sequence-databases-as-a-resource-for-antimicrobial-peptides
#6
REVIEW
W F Porto, A S Pires, O L Franco
Data mining has been recognized by many researchers as a hot topic in different areas. In the post-genomic era, the growing number of sequences deposited in databases has been the reason why these databases have become a resource for novel biological information. In recent years, the identification of antimicrobial peptides (AMPs) in databases has gained attention. The identification of unannotated AMPs has shed some light on the distribution and evolution of AMPs and, in some cases, indicated suitable candidates for developing novel antimicrobial agents...
February 12, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28209133/house-spider-genome-uncovers-evolutionary-shifts-in-the-diversity-and-expression-of-black-widow-venom-proteins-associated-with-extreme-toxicity
#7
Kerry L Gendreau, Robert A Haney, Evelyn E Schwager, Torsten Wierschin, Mario Stanke, Stephen Richards, Jessica E Garb
BACKGROUND: Black widow spiders are infamous for their neurotoxic venom, which can cause extreme and long-lasting pain. This unusual venom is dominated by latrotoxins and latrodectins, two protein families virtually unknown outside of the black widow genus Latrodectus, that are difficult to study given the paucity of spider genomes. Using tissue-, sex- and stage-specific expression data, we analyzed the recently sequenced genome of the house spider (Parasteatoda tepidariorum), a close relative of black widows, to investigate latrotoxin and latrodectin diversity, expression and evolution...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28207813/interacting-networks-of-resistance-virulence-and-core-machinery-genes-identified-by-genome-wide-epistasis-analysis
#8
Marcin J Skwark, Nicholas J Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Ying Ying Xu, Paul Turner, Simon R Harris, Stephen B Beres, James M Musser, Julian Parkhill, Stephen D Bentley, Erik Aurell, Jukka Corander
Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus) and Streptococcus pyogenes (group A Streptococcus)...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28205377/culture-independent-genomics-of-a-novel-chlamydial-pathogen-of-fish-provides-new-insight-into-host-specific-adaptations-utilised-by-these-intracellular-bacteria
#9
Alyce Taylor-Brown, Trestan Pillonel, Andrew Bridle, Weihong Qi, Nathan Bachmann, Terrence L Miller, Gilbert Greub, Barbara Nowak, Helena M B Seth-Smith, Lloyd Vaughan, Adam Polkinghorne
Several Chlamydiales families are associated with epitheliocystis, a common condition of the fish gill epithelium. These families share common ancestors with the Chlamydiaceae and environmental Chlamydiae. Due to the lack of culture systems, little is known about the biology of these chlamydial fish pathogens. We investigated epitheliocystis in cultured Orange-spotted grouper (Epinephelus coioides) from North Queensland, Australia. Basophilic inclusions were present in the gills of 22/31 fish and the presence of the chlamydial pathogen in the cysts was confirmed by in situ hybridisation...
February 15, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28203100/from-amino-acids-polymers-antimicrobial-peptides-and-histones-to-their-possible-role-in-the-pathogenesis-of-septic-shock-a-historical-perspective
#10
Isaac Ginsburg, Peter Vernon van Heerden, Erez Koren
This paper describes the evolution of our understanding of the biological role played by synthetic and natural antimicrobial cationic peptides and by the highly basic nuclear histones as modulators of infection, postinfectious sequelae, trauma, and coagulation phenomena. The authors discuss the effects of the synthetic polymers of basic poly α amino acids, poly l-lysine, and poly l-arginine on blood coagulation, fibrinolysis, bacterial killing, and blood vessels; the properties of natural and synthetic antimicrobial cationic peptides as potential replacements or adjuncts to antibiotics; polycations as opsonizing agents promoting endocytosis/phagocytosis; polycations and muramidases as activators of autolytic wall enzymes in bacteria, causing bacteriolysis and tissue damage; and polycations and nuclear histones as potential virulence factors and as markers of sepsis, septic shock, disseminated intravasclar coagulopathy, acute lung injury, pancreatitis, trauma, and other additional clinical disorders...
2017: Journal of Inflammation Research
https://www.readbyqxmd.com/read/28201991/plasmid-diversity-and-phylogenetic-consistency-in-the-lyme-disease-agent-borrelia-burgdorferi
#11
Sherwood R Casjens, Eddie B Gilcrease, Marija Vujadinovic, Emmanuel F Mongodin, Benjamin J Luft, Steven E Schutzer, Claire M Fraser, Wei-Gang Qiu
BACKGROUND: Bacteria from the genus Borrelia are known to harbor numerous linear and circular plasmids. We report here a comparative analysis of the nucleotide sequences of 236 plasmids present in fourteen independent isolates of the Lyme disease agent B. burgdorferi. RESULTS: We have sequenced the genomes of 14 B. burgdorferi sensu stricto isolates that carry a total of 236 plasmids. These individual isolates carry between seven and 23 plasmids. Their chromosomes, the cp26 and cp32 circular plasmids, as well as the lp54 linear plasmid, are quite evolutionarily stable; however, the remaining plasmids have undergone numerous non-homologous and often duplicative recombination events...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28196888/sulfide-responsive-transcriptional-repressor-sqrr-functions-as-a-master-regulator-of-sulfide-dependent-photosynthesis
#12
Takayuki Shimizu, Jiangchuan Shen, Mingxu Fang, Yixiang Zhang, Koichi Hori, Jonathan C Trinidad, Carl E Bauer, David P Giedroc, Shinji Masuda
Sulfide was used as an electron donor early in the evolution of photosynthesis, with many extant photosynthetic bacteria still capable of using sulfur compounds such as hydrogen sulfide (H2S) as a photosynthetic electron donor. Although enzymes involved in H2S oxidation have been characterized, mechanisms of regulation of sulfide-dependent photosynthesis have not been elucidated. In this study, we have identified a sulfide-responsive transcriptional repressor, SqrR, that functions as a master regulator of sulfide-dependent gene expression in the purple photosynthetic bacterium Rhodobacter capsulatus SqrR has three cysteine residues, two of which, C41 and C107, are conserved in SqrR homologs from other bacteria...
February 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28194138/phenotypic-microdiversity-and-phylogenetic-signal-analysis-of-traits-related-to-social-interaction-in-bacillus-spp-from-sediment-communities
#13
Dolores María Rodríguez-Torres, África Islas-Robles, Zulema Gómez-Lunar, Luis Delaye, Ismael Hernández-González, Valeria Souza, Michael Travisano, Gabriela Olmedo-Álvarez
Understanding the relationship between phylogeny and predicted traits is important to uncover the dimension of the predictive power of a microbial composition approach. Numerous works have addressed the taxonomic composition of bacteria in communities, but little is known about trait heterogeneity in closely related bacteria that co-occur in communities. We evaluated a sample of 467 isolates from the Churince water system of the Cuatro Cienegas Basin (CCB), enriched for Bacillus spp. The 16S rRNA gene revealed a random distribution of taxonomic groups within this genus among 11 sampling sites...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28193877/origin-of-microbial-biomineralization-and-magnetotaxis-during-the-archean
#14
Wei Lin, Greig A Paterson, Qiyun Zhu, Yinzhao Wang, Evguenia Kopylova, Ying Li, Rob Knight, Dennis A Bazylinski, Rixiang Zhu, Joseph L Kirschvink, Yongxin Pan
Microbes that synthesize minerals, a process known as microbial biomineralization, contributed substantially to the evolution of current planetary environments through numerous important geochemical processes. Despite its geological significance, the origin and evolution of microbial biomineralization remain poorly understood. Through combined metagenomic and phylogenetic analyses of deep-branching magnetotactic bacteria from the Nitrospirae phylum, and using a Bayesian molecular clock-dating method, we show here that the gene cluster responsible for biomineralization of magnetosomes, and the arrangement of magnetosome chain(s) within cells, both originated before or near the Archean divergence between the Nitrospirae and Proteobacteria This phylogenetic divergence occurred well before the Great Oxygenation Event...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28192724/enhancing-ammonium-oxidizing-bacteria-activity-was-key-to-single-stage-partial-nitrification-anammox-system-treating-low-strength-sewage-under-intermittent-aeration-condition
#15
Yuanyuan Miao, Liang Zhang, Baikun Li, Qian Zhang, Simeng Wang, Yongzhen Peng
Intermittent aeration and bio-augmentation were integrated to enhance single-stage partial nitrification-anammox (SPN/A) stability over 235-day operational period treating low-strength sewage. The effect of bio-augmentation sludge (with different abundances of ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB)) was determined. Partial nitrification sludge based bio-augmentation increased the total nitrogen (TN) removal efficiency from 29.1% to 70%, followed by the nitrification sludge (from 38...
January 27, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28192410/an-orthogonalized-platform-for-genetic-code-expansion-in-both-bacteria-and-eukaryotes
#16
James S Italia, Partha Sarathi Addy, Chester J J Wrobel, Lisa A Crawford, Marc J Lajoie, Yunan Zheng, Abhishek Chatterjee
In this study, we demonstrate the feasibility of expanding the genetic code of Escherichia coli using its own tryptophanyl-tRNA synthetase and tRNA (TrpRS-tRNA(Trp)) pair. This was made possible by first functionally replacing this endogenous pair with an E. coli-optimized counterpart from Saccharomyces cerevisiae, and then reintroducing the liberated E. coli TrpRS-tRNA(Trp) pair into the resulting strain as a nonsense suppressor, which was then followed by its directed evolution to genetically encode several new unnatural amino acids (UAAs)...
February 13, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28192223/emergence-of-multi-drug-resistance-among-soil-bacteria-exposing-to-insecticides
#17
Kirubakaran Rangasamy, Murugan Athiappan, Natarajan Devarajan, Javid A Parray
Impacts of pesticide exposure on the soil microbial flora and cross resistance to antibiotics have not been well documented. Development of antibiotic resistance is a common issue among soil bacteria which are exposing to pesticides continuously at sub-lethal concentration. The present study was focused to evaluate the correlation between pesticide exposures and evolution of multi drug resistance among isolates collected from soil applied with insecticides. Twenty five insecticide (Monochrotophos) degrading bacteria were isolated from contaminated agricultural soil...
February 9, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28188295/myroilysin-is-a-new-bacterial-member-of-the-m12a-family-of-metzincin-metallopeptidases-and-activated-by-a-cysteine-switch-mechanism
#18
Dongqing Xu, Jiale Zhou, Xiangdi Lou, Jianhua He, Tingting Ran, Weiwu Wang
Proteases play important roles in all living organisms and also have important industrial applications. Family M12A metalloproteases, mainly found throughout the animal kingdom, belong to the metzincin protease family and are synthesized as inactive precursors. So far, only flavastacin and myroilysin, isolated from bacteria, were reported to be M12A proteases, whilst the classification of myroilysin is still conflicting due to the lack of structural information. Here, we report the crystal structures of pro-myroilysin from bacterium Myroides sp...
February 9, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28188144/elevated-rate-of-genome-rearrangements-in-radiation-resistant-bacteria
#19
Jelena Repar, Fran Supek, Tin Klanjscek, Tobias Warnecke, Ksenija Zahradka, Davor Zahradka
A number of bacterial, archaeal, and eukaryotic species are known for their resistance to ionizing radiation. One of the challenges these species face is a potent environmental source of DNA double-strand breaks, potential drivers of genome structure evolution. Efficient and accurate DNA double-strand break repair systems have been demonstrated in several unrelated radiation-resistant species and are putative adaptations to the DNA damaging environment. Such adaptations are expected to compensate for the genome-destabilizing effect of environmental DNA damage and may be expected to result in a more conserved gene order in radiation-resistant species...
February 10, 2017: Genetics
https://www.readbyqxmd.com/read/28183996/antibiotic-tolerance-facilitates-the-evolution-of-resistance
#20
Irit Levin-Reisman, Irine Ronin, Orit Gefen, Ilan Braniss, Noam Shoresh, Nathalie Q Balaban
Controlled experimental evolution during antibiotic treatment can shed light on the processes leading to antibiotic resistance in bacteria. Recently, intermittent antibiotic exposures have been shown to lead rapidly to the evolution of tolerance, i.e., the ability to survive under treatment without developing resistance. However, whether tolerance delays or promotes the eventual emergence of resistance is unclear. Here, we used in vitro evolution experiments to explore this question. We found that in all cases tolerance preceded resistance...
February 9, 2017: Science
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