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Bacteria evolution

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https://www.readbyqxmd.com/read/29150506/the-swinholide-biosynthetic-gene-cluster-from-a-terrestrial-cyanobacterium-nostoc-sp-uhcc-0450
#1
Anu Humisto, Jouni Jokela, Liwei Liu, Matti Wahlsten, Hao Wang, Perttu Permi, João Paulo Machado, Agostinho Antunes, David P Fewer, Kaarina Sivonen
Swinholides are 42-carbon ring polyketides with a twofold axis of symmetry. They are potent cytotoxins that disrupt the actin cytoskeleton. Swinholides were discovered from the marine sponge Theonella sp. and were long-suspected to be produced by symbiotic bacteria. Misakinolide, a structural variant of swinholide, was recently demonstrated to be the product of the symbiotic heterotrophic proteobacterium. Here we report the production of swinholide A by an axenic strain of the terrestrial cyanobacterium Nostoc sp...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29149207/evolution-of-the-metabolome-in-response-to-selection-for-increased-immunity-in-populations-of-drosophila-melanogaster
#2
Navdeep Gogna, Rakesh Sharma, Vanika Gupta, Kavita Dorai, N G Prasad
We used NMR-based metabolomics to test two hypotheses-(i) there will be evolved differences in the metabolome of selected and control populations even under un-infected conditions and (ii) post infection, the metabolomes of the selected and control populations will respond differently. We selected replicate populations of Drosophila melanogaster for increased survivorship (I) against a gram-negative pathogen. We subjected the selected (I) and their control populations (S) to three different treatments: (1) infected with heat-killed bacteria (i), (2) sham infected (s), and (3) untreated (u)...
2017: PloS One
https://www.readbyqxmd.com/read/29147114/antibiotic-resistant-bacterial-isolates-from-captive-green-turtles-and-in-vitro-sensitivity-to-bacteriophages
#3
Alessandro Delli Paoli Carini, Ellen Ariel, Jacqueline Picard, Lisa Elliott
This study aimed to test multidrug resistant isolates from hospitalised green turtles (Chelonia mydas) and their environment in North Queensland, Australia, for in vitro susceptibility to bacteriophages. Seventy-one Gram-negative bacteria were isolated from green turtle eye swabs and water samples. Broth microdilution tests were used to determine antibiotic susceptibility. All isolates were resistant to at least two antibiotics, with 24% being resistant to seven of the eight antibiotics. Highest resistance rates were detected to enrofloxacin (77%) and ampicillin (69...
2017: International Journal of Microbiology
https://www.readbyqxmd.com/read/29146443/differential-responses-of-a-thioredoxin-like-protein-gene-to-vibrio-parahaemolyticus-challenge-in-the-noble-scallop-chlamys-nobilis-with-different-total-carotenoids-content
#4
Hongkuan Zhang, Dewei Cheng, Hongxing Liu, Huaiping Zheng
Being lack of specific immune system, both enzymes and non-enzymatic antioxidants play crucial roles in immune of invertebrates. In the present study, in order to investigate immune roles of enzyme (thioredoxin, TRX) and antioxidants (carotenoids), Golden scallops with golden shell and golden muscle rich in carotenoids content and Brown scallops with brown shell and white muscle less carotenoids content of the noble scallop Chlamys nobilis were challenged by Vibrio parahaemolyticus for 48 h. Firstly, a cDNA of TRX protein gene from the scallop (named as CnTRX) was cloned and characterized...
November 13, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29145803/unraveling-the-evolution-and-coevolution-of-small-regulatory-rnas-and-coding-genes-in-listeria
#5
Franck Cerutti, Ludovic Mallet, Anaïs Painset, Claire Hoede, Annick Moisan, Christophe Bécavin, Mélodie Duval, Olivier Dussurget, Pascale Cossart, Christine Gaspin, Hélène Chiapello
BACKGROUND: Small regulatory RNAs (sRNAs) are widely found in bacteria and play key roles in many important physiological and adaptation processes. Studying their evolution and screening for events of coevolution with other genomic features is a powerful way to better understand their origin and assess a common functional or adaptive relationship between them. However, evolution and coevolution of sRNAs with coding genes have been sparsely investigated in bacterial pathogens. RESULTS: We designed a robust and generic phylogenomics approach that detects correlated evolution between sRNAs and protein-coding genes using their observed and inferred patterns of presence-absence in a set of annotated genomes...
November 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29139344/aeropyrum-pernix-membrane-topology-of-protein-vkor-promotes-protein-disulfide-bond-formation-in-two-subcellular-compartments
#6
Stijntje Hibender, Cristina Landeta, Mehmet Berkmen, Jon Beckwith, Dana Boyd
Disulfide bonds confer stability and activity to proteins. Bioinformatic approaches allow predictions of which organisms make protein disulfide bonds and in which subcellular compartments disulfide bond formation takes place. Such an analysis, along with biochemical and protein structural data, suggests that many of the extremophile Crenarachaea make protein disulfide bonds in both the cytoplasm and the cell envelope. We have sought to determine the oxidative folding pathways in the sequenced genomes of the Crenarchaea, by seeking homologues of the enzymes known to be involved in disulfide bond formation in bacteria...
November 15, 2017: Microbiology
https://www.readbyqxmd.com/read/29138003/serine-threonine-protein-kinases-from-bacteria-archaea-and-eukarya-share-a-common-evolutionary-origin-deeply-rooted-in-the-tree-of-life
#7
Ivan Andreas Stancik, Martin Sebastijan Šestak, Boyang Ji, Marina Axelson-Fisk, Damjan Franjevic, Carsten Jers, Tomislav Domazet-Lošo, Ivan Mijakovic
The main family of serine/threonine/tyrosine protein kinases present in eukarya was defined and described by Hanks et al. in 1988. It was initially believed that these kinases do not exist in bacteria, but extensive genome sequencing revealed their existence in many bacteria. For historical reasons, the term "eukaryotic-type kinases" propagated in the literature to describe bacterial members of this protein family. Here, we argue that this term should be abandoned as a misnomer, and we provide several lines of evidence to support this claim...
November 11, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29136611/gut-microbiota-in-health-and-disease
#8
Yuichiro Yamashiro
Intestinal regulatory T (Treg) cells are critical to maintaining immune tolerance to dietary antigens and gut microbiota. This paper reviews several papers on this topic that were recently published by Japanese researchers. Specifically, Prof. K. Honda and his group have found that commensal microbiota capable of metabolizing butyrate induces the differentiation of colonic Treg cells. In a separate work, Prof. Y. Yokoyama and his group used a novel, culture-independent analytical method (the Yakult Intestinal Flora-Scan) for detection of bacteria in the bloodstream...
November 14, 2017: Annals of Nutrition & Metabolism
https://www.readbyqxmd.com/read/29133443/the-thermodynamic-efficiency-of-computations-made-in-cells-across-the-range-of-life
#9
Christopher P Kempes, David Wolpert, Zachary Cohen, Juan Pérez-Mercader
Biological organisms must perform computation as they grow, reproduce and evolve. Moreover, ever since Landauer's bound was proposed, it has been known that all computation has some thermodynamic cost-and that the same computation can be achieved with greater or smaller thermodynamic cost depending on how it is implemented. Accordingly an important issue concerning the evolution of life is assessing the thermodynamic efficiency of the computations performed by organisms. This issue is interesting both from the perspective of how close life has come to maximally efficient computation (presumably under the pressure of natural selection), and from the practical perspective of what efficiencies we might hope that engineered biological computers might achieve, especially in comparison with current computational systems...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29131360/bacterial-diversity-and-community-structure-during-fermentation-of-chinese-sauerkraut-with-lactobacillus-casei-11mz-5-1-by-illumina-miseq-sequencing
#10
Renpeng Du, Gang Song, Dan Zhao, Jian Sun, Wenxiang Ping, Jingping Ge
The bacterial diversity and community structure involved in Chinese sauerkraut is one of the most important factors shaping the final characteristics of traditional foods. In this research, Lactobacillus casei 11MZ-5-1 was applied in Chinese sauerkraut fermentation as a starter culture. Illumina Miseq sequencing analysis was used to reveal the bacterial diversity and community structure during Chinese sauerkraut fermentation. A total of 177283 high quality reads of 16S rRNA V4 regions were obtained. The inoculation of L...
November 13, 2017: Letters in Applied Microbiology
https://www.readbyqxmd.com/read/29129755/phylogenetic-analysis-predicts-structural-divergence-for-proteobacterial-clpc-proteins
#11
Justin M Miller, Hamza Chaudhary, Justin D Marsee
Regulated proteolysis is required in all organisms for the removal of misfolded or degradation-tagged protein substrates in cellular quality control pathways. The molecular machines that catalyze this process are known as ATP-dependent proteases with examples that include ClpAP and ClpCP. Clp/Hsp100 subunits form ring-structures that couple the energy of ATP binding and hydrolysis to protein unfolding and subsequent translocation of denatured protein into the compartmentalized ClpP protease for degradation...
November 9, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/29129605/evolution-and-adaptation-of-single-pass-transmembrane-proteins
#12
Irina D Pogozheva, Andrei L Lomize
A comparative analysis of 6,039 single-pass (bitopic) membrane proteins from six evolutionarily distant organisms was performed based on data from the Membranome database. The observed repertoire of bitopic proteins is significantly enlarged in eukaryotic cells and especially in multicellular organisms due to the diversification of enzymes, emergence of proteins involved in vesicular trafficking, and expansion of receptors, structural, and adhesion proteins. The majority of bitopic proteins in multicellular organisms are located in the plasma membrane (PM) and involved in cell communication...
November 9, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29128642/the-evolution-of-metabolic-regulation-in-animals
#13
Frank Seebacher
Energy metabolism is determined by a suite of regulatory mechanism, and their increasing complexity over evolutionary time provides the key to understanding the emergence of different metabolic phenotypes. Energy metabolism is at the core of biological processes because all organisms must maintain energy balance against thermodynamic gradients. Energy metabolism is regulated by a bewildering array of interacting molecular mechanisms, and much of what is known about metabolic regulation comes from the medical literature...
November 8, 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/29126700/structure-and-function-of-haemoglobins
#14
REVIEW
David A Gell
Haemoglobin (Hb) is widely known as the iron-containing protein in blood that is essential for O2 transport in mammals. Less widely recognised is that erythrocyte Hb belongs to a large family of Hb proteins with members distributed across all three domains of life-bacteria, archaea and eukaryotes. This review, aimed chiefly at researchers new to the field, attempts a broad overview of the diversity, and common features, in Hb structure and function. Topics include structural and functional classification of Hbs; principles of O2 binding affinity and selectivity between O2/NO/CO and other small ligands; hexacoordinate (containing bis-imidazole coordinated haem) Hbs; bacterial truncated Hbs; flavohaemoglobins; enzymatic reactions of Hbs with bioactive gases, particularly NO, and protection from nitrosative stress; and, sensor Hbs...
October 31, 2017: Blood Cells, Molecules & Diseases
https://www.readbyqxmd.com/read/29126241/lactobacillus-backii-and-pediococcus-damnosus-isolated-from-170-year-old-beer-recovered-from-a-shipwreck-lack-the-metabolic-activities-required-to-grow-in-modern-lager-beer
#15
Ilkka Kajala, Jordyn Bergsveinson, Vanessa Friesen, Anna Redekop, Riikka Juvonen, Erna Storgårds, Barry Ziola
In 2010, bottles of beer containing viable bacteria of the common beer-spoilage species Lactobacillus backii and Pediococcus damnosus were recovered from a shipwreck near the Åland Islands, Finland. The 170-year quiescent state maintained by the shipwreck bacteria presented a unique opportunity to study lactic acid bacteria (LAB) evolution vis a vis growth and survival in the beer environment. Three shipwreck bacteria (one L. backii strain and two P. damnosus strains) and modern-day beer-spoilage isolates of the same two species were genome sequenced, characterized for hop iso-α-acid tolerance, and growth in degassed lager and wheat beer...
November 8, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29120463/compartmentalized-partnered-replication-for-the-directed-evolution-of-genetic-parts-and-circuits
#16
Zhanar Abil, Jared W Ellefson, Jimmy D Gollihar, Ella Watkins, Andrew D Ellington
Compartmentalized partnered replication (CPR) is an emulsion-based directed evolution method based on a robust and modular phenotype-genotype linkage. In contrast to other in vivo directed evolution approaches, CPR largely mitigates host fitness effects due to a relatively short expression time of the gene of interest. CPR is based on gene circuits in which the selection of a 'partner' function from a library leads to the production of a thermostable polymerase. After library preparation, bacteria produce partner proteins that can potentially lead to enhancement of transcription, translation, gene regulation, and other aspects of cellular metabolism that reinforce thermostable polymerase production...
December 2017: Nature Protocols
https://www.readbyqxmd.com/read/29118137/defector-clustering-is-linked-to-cooperation-in-a-pathogenic-bacterium
#17
Edward W Tekwa, Dao Nguyen, Michel Loreau, Andrew Gonzalez
Spatial clustering is thought to favour the evolution of cooperation because it puts cooperators in a position to help each other. However, clustering also increases competition. The fate of cooperation may depend on how much cooperators cluster relative to defectors, but these clustering differences have not been the focus of previous models and experiments. By competing siderophore-producing cooperator and defector strains of the opportunistic pathogen Pseudomonas aeruginosa in experimental microhabitats, we found that at the spatial scale of individual interactions, cooperator clustering lowers cooperation, but defector clustering favours cooperation...
November 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29116640/strain-diversity-and-the-evolution-of-antibiotic-resistance
#18
Sonia Borrell, Andrej Trauner
Drug resistance is best thought of as an ongoing biological process. Resistant bacteria must emerge, become established and ultimately transmit in order to be relevant to human health. In this context, genetic diversity can influence the rate and likelihood of resistance emerging; it can also modulate the net physiological impact of resistance and the propensity of an organism to improve any defects that arise from it. Combined, these effects can have an impact on a larger scale, with highly transmissible drug-resistant bacterial strains posing a formidable threat to global health...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29114218/periodontitis-microbiomes-and-their-role-in-alzheimer-s-disease
#19
Anna B Pritchard, StJohn Crean, Ingar Olsen, Sim K Singhrao
As far back as the eighteenth and early nineteenth centuries, microbial infections were responsible for vast numbers of deaths. The trend reversed with the introduction of antibiotics coinciding with longer life. Increased life expectancy however, accompanied the emergence of age related chronic inflammatory states including the sporadic form of Alzheimer's disease (AD). Taken together, the true challenge of retaining health into later years of life now appears to lie in delaying and/or preventing the progression of chronic inflammatory diseases, through identifying and influencing modifiable risk factors...
2017: Frontiers in Aging Neuroscience
https://www.readbyqxmd.com/read/29114057/directed-evolution-of-secb-chaperones-toward-toxin-antitoxin-systems
#20
Ambre Julie Sala, Patricia Bordes, Sara Ayala, Nawel Slama, Samuel Tranier, Michèle Coddeville, Anne-Marie Cirinesi, Marie-Pierre Castanié-Cornet, Lionel Mourey, Pierre Genevaux
SecB chaperones assist protein export in bacteria. However, certain SecB family members have diverged to become specialized toward the control of toxin-antitoxin (TA) systems known to promote bacterial adaptation to stress and persistence. In such tripartite TA-chaperone (TAC) systems, the chaperone was shown to assist folding and to prevent degradation of its cognate antitoxin, thus facilitating inhibition of the toxin. Here, we used both the export chaperone SecB of Escherichia coli and the tripartite TAC system of Mycobacterium tuberculosis as a model to investigate how generic chaperones can specialize toward the control of TA systems...
November 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
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