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bacteria clock

Tanai Cardona, Patricia Sánchez-Baracaldo, A William Rutherford, Anthony W Larkum
Photosystem II is a photochemical reaction center that catalyzes the light-driven oxidation of water to molecular oxygen. Water oxidation is the distinctive photochemical reaction that permitted the evolution of oxygenic photosynthesis and the eventual rise of eukaryotes. At what point during the history of life an ancestral photosystem evolved the capacity to oxidize water still remains unknown. Here, we study the evolution of the core reaction center proteins of Photosystem II using sequence and structural comparisons in combination with Bayesian relaxed molecular clocks...
November 9, 2018: Geobiology
Michele Monti, David K Lubensky, Pieter Rein Ten Wolde
To estimate the time, many organisms, ranging from cyanobacteria to animals, employ a circadian clock which is based on a limit-cycle oscillator that can tick autonomously with a nearly 24 h period. Yet, a limit-cycle oscillator is not essential for knowing the time, as exemplified by bacteria that possess an "hourglass": a system that when forced by an oscillatory light input exhibits robust oscillations from which the organism can infer the time, but that in the absence of driving relaxes to a stable fixed point...
August 17, 2018: Physical Review Letters
Prassanna Rao, Tania A Rozgaja, Abdulaziz Alqahtani, Julia E Grimwade, Alan C Leonard
Although the mechanisms that precisely time initiation of chromosome replication in bacteria remain unclear, most clock models are based on accumulation of the active initiator protein, DnaA-ATP. During each cell division cycle, sufficient DnaA-ATP must become available to interact with a distinct set of low affinity recognition sites in the unique chromosomal replication origin, oriC , and assemble the pre-replicative complex (orisome) that unwinds origin DNA and helps load the replicative helicase. The low affinity oriC -DnaA-ATP interactions are required for the orisome's mechanical functions, and may also play a role in timing of new rounds of DNA synthesis...
2018: Frontiers in Microbiology
Ayodeji O Olakanye, T Komang Ralebitso-Senior
To gain a better understanding of how environmental microbiota respond to cadaver decomposition, a forensic ecogenomic study was made with soil only control and 4g each of Sus scrofa domesticus and plant litter (Agrostis/Festuca spp.) buried individually in a sandy clay loam (80g) in sealed but perforated triplicate microcosms. The next-generation sequencing (Illumina Miseq) of the soil bacteria (16S rRNA gene) clade revealed seasonal taxomonic shifts at genus-level for the pig and plant litter microcosms compared to the non-burial controls...
July 2018: Forensic Science International
Adrián A Davín, Eric Tannier, Tom A Williams, Bastien Boussau, Vincent Daubin, Gergely J Szöllősi
Biodiversity has always been predominantly microbial, and the scarcity of fossils from bacteria, archaea and microbial eukaryotes has prevented a comprehensive dating of the tree of life. Here, we show that patterns of lateral gene transfer deduced from an analysis of modern genomes encode a novel and abundant source of information about the temporal coexistence of lineages throughout the history of life. We use state-of-the-art species tree-aware phylogenetic methods to reconstruct the history of thousands of gene families and demonstrate that dates implied by gene transfers are consistent with estimates from relaxed molecular clocks in Bacteria, Archaea and Eukarya...
May 2018: Nature Ecology & Evolution
Vincent Lôme, Jean-Michel Brunel, Jean-Marie Pagès, Jean-Michel Bolla
Antibiotic resistance is now a worldwide therapeutic problem. Since the beginning of anti-infectious treatment bacteria have rapidly shown an incredible ability to develop and transfer resistance mechanisms. In the last decades, the design variation of pioneer bioactive molecules has strongly improved their activity and the pharmaceutical companies partly won the race against the clock. Since the 1980s, the new classes of antibiotics that emerged were mainly directed to Gram-positive bacteria. Thus, we are now facing to multidrug-resistant Gram-negative bacteria, with no therapeutic options to deal with them...
2018: Frontiers in Microbiology
Hadi Taghvafard, Hildeberto Jardón-Kojakhmetov, Ming Cao
We develop a tool based on bifurcation analysis for parameter-robustness analysis for a class of oscillators and, in particular, examine a biochemical oscillator that describes the transition phase between social behaviours of myxobacteria. Myxobacteria are a particular group of soil bacteria that have two dogmatically different types of social behaviour: when food is abundant they live fairly isolated forming swarms, but when food is scarce, they aggregate into a multicellular organism. In the transition between the two types of behaviours, spatial wave patterns are produced, which is generally believed to be regulated by a certain biochemical clock that controls the direction of myxobacteria's motion...
January 2018: Proceedings. Mathematical, Physical, and Engineering Sciences
C Magnabosco, K R Moore, J M Wolfe, G P Fournier
Phototrophic bacteria are among the most biogeochemically significant organisms on Earth and are physiologically related through the use of reaction centers to collect photons for energy metabolism. However, the major phototrophic lineages are not closely related to one another in bacterial phylogeny, and the origins of their respective photosynthetic machinery remain obscured by time and low sequence similarity. To better understand the co-evolution of Cyanobacteria and other ancient anoxygenic phototrophic lineages with respect to geologic time, we designed and implemented a variety of molecular clocks that use horizontal gene transfer (HGT) as additional, relative constraints...
March 2018: Geobiology
Tingting Guo, Yongping Xin, Chenchen Zhang, Jian Kong
In double-stranded DNA bacteriophages, infection cycles are ended by host cell lysis through the action of phage-encoded endolysins and holins. The precise timing of lysis is regulated by the holin inhibitors, named antiholins. Sequence analysis has revealed that holins with a single transmembrane domain (TMD) are prevalent in Lactobacillus bacteriophages. A temperate bacteriophage of Lactobacillus fermentum , ϕPYB5, has a two-component lysis cassette containing endolysin Lyb5 and holin Hyb5. The hyb5 gene is 465 bp long, encoding 154 amino acid residues with an N-terminal TMD and a large cytoplasmic C-terminal domain...
March 15, 2018: Applied and Environmental Microbiology
Kira S Makarova, Michael Y Galperin, Eugene V Koonin
All organisms must adapt to ever-changing environmental conditions and accordingly have evolved diverse signal transduction systems. In bacteria, the most abundant networks are built around the two-component signal transduction systems that include histidine kinases and receiver domains. In contrast, eukaryotic signal transduction is dominated by serine/threonine/tyrosine protein kinases. Both of these systems are also found in archaea, but they are not as common and diversified as their bacterial and eukaryotic counterparts, suggesting the possibility that archaea have evolved other, still uncharacterized signal transduction networks...
December 5, 2017: MBio
Yasmine M Cissé, Jeremy C Borniger, Elise Lemanski, William H Walker, Randy J Nelson
An important entraining signal for the endogenous circadian clock, independent of light, is food intake. The circadian and immune systems are linked; forced desynchrony of the circadian clock via nighttime light exposure or genetic ablation of core clock components impairs immune function. The timing of food intake affects various aspects of the circadian clock, but its effects on immune function are unknown. We tested the hypothesis that temporal desynchrony of food intake alters innate immune responses. Adult male Swiss Webster mice were provided with food during the night, the day, or ad libitum for 4 wk, followed by administration of LPS prior to the onset of either the active phase (zeitgeber time [ZT]12: Experiment 1) or the inactive phase (ZT0: Experiment 2)...
January 15, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
Albert Goldbeter
Sustained oscillations abound in biological systems. They occur at all levels of biological organization over a wide range of periods, from a fraction of a second to years, and with a variety of underlying mechanisms. They control major physiological functions, and their dysfunction is associated with a variety of physiological disorders. The goal of this review is (i) to give an overview of the main rhythms observed at the cellular and supracellular levels, (ii) to briefly describe how the study of biological rhythms unfolded in the course of time, in parallel with studies on chemical oscillations, (iii) to present the major roles of biological rhythms in the control of physiological functions, and (iv) the pathologies associated with the alteration, disappearance, or spurious occurrence of biological rhythms...
October 2017: Chaos
Jessica Handke, Noemi Procopio, Michael Buckley, Dieudonne van der Meer, Graham Williams, Martin Carr, Anna Williams
AIMS: Bacteria are considered one of the major driving forces of the mammalian decomposition process and have only recently been recognised as forensic tools. At this point, little is known about their potential use as 'post-mortem clocks'. This study aimed to establish the proof of concept for using bacterial identification as post-mortem interval (PMI) indicators, using a multi-omics approach. METHODS AND RESULTS: Pieces of pork were placed in the University's outdoor facility and surface swabs were taken at regular intervals up to 60 days...
December 2017: Forensic Science International
Andreas Neueder, Theresa A Gipson, Sophie Batterton, Hayley J Lazell, Pamela P Farshim, Paolo Paganetti, David E Housman, Gillian P Bates
The heat shock response (HSR) is a mechanism to cope with proteotoxic stress by inducing the expression of molecular chaperones and other heat shock response genes. The HSR is evolutionarily well conserved and has been widely studied in bacteria, cell lines and lower eukaryotic model organisms. However, mechanistic insights into the HSR in higher eukaryotes, in particular in mammals, are limited. We have developed an in vivo heat shock protocol to analyze the HSR in mice and dissected heat shock factor 1 (HSF1)-dependent and -independent pathways...
October 2, 2017: Scientific Reports
Nicolas M Schmelling, Robert Lehmann, Paushali Chaudhury, Christian Beck, Sonja-Verena Albers, Ilka M Axmann, Anika Wiegard
BACKGROUND: Circadian clocks are found in organisms of almost all domains including photosynthetic Cyanobacteria, whereby large diversity exists within the protein components involved. In the model cyanobacterium Synechococcus elongatus PCC 7942 circadian rhythms are driven by a unique KaiABC protein clock, which is embedded in a network of input and output factors. Homologous proteins to the KaiABC clock have been observed in Bacteria and Archaea, where evidence for circadian behavior in these domains is accumulating...
July 21, 2017: BMC Evolutionary Biology
Christopher Staley, Abigail P Ferrieri, Malak M Tfaily, Yaya Cui, Rosalie K Chu, Ping Wang, Jared B Shaw, Charles K Ansong, Heather Brewer, Angela D Norbeck, Meng Markillie, Fernanda do Amaral, Thalita Tuleski, Tomás Pellizzaro, Beverly Agtuca, Richard Ferrieri, Susannah G Tringe, Ljiljana Paša-Tolić, Gary Stacey, Michael J Sadowsky
BACKGROUND: The circadian clock regulates plant metabolic functions and is an important component in plant health and productivity. Rhizosphere bacteria play critical roles in plant growth, health, and development and are shaped primarily by soil communities. Using Illumina next-generation sequencing and high-resolution mass spectrometry, we characterized bacterial communities of wild-type (Col-0) Arabidopsis thaliana and an acyclic line (OX34) ectopically expressing the circadian clock-associated cca1 transcription factor, relative to a soil control, to determine how cycling dynamics affected the microbial community...
June 24, 2017: Microbiome
Utpal Bhadra, Nirav Thakkar, Paromita Das, Manika Pal Bhadra
The human body persists in its rhythm as per its initial time zone, and transition always occur according to solar movements around the earth over 24 h. While traveling across different latitudes and longitudes, at the pace exceeding the earth's movement, the changes in the external cues exceed the level of toleration of the body's biological clock. This poses an alteration in our physiological activities of sleep-wake pattern, mental alertness, organ movement, and eating habits, causing them to temporarily lose the track of time...
July 2017: Sleep Medicine
Bradon R McDonald, Cameron R Currie
Lateral gene transfer (LGT) profoundly shapes the evolution of bacterial lineages. LGT across disparate phylogenetic groups and genome content diversity between related organisms suggest a model of bacterial evolution that views LGT as rampant and promiscuous. It has even driven the argument that species concepts and tree-based phylogenetics cannot be applied to bacteria. Here, we show that acquisition and retention of genes through LGT are surprisingly rare in the ubiquitous and biomedically important bacterial genus Streptomyces Using a molecular clock, we estimate that the Streptomyces bacteria are ~380 million years old, indicating that this bacterial genus is as ancient as land vertebrates...
June 6, 2017: MBio
Luis Delaye, Cecilio Valadez-Cano, Bernardo Pérez-Zamorano
The ancestor of Paulinella chromatophora established a symbiotic relationship with cyanobacteria related to the Prochloroccocus/Synechococcus clade. This event has been described as a second primary endosymbiosis leading to a plastid in the making. Based on the rate of pseudogene disintegration in the endosymbiotic bacteria Buchnera aphidicola, it was suggested that the chromatophore in P. chromatophora has a minimum age of ~60 Myr. Here we revisit this estimation by using a lognormal relaxed molecular clock on the 18S rRNA of P...
March 15, 2016: PLoS Currents
Jingqiu Liao, Martin Wiedmann, Jasna Kovac
Sequencing of single genes remains an important tool that allows the rapid classification of bacteria. Sequencing of a portion of sigB , which encodes a stress-responsive alternative sigma factor, has emerged as a commonly used molecular tool for the initial characterization of diverse Listeria isolates. In this study, evolutionary approaches were used to assess the validity of sigB allelic typing for Listeria For a data set of 4,280 isolates, sigB allelic typing showed a Simpson's index of diversity of 0.96...
June 15, 2017: Applied and Environmental Microbiology
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