Complete nitrification by a single microorganism (Comammox)

Nitrification is a two-step process where ammonia is first oxidized to nitrite by ammonia-oxidizing bacteria and/or archaea, and subsequently to nitrate by nitrite-oxidizing bacteria. Already described by Winogradsky in 1890, this division of labour between the two functional groups is a generally accepted characteristic of the biogeochemical nitrogen cycle. Complete oxidation of ammonia to nitrate in one organism (complete ammonia oxidation; comammox) is energetically feasible, and it was postulated that this process could occur under conditions selecting for species with lower growth rates but higher growth yields than canonical ammonia-oxidizing microorganisms. Still, organisms catalysing this process have not yet been discovered. Here we report the enrichment and initial characterization of two Nitrospira species that encode all the enzymes necessary for ammonia oxidation via nitrite to nitrate in their genomes, and indeed completely oxidize ammonium to nitrate to conserve energy. Their ammonia monooxygenase (AMO) enzymes are phylogenetically distinct from currently identified AMOs, rendering recent acquisition by horizontal gene transfer from known ammonia-oxidizing microorganisms unlikely. We also found highly similar amoA sequences (encoding the AMO subunit A) in public sequence databases, which were apparently misclassified as methane monooxygenases. This recognition of a novel amoA sequence group will lead to an improved understanding of the environmental abundance and distribution of ammonia-oxidizing microorganisms. Furthermore, the discovery of the long-sought-after comammox process will change our perception of the nitrogen cycle.



a, Co-aggregation of Nitrospira and Brocadia in the enrichment. Cells are stained by FISH with probes for all bacteria (EUB338mix, blue), and specific for Nitrospira (Ntspa712, green, resulting in cyan) and anammox bacteria (Amx820, red, resulting in magenta). b, AMO labelling by FTCP (green). Nitrospira was counterstained by FISH (probes Ntspa662 (blue) and Ntspa476 (red), resulting in white). c, Ammonium-dependent CO₂ fixation by Nitrospira shown by FISH-MAR. Silver grain deposition (black) above cell clusters indicates ¹⁴CO₂ incorporation. Nitrospira was stained by FISH (probes Ntspa476 (red) and Ntspa662 (blue), resulting in magenta). Images in b and c are representative of two individual experiments, with three (b) or two (c) technical replicates each. Scale bars in all panels represent 10 μm.

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¿Cómo cultivar microorganismos no cultivables?

Many microorganisms are "unculturable," or at least not able to grow in known media. Now, a new tool enables researchers to predict what nutrients organisms need to thrive in the lab, eliminating most of the guesswork involved in setting up new cultures. Read more...

Studying microbes has provided unparalleled insights into the molecular mechanisms governing cell functions, but expanding on such studies with new microbes depends on finding the right media for culturing the bacteria. Now, Matthew Oberhardt, a postdoctoral fellow at the Center for Bioinformatics and Computational Biology at the University of Maryland, and his colleagues present a new way to approach these “unculturables” in the journal Nature Communications.

“We had a very simple question in mind. Could we try to predict the minimal media needed to actually grow organisms?” he said. To find the answer, Oberhardt and his fellow researchers turned to the Leibniz Institute German Collection of Microorganisms and Cell Cultures, which hosts a repository of around 1300 media recipes for 23,000 microbes. “We thought that we might be able to extract a lot of information and create a new paradigm where we could do some predictive modeling.”
The team combed through recipe files and extracted details such as ingredient lists and salt concentrations to create a Known Media Database (KOMODO) that includes more than 18,000 strain-media combinations as well as more than 3000 media variants and compound concentrations.
Oberhardt and his colleagues then leveraged the database to predict which organisms would grow well in which media. By looking at media that support multiple microbes and applying the transitive property and a phylogeny-based filter, they were able to predict which microbes would grow in new in vitro experiments with approximately 83% accuracy.
“No one has really looked at this problem this way before, and we’ve been able to set a new framework,” Oberhardt said. “We’re not done yet. We’re going to improve the database by including more biogenetic data and ecological data. But we think this is a really good starting point, and we can use more sophisticated machine learning methods to help us create good metabolic models in the future.”

Reference
Oberhardt MA, Zarecki R, Gronow S, Lang E, Klenk HP, Gophna U, Ruppin E. Harnessing the landscape of microbial culture media to predict new organism-media pairings. Nat Commun. 2015 Oct 13;6:8493. doi: 10.1038/ncomms9493.  

Novel antibody–antibiotic conjugate eliminates intracellular S. aureus

Staphylococcus aureus is considered to be an extracellular pathogen. However, survival of S. aureus within host cells may provide a reservoir relatively protected from antibiotics, thus enabling long-term colonization of the host and explaining clinical failures and relapses after antibiotic therapy. Here we confirm that intracellular reservoirs of S. aureus in mice comprise a virulent subset of bacteria that can establish infection even in the presence of vancomycin, and we introduce a novel therapeutic that effectively kills intracellular S. aureus. This antibody–antibiotic conjugate consists of an anti-S. aureus antibody conjugated to a highly efficacious antibiotic that is activated only after it is released in the proteolytic environment of the phagolysosome. The antibody–antibiotic conjugate is superior to vancomycin for treatment of bacteraemia and provides direct evidence that intracellular S. aureus represents an important component of invasive infections.



a, Model of AAC (not drawn to scale). b, Mechanism of AAC action. c, Binding of Alexa-488 anti-β-GlcNAC WTA monoclonal antibody (mAb) or anti-α-GlcNAC WTA monoclonal antibody, or isotype control antibody, anti-cytomegalovirus glycoprotein-D (gD) to USA300 isolated from infected kidneys (n = 3). MFI, mean fluorescence intensity. d, Binding of anti-GlcNAC WTA antibodies (red) or isotype control (grey) to protein-A-deficient USA300 lacking tarM or tarS (n = 3). WT, wild type. e, Crystal structure of anti-β-GlcNAc WTA Fab bound to a synthetic minimal β-WTA unit. Antibody light chain (pink) and heavy chain (blue) are shown. f, MIC determination for rifampicin and rifalogue on USA300 (n = 5). g, Survival of stationary phase USA300 incubated with 1 × 10−6 M rifampicin or rifalogue (n = 4). h, USA300 bacteria were incubated without antibiotic (black) or with 3 μg ml−1 ciprofloxacin (Cipro; green, red and grey). 1 μg ml−1 of rifalogue (red) or rifampicin (grey) was added as indicated (n = 3). i, Intact AAC does not kill planktonic bacteria but does after pre-treatment with cathepsin-B (n = 3). g–i, Error bars show s.d. for triplicate samples (n = biological repeats).

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Premio Nobel de Química 2015 para los padres de los mecanismos de reparación del ADN

La Real Academia de las Ciencias Sueca ha galardonado con el Nobel de Química 2015 a Tomas Lindahl, Paul Modrich y Aziz Sancarr, considerados los padres de los mecanismos de reparación del ADN, cuyo conocimiento ha permitido, por ejemplo, desarrollar tratamientos para enfermedades como el cáncer.

Tomas Lindahl

Prize share: 1/3

Paul Modrich

Prize share: 1/3

Aziz Sancar

Prize share: 1/3

El jurado ha considerado que los trabajos de los tres investigadores han sido clave para aprender cómo reparan las células su ADN y cómo salvaguardan su material genético.

Lindahl (Estocolmo, 1938) trabaja en el Instituto Francis Crick del Reino Unido, Modrich (1946) es investigador de la Universidad de Duke (EEUU) mientras que Sancar (de origen turco, aunque con pasaporte estadounidense) es investigador de la Universidad de Carolina del Norte. Como ha explicado el jurado, nuestras células sufren cada día cientos de alteraciones provocadas por agentes como el tabaco, las radiaciones solares o los radicales libres; "incluso sin esos ataques, el ADN es altamente inestable". Lo que los nuevos Nobel de Química descubrieron en sus laboratorios desde los años 70 es que existe todo un complejo sistema de reparación del material genético de las células para impedir que estos cambios se traduzcan en un completo "caos celular".

El Nobel de Medicina premia nuevos tratamientos contra infecciones de parásitos y malaria

De izquierda a derecha: William C. Campbell, Satoshi Omura y Yoyou Tu

El Nobel de Medicina y Fisiología ha premiado este año avances cruciales contra enfermedades provocadas por parásitos que durante milenios han asolado a la Humanidad y hoy siguen constituyendo uno de los problemas sanitarios más graves del mundo actual, sobre todo en los países más pobres. El Instituto Karolinska ha anunciado en Estocolmo el galardón, que comparten William C. Campbell y Satoshi Omura por descubrir una nueva terapia contra infecciones de lombrices redondas (nemátodos) y Youyou Tu por desarrollar un tratamiento novedoso contra la malaria. Los galardonados compartirán un premio económico de ocho millones de coronas suecas (855.000 euros, 954.000 dólares).

Según informó el comité al dar a conocer el nombre de los galardonados, los tres premiados este año "han desarrollado terapias que han revolucionado el tratamiento de algunas de las más devastadoras enfermedades parasitarias".

El irlandés Campbell y el japonés Omura descubrieron un nuevo fármaco, la Ivermectina, que ha logrado reducir de forma radical la incidencia de la oncocercosis o ceguera de los ríos y la filariasis linfática o elefantiasis, además de mostrar una eficacia parcial contra otras enfermedades parasitarias. La científica china Youyou Tu, por su parte, descubrió la Artemisina, una droga que ha reducido de manera muy significativa la mortalidad por malaria.

Un fármaco 'revolucionario'

El primer compuesto se desarrolló en los años '80 y, según los expertos, rompió todos los esquemas, primero en el mercado veterinario. Mataba parásitos de dos tipos, los que viven en la piel y los que proceden del intestino. Al poco tiempo, este fármaco demostró eficacia contra un parásito 'primo hermano' del que causa la oncocercosis en caballos. Dados los resultados y teniendo en cuenta el grave problema que había en África y Latinoamérica con la ceguera de los ríos en humanos, se pusieron en marcha ensayos clínicos. Se comprobó que en personas, la Ivermectina "no era capaz de matar al parásito (Onchocerca volvulus), pero sí lo dejaba estéril, es decir, conseguía prevenir la enfermedad durante un periodo de tiempo", expone a EL MUNDO Carlos Chaccour, médico e investigador de la Universidad de Navarra.

Desde entonces, como medida de prevención, argumenta Chaccour, "en estas zonas de riesgo, donde la oncocercosis causaba estragos y dejaba a poblaciones enteras ciegas, se toma este fármaco aproximadamente una vez al año. En el Amazonas incluso hasta cuatro veces al año". Tales eran los efectos que la farmacéutica Merck & Co., la empresa que descubrió y fabrica el fármaco, decidió donarlo a los países donde la oncocercosis es endémica. Gracias a ello, se han tratado anualmente a unos 60-80 millones de personas.

La Ivermectina no sólo previene la ceguera de los ríos, también está autorizada en Francia, por ejemplo, para la sarna complicada y actúa frente a otros parásitos como la filariasis linfática o elefantiasis (una enfermedad tropical que puede producir alteraciones del sistema linfático e hipertrofia anormal de algunas partes del cuerpo, causando dolor, discapacidad grave y estigma social), entre otras enfermedades parasitarias.

Tomado de "El Mundo"

Los virus se defienden de nuevo

The battle for survival between bacteria and the viruses that infect them (phages) has led to the evolution of many bacterial defence systems and phage-encoded antagonists of these systems. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated (cas) genes comprise an adaptive immune system that is one of the most widespread means by which bacteria defend themselves against phages. We identified the first examples of proteins produced by phages that inhibit a CRISPR–Cas system. Here we performed biochemical and in vivo investigations of three of these anti-CRISPR proteins, and show that each inhibits CRISPR–Cas activity through a distinct mechanism. Two block the DNA-binding activity of the CRISPR–Cas complex, yet do this by interacting with different protein subunits, and using steric or non-steric modes of inhibition. The third anti-CRISPR protein operates by binding to the Cas3 helicase–nuclease and preventing its recruitment to the DNA-bound CRISPR–Cas complex. In vivo, this anti-CRISPR can convert the CRISPR–Cas system into a transcriptional repressor, providing the first example—to our knowledge—of modulation of CRISPR–Cas activity by a protein interactor. The diverse sequences and mechanisms of action of these anti-CRISPR proteins imply an independent evolution, and foreshadow the existence of other means by which proteins may alter CRISPR–Cas function.

Tomado de: 

Multiple mechanisms for CRISPR–Cas inhibition by anti-CRISPR protein

Nature

(2015)

doi:10.1038/nature15254

Received

21 November 2014s

Accepted

29 July 2015

Published online

23 September 2015       

Eye-like ocelloids are built from different endosymbiotically acquired components

Multicellularity is often considered a prerequisite for morphological complexity, as seen in the camera-type eyes found in several groups of animals. A notable exception exists in single-celled eukaryotes called dinoflagellates, some of which have an eye-like ‘ocelloid’ consisting of subcellular analogues to a cornea, lens, iris, and retina¹. These planktonic cells are uncultivated and rarely encountered in environmental samples, obscuring the function and evolutionary origin of the ocelloid. Here we show, using a combination of electron microscopy, tomography, isolated-organelle genomics, and single-cell genomics, that ocelloids are built from pre-existing organelles, including a cornea-like layer made of mitochondria and a retinal body made of anastomosing plastids. We find that the retinal body forms the central core of a network of peridinin-type plastids, which in dinoflagellates and their relatives originated through an ancient endosymbiosis with a red alga². As such, the ocelloid is a chimaeric structure, incorporating organelles with different endosymbiotic histories. The anatomical complexity of single-celled organisms may be limited by the components available for differentiation, but the ocelloid shows that pre-existing organelles can be assembled into a structure so complex that it was initially mistaken for a multicellular eye³. Although mitochondria and plastids are acknowledged chiefly for their metabolic roles, they can also be building blocks for greater structural complexity.

a, Illustration of Nematodinium showing the basic components of the ocelloid with their putative organellar origins. b, TEM of the ocelloid of Erythropsidinium, including the lens (L) and retinal body (r). c, TEM of the ocelloid of Nematodinium, depicting the edge of the lens (L) where it is overlain by a cornea-like layer of mitochondria (m). d, Genomic reads amplified from five whole cells of Nematodinium; arrow, retinal body. e, Genomic reads amplified from five retinal bodies (arrow) after they were micro-dissected from individual cells of Nematodinium.

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CRISRP-Cas: una revolución similar a la PCR

Tomado de 

Deep-sea hydrothermal vent bacteria related to human pathogenic Vibrio species

During Alvin and Nautile dives in 1999, samples were collected from water surrounding sulfide chimneys of a hydrothermal vent along the East Pacific Rise and four mesophilic bacteria were isolated, including a novel Vibrio species, Vibrio antiquarius. Genomic, functional, and phylogenetic analyses indicate an intriguing blend of genomic features related to adaptation and animal symbiotic association, and also revealed the presence of virulence genes commonly found in Vibrio species pathogenic for humans. The presence of these virulence genes in an ecologically distinct Vibrio species was surprising. It is concluded that pathogenicity genes serve a far more fundamental ecological role than solely causation of human disease.

Vibrio species are both ubiquitous and abundant in marine coastal waters, estuaries, ocean sediment, and aquaculture settings worldwide. We report here the isolation, characterization, and genome sequence of a novel Vibrio species, Vibrio antiquarius, isolated from a mesophilic bacterial community associated with hydrothermal vents located along the East Pacific Rise, near the southwest coast of Mexico. Genomic and phenotypic analysis revealed V. antiquarius is closely related to pathogenic Vibrio species, namely Vibrio alginolyticus, Vibrio parahaemolyticus, Vibrio harveyi, and Vibrio vulnificus, but sufficiently divergent to warrant a separate species status. The V. antiquarius genome encodes genes and operons with ecological functions relevant to the environment conditions of the deep sea and also harbors factors known to be involved in human disease caused by freshwater, coastal, and brackish water vibrios. The presence of virulence factors in this deep-sea Vibrio species suggests a far more fundamental role of these factors for their bacterial host. Comparative genomics revealed a variety of genomic events that may have provided an important driving force in V. antiquarius evolution, facilitating response to environmental conditions of the deep sea.                          

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Las levaduras pueden producir morfina y opiáceos

Biotechnology is about to make morphine production as simple as brewing beer. A paper published on 18 May in Nature Chemical Biology reports the creation of a yeast strain containing the first half of a biochemical pathway that turns simple sugars into morphine — mimicking the process by which poppies make opiates. Combined with other advances, researchers predict that it will be only a few years — or even months — before a single engineered yeast strain can complete the entire process.

Dueber and colleagues’ work does not reach that goal. But it demonstrates that, given the right genes and biochemical machinery, yeast can convert glucose into the intermediate compound (S)-reticuline — the first half of the poppy’s morphine-production pathway.

Benzylisoquinoline alkaloids (BIAs) are a diverse family of plant-specialized metabolites that include the pharmaceuticals codeine and morphine and their derivatives. Microbial synthesis of BIAs holds promise as an alternative to traditional crop-based manufacturing. Here we demonstrate the production of the key BIA intermediate (S)-reticuline from glucose in Saccharomyces cerevisiae. To aid in this effort, we developed an enzyme-coupled biosensor for the upstream intermediate L-3,4-dihydroxyphenylalanine (L-DOPA). Using this sensor, we identified an active tyrosine hydroxylase and improved its L-DOPA yields by 2.8-fold via PCR mutagenesis. Coexpression of DOPA decarboxylase enabled what is to our knowledge the first demonstration of dopamine production from glucose in yeast, with a 7.4-fold improvement in titer obtained for our best mutant enzyme. We extended this pathway to fully reconstitute the seven-enzyme pathway from L-tyrosine to (S)-reticuline. Future work to improve titers and connect these steps with downstream pathway branches, already demonstrated in S. cerevisiae, will enable low-cost production of many high-value BIAs.

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X-domain of peptide synthetases recruits oxygenases crucial for glycopeptide biosynthesis

Non-ribosomal peptide synthetase (NRPS) mega-enzyme complexes are modular assembly lines that are involved in the biosynthesis of numerous peptide metabolites independently of the ribosome¹. The multiple interactions between catalytic domains within the NRPS machinery are further complemented by additional interactions with external enzymes, particularly focused on the final peptide maturation process. An important class of NRPS metabolites that require extensive external modification of the NRPS-bound peptide are the glycopeptide antibiotics (GPAs), which include vancomycin and teicoplanin^{2, 3}. These clinically relevant peptide antibiotics undergo cytochrome P450-catalysed oxidative crosslinking of aromatic side chains to achieve their final, active conformation^{4, 5, 6, 7, 8, 9, 10, 11, 12}. However, the mechanism underlying the recruitment of the cytochrome P450 oxygenases to the NRPS-bound peptide was previously unknown. Here we show, through in vitro studies, that the X-domain^{13, 14}, a conserved domain of unknown function present in the final module of all GPA NRPS machineries, is responsible for the recruitment of oxygenases to the NRPS-bound peptide to perform the essential side-chain crosslinking. X-ray crystallography shows that the X-domain is structurally related to condensation domains, but that its amino acid substitutions render it catalytically inactive. We found that the X-domain recruits cytochrome P450 oxygenases to the NRPS and determined the interface by solving the structure of a P450–X-domain complex. Additionally, we demonstrated that the modification of peptide precursors by oxygenases in vitro—in particular the installation of the second crosslink in GPA biosynthesis—occurs only in the presence of the X-domain. Our results indicate that the presentation of peptidyl carrier protein (PCP)-bound substrates for oxidation in GPA biosynthesis requires the presence of the NRPS X-domain to ensure conversion of the precursor peptide into a mature aglycone, and that the carrier protein domain alone is not always sufficient to generate a competent substrate for external cytochrome P450 oxygenases.




Domain labels for NRPS proteins (Tcp9–12): A, adenylation (selected amino acids indicated above the module: Hpg, 4-hydroxyphenylglycine; Dpg, 3,5-dihydroxyphenylglycine); C, condensation; E, epimerization; T, thiolation/peptidyl carrier protein (PCP); TE, thioesterase; X, domain of unknown function. Essential P450-catalysed aglycone rigidification takes place through crosslinking of aromatic side chains (OxyA–C, OxyE). Each crosslinking reaction is performed by a specific Oxy protein, with the products of each Oxy protein indicated schematically; standard ring nomenclature is indicated on the teicoplanin aglycone in red lettering.

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Complex archaea that bridge the gap between prokaryotes and eukaryotes

The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of ‘Lokiarchaeota’, a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. 

Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic ‘starter-kit’ to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.


a, Schematic overview of the metagenomics approach. BI, Bayesian inference; ML, maximum likelihood. b, Bayesian phylogeny of concatenated alignments comprising 36 conserved phylogenetic marker proteins using sophisticated models of protein evolution (Methods), showing eukaryotes branching within Lokiarchaeota. Numbers above and below branches refer to Bayesian posterior probability and maximum-likelihood bootstrap support values, respectively. Posterior probability values above 0.7 and bootstrap support values above 70 are shown. Scale indicates the number of substitutions per site. c, Phylogenetic breakdown of the Lokiarchaeum proteome, in comparison with proteomes of Korarchaeota, Aigarchaeota (Caldiarchaeum) and Miscellaneous Crenarchaeota Group (MCG) archaea. Category ‘Other’ contains proteins assigned to the root of cellular organisms, to viruses and to unclassified proteins.

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ParMRC es la maquinaria mitótica conocida mas simple

Structures of actin-like ParM filaments show architecture of plasmid-segregating spindles

Active segregation of Escherichia coli low-copy-number plasmid R1 involves formation of a bipolar spindle made of left-handed double-helical actin-like ParM filaments^{1, 2, 3, 4, 5, 6}. ParR links the filaments with centromeric parC plasmid DNA, while facilitating the addition of subunits to ParM filaments^{3, 7, 8, 9}. Growing ParMRC spindles push sister plasmids to the cell poles^{9, 10}. Here, using modern electron cryomicroscopy methods, we investigate the structures and arrangements of ParM filaments in vitro and in cells, revealing at near-atomic resolution how subunits and filaments come together to produce the simplest known mitotic machinery. To understand the mechanism of dynamic instability, we determine structures of ParM filaments in different nucleotide states. The structure of filaments bound to the ATP analogue AMPPNP is determined at 4.3 Å resolution and refined. The ParM filament structure shows strong longitudinal interfaces and weaker lateral interactions. Also using electron cryomicroscopy, we reconstruct ParM doublets forming antiparallel spindles. Finally, with whole-cell electron cryotomography, we show that doublets are abundant in bacterial cells containing low-copy-number plasmids with the ParMRC locus, leading to an asynchronous model of R1 plasmid segregation.


Fig. a, A mutant of ParM that hydrolyses ATP more slowly (D170A) was overexpressed in E. coli cells. Tomographic slices show large bundles of ParM blocking cell division. This experiment was performed two times. b, The ParMRC operon driven from high‐copy‐number plasmid pDD19. Tomographic slice showing an example of observed doublets. c, Tomographic slice for a medium‐copy‐number plasmid (pKG321). d, Tomographic slice for a low‐copy‐number plasmid, emulating the native low‐copy‐number R1 plasmids (pKG491, ‘mini‐R1’ replicon) in E. coli (see Supplementary Videos 5 and 6 to view entire tomograms). Each experiment with different copy‐number plasmids was performed once. e, Schematic depicting proposed asynchronous plasmid DNA segregation. Bipolar ParM spindles are seeded when replication has produced two parC centromeric regions, still in close proximity. Each seeds one unipolar ParM filament, which then come together in an antiparallel fashion to form the segregating bipolar spindle. Non‐productive unipolar filaments or spindles that lack plasmid attachment will be destroyed through the dynamic instability of ParM. This is in contrast to earlier ideas in which all sister plasmids would be segregated through one bundle of filaments, containing double the number of unipolar filaments as the copy number of the plasmid in the cell¹⁹.

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Bacterias que se comportan como cristales vivos

Fast-Moving Bacteria Self-Organize into Active Two-Dimensional Crystals of Rotating Cells

We investigate a new form of collective dynamics displayed by Thiovulum majus, one of the fastest-swimming bacteria known. Cells spontaneously organize on a surface into a visually striking two-dimensional hexagonal lattice of rotating cells. As each constituent cell rotates its flagella, it creates a tornadolike flow that pulls neighboring cells towards and around it. As cells rotate against their neighbors, they exert forces on one another, causing the crystal to rotate and cells to reorganize. We show how these dynamics arise from hydrodynamic and steric interactions between cells. We derive the equations of motion for a crystal, show that this model explains several aspects of the observed dynamics, and discuss the stability of these active crystals.


Fig. 1. A large bacterial crystal in dark-field illumination. The bright glow of individual cells results from light scattering off intercellular sulfur globules. The illumination of cells differs because the concentration of sulfur globules varies between cells. The scale bar is 10  μm.

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The future of the postdoc

There is a growing number of postdocs and few places in academia for them to go. But change could be on the way.



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An Escherichia coli Mutant That Makes Exceptionally Long Cells

Although Escherichia coli is a very small (1- to 2-μm) rod-shaped cell, here we describe an E. coli mutant that forms enormously long cells in rich media such as Luria broth, as long indeed as 750 μm. These extremely elongated (eel) cells are as long as the longest bacteria known and have no internal subdivisions. They are metabolically competent, elongate rapidly, synthesize DNA, and distribute cell contents along this length. They lack only the ability to divide. The concentration of the essential cell division protein FtsZ is reduced in these eel cells, and increasing this concentration restores division.

IMPORTANCE Escherichia coli is usually a very small bacterium, 1 to 2 μm long. We have isolated a mutant that forms enormously long cells, 700 times longer than the usual E. coli cell. E. coli filaments that form under other conditions usually die within a few hours, whereas our mutant is fully viable even when it reaches such lengths. This mutant provides a useful tool for the study of aspects of E. coli physiology that are difficult to investigate with small cells.      

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Diverse uncultivated ultra-small bacterial cells in groundwater

Bacteria from phyla lacking cultivated representatives are widespread in natural systems and some have very small genomes. Here we test the hypothesis that these cells are small and thus might be enriched by filtration for coupled genomic and ultrastructural characterization. Metagenomic analysis of groundwater that passed through a ~0.2-μm filter reveals a wide diversity of bacteria from the WWE3, OP11 and OD1 candidate phyla. Cryogenic transmission electron microscopy demonstrates that, despite morphological variation, cells consistently have small cell size (0.009±0.002 μm³). Ultrastructural features potentially related to cell and genome size minimization include tightly packed spirals inferred to be DNA, few densely packed ribosomes and a variety of pili-like structures that might enable inter-organism interactions that compensate for biosynthetic capacities inferred to be missing from genomic data. The results suggest that extremely small cell size is associated with these relatively common, yet little known organisms.



Cryo-electron tomography images from 3D reconstructions of ultra-small bacteria.

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CRISPR/Cas is all the rage—and getting more precise and efficient.

Una reciente revisión:

CRISPR (clustered, regularly interspaced, short palindromic repeats) is named for particular DNA loci that are found in many archaea and bacteria. CRISPR works with associated nucleases, including Cas9, to protect the cells from viral infection by inserting short snippets of viral DNA into the CRISPR cassette. By combining the Cas9 nuclease with a short guide RNA that’s custom-designed to bind a specific target, CRISPR/Cas can easily edit any gene you want. Just in the past year, for example, it has allowed researchers to cure a rare liver disease in mice, to excise HIV-inserted genes from human immune cells, and to block HIV from entering blood stem cells. CRISPR/Cas is easier than the other nuclease-based editing technologies, says John Schimenti of Cornell University; scientists are basically a reagent catalog and a round of PCR away from having everything they need to utilize CRISPR.

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Recoded organisms engineered to depend on synthetic amino acids

Genetically modified organisms (GMOs) are increasingly used in research and industrial systems to produce high-value pharmaceuticals, fuels and chemicals. Genetic isolation and intrinsic biocontainment would provide essential biosafety measures to secure these closed systems and enable safe applications of GMOs in open systems, which include bioremediation and probiotics. Although safeguards have been designed to control cell growth by essential gene regulation, inducible toxin switches and engineered auxotrophies, these approaches are compromised by cross-feeding of essential metabolites, leaked expression of essential genes, or genetic mutations.

Here we describe the construction of a series of genomically recoded organisms (GROs) whose growth is restricted by the expression of multiple essential genes that depend on exogenously supplied synthetic amino acids (sAAs). We introduced a Methanocaldococcus jannaschii tRNA:aminoacyl-tRNA synthetase pair into the chromosome of a GRO derived from Escherichia coli that lacks all TAG codons and release factor 1, endowing this organism with the orthogonal translational components to convert TAG into a dedicated sense codon for sAAs. Using multiplex automated genome engineering, we introduced in-frame TAG codons into 22 essential genes, linking their expression to the incorporation of synthetic phenylalanine-derived amino acids. Of the 60 sAA-dependent variants isolated, a notable strain harbouring three TAG codons in conserved functional residuesof MurG, DnaA and SerS and containing targeted tRNA deletions maintained robust growth and exhibited undetectable escape frequencies upon culturing ~10¹¹ cells on solid media for 7 days or in liquid media for 20 days. This is a significant improvement over existing biocontainment approaches.

We constructed synthetic auxotrophs dependent on sAAs that were not rescued by cross-feeding in environmental growth assays. These auxotrophic GROs possess alternative genetic codes that impart genetic isolation by impeding horizontal gene transfer and now depend on the use of synthetic biochemical building blocks, advancing orthogonal barriers between engineered organisms and the environment.

Nature 518, 89–93 (05 February 2015) doi:10.1038/nature14095

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Un nuevo antibiótico de un microorganismo "no cultivable"

Antibiotic resistance is spreading faster than the introduction of new compounds into clinical practice, causing a public health crisis. Most antibiotics were produced by screening soil microorganisms, but this limited resource of cultivable bacteria was overmined by the 1960s. Synthetic approaches to produce antibiotics have been unable to replace this platform. Uncultured bacteria make up approximately 99% of all species in external environments, and are an untapped source of new antibiotics. We developed several methods to grow uncultured organisms by cultivation in situ or by using specific growth factors. Here we report a new antibiotic that we term teixobactin, discovered in a screen of uncultured bacteria. Teixobactin inhibits cell wall synthesis by binding to a highly conserved motif of lipid II (precursor of peptidoglycan) and lipid III (precursor of cell wall teichoic acid). We did not obtain any mutants of Staphylococcus aureus or Mycobacterium tuberculosis resistant to teixobactin. The properties of this compound suggest a path towards developing antibiotics that are likely to avoid development of resistance.



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