jueves, 15 de marzo de 2018

Nuevo sistema TA en Corynebacterium glutamicum

Glutamine-rich toxic proteins GrtA, GrtB, and GrtC together with the antisense RNA AsgR constitute a toxin–antitoxin-like system in Corynebacterium glutamicum.

The Corynebacterium glutamicum R grtA (cgR_2936), grtB (cgR_2934), and grtC (cgR_2933) genes were identified as paralogs encoding glutamine-rich toxic proteins. We also identified a new antisense small RNA AsgR (antisense sRNA for grtA) that overlaps the 3′ end of the grtA gene. Single over-expressions of grtA, grtB, and grtC resulted in complete inhibition of Escherichia coli cell growth. This growth was rescued by co-expression of AsgR. Similar effects were observed in C. glutamicum, although the toxicities of these proteins were moderate. Inhibition of AsgR transcription resulted in increased levels and prolonged half-lives of grtA, grtB, and grtC mRNAs. We also found that the expression levels of grtA, grtB, and grtC were increased in an RNase III deletion mutant. Primer extension analysis revealed the RNase III cleavage site to be in the 3′ untranslated region (3′-UTR) of the grtA mRNA. The expression levels of grtA, grtB, and grtC were increased after exposure to several stresses, including heat shock, treatment with penicillin G, lysozyme, or H2O2. The deletions of grtABC and asgR genes resulted in decreased survival rate under several stresses. These results indicate that GrtABC and AsgR constitute a type I toxin–antitoxin-like system in C. glutamicum.

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jueves, 22 de febrero de 2018

Peptidoglycan synthesis drives an FtsZ-treadmilling-independent step of cytokinesis

Peptidoglycan is the main component of the bacterial wall and protects cells from the mechanical stress that results from high intracellular turgor. Peptidoglycan biosynthesis is very similar in all bacteria; bacterial shapes are therefore mainly determined by the spatial and temporal regulation of peptidoglycan synthesis rather than by the chemical composition of peptidoglycan. The form of rod-shaped bacteria, such as Bacillus subtilis or Escherichia coli, is generated by the action of two peptidoglycan synthesis machineries that act at the septum and at the lateral wall in processes coordinated by the cytoskeletal proteins FtsZ and MreB, respectively1,2. The tubulin homologue FtsZ is the first protein recruited to the division site, where it assembles in filaments—forming the Z ring—that undergo treadmilling and recruit later divisome proteins3,4. The rate of treadmilling in B. subtilis controls the rates of both peptidoglycan synthesis and cell division3. The actin homologue MreB forms discrete patches that move circumferentially around the cell in tracks perpendicular to the long axis of the cell, and organize the insertion of new cell wall during elongation5,6. Cocci such as Staphylococcus aureus possess only one type of peptidoglycan synthesis machinery7,8, which is diverted from the cell periphery to the septum in preparation for division9. The molecular cue that coordinates this transition has remained elusive. Here we investigate the localization of S. aureus peptidoglycan biosynthesis proteins and show that the recruitment of the putative lipid II flippase MurJ to the septum, by the DivIB–DivIC–FtsL complex, drives peptidoglycan incorporation to the midcell. MurJ recruitment corresponds to a turning point in cytokinesis, which is slow and dependent on FtsZ treadmilling before MurJ arrival but becomes faster and independent of FtsZ treadmilling after peptidoglycan synthesis activity is directed to the septum, where it provides additional force for cell envelope constriction.

a, Schematic of the peptidoglycan synthesis pathway in S. aureus. UDP, uridine diphosphate. b, Structured illumination microscopy (SIM) images of S. aureus cells expressing fluorescent derivatives of PG synthesis proteins. Scale bars, 0.5 μm. Images are representative of three biological replicates. c, Ratios between fluorescence signal at the septum and the peripheral membrane, measured in cells with a complete septum (phase 3). Blue, membrane proteins with fluorescence ratio of approximately 2, similar to Nile Red staining of COL membrane (expected as the septum contains two membranes versus one in the cell periphery). Green, septal enriched proteins with 2.5 < fluorescence ratio < 3.5. Red, septal proteins with fluorescence ratio > 4. Data are represented as column graphs in which the height of the column is the mean and whiskers are s.d. From left to right, n = 439, 533, 516, 513, 512, 622, 503, 517, 503, 689, 1,321, 488 and 516 cells. AU, arbitrary unit. d, Schematic of the S. aureuscell cycle. Phase 1 cells have not initiated septum synthesis, phase 2 cells are undergoing septum synthesis and phase 3 cells have a complete septum undergoing maturation in preparation for splitting.

miércoles, 21 de febrero de 2018

Construcción de cepas de Escherichia coli a partir de minicélulas por transferencia lateral de genes

Recently, artificial life is created with artificial materials and methods. Life can be born, when genomic DNA molecule integrated in liposomes containing biochemical reactions for biogenic needs. However, it is not yet known whether the integration of these parts will be able to occur in nature, and constitute a living system. I planned to regenerate bacteria from biologically active liposomes by inserting genomic DNA using all natural materials and methods. The mini-cells of Escherichia coli, containing plasmids and activated SOS proteins, act as protocells. Four new E. coli strains were regenerated from mini-cells by inserting the genomes with the conjugation system between F- and Hfr strains. Four regenerated cells showed the same genetic markers as two genome donors. The pulse field gel electrophoresis of their genomes showed admixing of those of both two donors. In addition, the genome of 4 regenerated cells had chimera genome of two donors. Our results represent synthesis of life can occur in nature without artificial arrangement.
IMPORTANCE What is the difference between inanimate objects and organisms? Organisms have genomic DNA by all means. When organisms lose their genome, they cannot neither grow nor reproduce. As the result, organisms turn into inanimate objects without their genome. In this manuscript, I regenerated microbes from the cell corpse that lost its genome by inserting another genome. All steps of regeneration applied natural behavior of microbes. The same regeneration of microbes would happen in nature. The primitive lives have plasticity, which accelerates evolution and provides various kinds of lives in the world.

miércoles, 7 de febrero de 2018

Sistemas de inyección contráctil de bacteriófagos

Bacteria and bacteriophages utilize a  rigid  tube-contractile  sheath  mechanism  for delivering proteins and DNA across the cell envelope. Here we describe conserved features of these contractile assemblies and propose their evolutionary pathway. The complexity of today’s systems is a result of gene duplication and subsequent specialization of function.

Contractile    tail    bacteriophages, or    myobacteriophages, use    a    sophisticated biomolecular structure to inject their genome into the bacterial host cell.  This structure consists of a contractile sheath enveloping a rigid tube that is sharpened by a spike-shaped protein complex at its tip. The spike complex forms the centerpiece of a baseplate complex that terminates the sheath and the tube.  The baseplate anchors the tail to the target  cell membrane  with  the  help  of  fibrous  proteins  emanating  from  it  and  triggers  contraction  of  the sheath. The contracting sheath drives the tube with its spiky tip through the target cell membrane.  Subsequently, the bacteriophage genome  is  injected  through  the tube.  The structural transformation of  the  bacteriophage  T4  baseplate  upon  binding  to  the  host  cell  has  been  recently  described  in  near-atomic  detail. 

martes, 30 de enero de 2018

El animal que no cumple la «ley natural» del envejecimiento

Una investigación publicada recientemente ha presentado resultados que indican que las ratas topo desnudas (Heterocephalus glaber), unos roedores lampiños y armados con dos exagerados dientes, no cumplen la fórmula de Gompertz. Después de alcanzar la edad adulta, a los seis meses, su probabilidad de morir permanece constante e incluso disminuye un poco con el tiempo. Por eso, quizás, estos animales alcanzan los 30 años de edad en cautividad, frente a los cuatro de otros roedores también criados en jaulas. Estos animales tienen una elevada actividad reparadora de ADN y, por otra, altos niveles de chaperonas, unas proteínas que ayudan a otras a plegarse para funcionar adecuadamente. 

En el mundo de los animales de laboratorio, dominado por ratas albinas y moscas, las ratas topo desnudas son súperestrellas. Muy raramente tienen cáncer, son inmunes a ciertos tipos de dolor (como el de las quemaduras), pueden sobrevivir 18 minutos sin oxígeno, cambiando su metabolismo, y son increíblemente longevas: les correspondería vivir seis años, pero pueden llegar a los 30, y conservando su fertilidad. Por todo esto, no llama la atención que los investigadores quieran estudiarlas en beneficio de la salud humana.

viernes, 26 de enero de 2018

Nuevos sistemas de defensa frente a fagos en bacterias

The arms race between bacteria and phages led to the development of sophisticated antiphage defense systems, including CRISPR-Cas and restriction-modification systems. Evidence suggests that unknown defense systems are located in “defense islands” in microbial genomes. 

We comprehensively characterized the bacterial defensive arsenal by examining gene families that are clustered next to known defense genes in prokaryotic genomes. Candidate defense systems were systematically engineered and validated in model bacteria for their antiphage activities. 

We report nine previously unknown antiphage systems and one antiplasmid system that are widespread in microbes and strongly protect against foreign invaders. These include systems that adopted components of the bacterial flagella and condensin complexes. Our data also suggest a common, ancient ancestry of innate immunity components shared between animals, plants, and bacteria.

Bacteria and archaea are frequently attacked by viruses (phages), and as a result have developed multiple, sophisticated lines of active defense (13) that can collectively be referred to as the prokaryotic “immune system.” Antiphage defense strategies include restriction-modification (R-M) systems that target specific sequences on the invading phage (4), CRISPR-Cas, which provides acquired immunity through memorization of past phage attacks (5), abortive infection systems (Abi) that lead to cell death or metabolic arrest upon infection (6), and additional systems whose mechanism of action is not yet clear such as BREX (7), prokaryotic Argonautes (pAgos) (8) and DISARM (9). Different bacteria encode different sets of defense systems: CRISPR-Cas systems are found in about 40% of all sequenced bacteria (1011), R-M systems are found in about 75% of prokaryote genomes (12) while pAgos and BREX appear in about 10% (713). It has been suggested that many currently unknown defense systems reside in genomes and plasmids of nonmodel bacteria and archaea and await discovery (214).
Antiphage defense systems were found to be frequently physically clustered in bacterial and archaeal genomes such that, for example, genes encoding restriction enzymes commonly reside in the vicinity of genes encoding abortive infection systems and other phage resistance systems (1415). The observation that defense systems are clustered in genomic “defense islands” has led to the suggestion that genes of unknown function residing within such defense islands may also participate in antiphage defense (1516). Indeed, recent studies that focused on individual genes enriched next to known defense genes resulted in the discovery of new systems that protect bacteria against phages (7917).

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A global atlas of the dominant bacteria found in soil

The immense diversity of soil bacterial communities has stymied efforts to characterize individual taxa and document their global distributions. We analyzed soils from 237 locations across six continents and found that only 2% of bacterial phylotypes (~500 phylotypes) consistently accounted for almost half of the soil bacterial communities worldwide. Despite the overwhelming diversity of bacterial communities, relatively few bacterial taxa are abundant in soils globally. We clustered these dominant taxa into ecological groups to build the first global atlas of soil bacterial taxa. Our study narrows down the immense number of bacterial taxa to a “most wanted” list that will be fruitful targets for genomic and cultivation-based efforts aimed at improving our understanding of soil microbes and their contributions to ecosystem functioning.