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Two small RNAs, CrcY and CrcZ, act in concert to sequester the Crc global regulator in Pseudomonas putida, modulating catabolite repression |
Mol Microbiol. 2012 Jan;83(1):24-40
Moreno R, Fonseca P, Rojo F.
 The Crc protein is a translational repressor that recognizes a specific
target at some mRNAs, controlling catabolite repression and
co-ordinating carbon metabolism in pseudomonads. In Pseudomonas aeruginosa, the levels of free Crc protein are controlled by CrcZ, a sRNA that sequesters Crc, acting as an antagonist.
We show that, in Pseudomonas putida,
the levels of free Crc are controlled by CrcZ and by a novel 368 nt
sRNA named CrcY. CrcZ and CrcY, which contain six potential targets for
Crc, were able to bind Crc specifically in vitro. The levels of
CrcZ and CrcY were low under conditions generating a strong catabolite
repression, and increased strongly when catabolite repression was
absent. Deletion of either crcZ or crcY had no effect
on catabolite repression, but the simultaneous absence of both sRNAs led
to constitutive catabolite repression that compromised growth on some
carbon sources. Overproduction of CrcZ or CrcY significantly reduced
repression. We propose that CrcZ and CrcY act in concert, sequestering
and modulating the levels of free Crc according to metabolic conditions.
The CbrA/CbrB two-component system activated crcZ transcription, but had little effect on crcY. CrcY was detected in P. putida, Pseudomonas fluorescens and Pseudomonas syringae, but not in P. aeruginosa. |
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Resolving structure and mechanical properties at the nanoscale of viruses with frequency modulation atomic force microscopy |
PLoS ONE 2012;7(1):e30204
Martinez-Martin D, Carrasco C, Hernando-Perez M, de Pablo PJ, Gomez-Herrero J, Perez R, Mateu MG, Carrascosa JL, Kiracofe D, Melcher J, Raman A.
 Structural Biology (SB) techniques are particularly successful in solving virus structures. Taking advantage of the symmetries, a heavy averaging on the data of a large number of specimens, results in an accurate determination of the structure of the sample. However, these techniques do not provide true single molecule information of viruses in physiological conditions.
To answer many fundamental questions about the quickly expanding physical virology it is important to develop techniques with the capability to reach nanometer scale resolution on both structure and physical properties of individual molecules in physiological conditions. Atomic force microscopy (AFM) fulfills these requirements providing images of individual virus particles under physiological conditions, along with the characterization of a variety of properties including local adhesion and elasticity. Using conventional AFM modes is easy to obtain molecular resolved images on flat samples, such as the purple membrane, or large viruses as the Giant Mimivirus. On the contrary, small virus particles (25–50 nm) cannot be easily imaged. In this work we present Frequency Modulation atomic force microscopy (FM-AFM) working in physiological conditions as an accurate and powerful technique to study virus particles. Our interpretation of the so called “dissipation channel” in terms of mechanical properties allows us to provide maps where the local stiffness of the virus particles are resolved with nanometer resolution. FM-AFM can be considered as a non invasive technique since, as we demonstrate in our experiments, we are able to sense forces down to 20 pN. The methodology reported here is of general interest since it can be applied to a large number of biological samples. In particular, the importance of mechanical interactions is a hot topic in different aspects of biotechnology ranging from protein folding to stem cells differentiation where conventional AFM modes are already being used. |
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The Escherichia coli SOS gene dinF protects against oxidative stress and bile salts |
PLoS ONE
Rodríguez-Beltrán J, Rodríguez-Rojas A, Guelfo JR, Couce A, Blázquez J.
 DNA is constantly damaged by physical and chemical factors, including
reactive oxygen species (ROS), such as superoxide radical (O2−), hydrogen peroxide (H2O2)
and hydroxyl radical (•OH). Specific mechanisms to protect and repair
DNA lesions produced by ROS have been developed in living beings.
In Escherichia coli
the SOS system, an inducible response activated to rescue cells from
severe DNA damage, is a network that regulates the expression of more
than 40 genes in response to this damage, many of them playing important
roles in DNA damage tolerance mechanisms. Although the function of most
of these genes has been elucidated, the activity of some others, such
as dinF, remains unknown. The DinF deduced polypeptide sequence
shows a high homology with membrane proteins of the multidrug and toxic
compound extrusion (MATE) family. We describe here that expression of dinF protects against bile salts, probably by decreasing the effects of ROS, which is consistent with the observed decrease in H2O2-killing
and protein carbonylation. These results, together with its ability to
decrease the level of intracellular ROS, suggests that DinF can
detoxify, either direct or indirectly, oxidizing molecules that can
damage DNA and proteins from both the bacterial metabolism and the
environment. Although the exact mechanism of DinF activity remains to be
identified, we describe for the first time a role for dinF. |
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Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling |
Plant Journal
Hornitschek P, Kohnen MV, Lorrain S, Rougemont J, Ljung K, López-Vidriero I, Franco-Zorrilla JM, Solano R, Trevisan M, Pradervand S, Xenarios I, Fankhauser C.
 Plant growth is strongly influenced by the presence of neighbors competing for light resources. In response to vegetational shading shade-intolerant plants such as Arabidopsis display a suite of developmental responses known as the shade avoidance syndrome (SAS).
The phytochrome B (phyB) photoreceptor is the major light sensor mediating this adaptive response. The control of the SAS occurs in part with phyB directly controlling protein abundance of Phytochrome Interacting Factors 4 and 5 (PIF4 and PIF5). The shade avoidance response also requires rapid biosynthesis of auxin and its transport to promote elongation growth. The identification of genome-wide PIF5 binding sites during shade avoidance reveals that this bHLH transcription factor regulates the expression of a subset of previously identified SAS genes. Moreover our study suggests that PIF4 and PIF5 regulate elongation growth by directly controlling the expression of genes coding for auxin biosynthesis and auxin signaling components. |
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The genetic network of the TOL plasmid pWW0 of the soil bacterium Pseudomonas putida mt-2 for catabolism of m-xylene is an archetypal model for environmental biodegradation of aromatic pollutants.
Although nearly every metabolic and transcriptional component of this regulatory system
is known to an extraordinary molecular detail, the complexity of its architecture
is still perplexing.