Research in Microbiology (RES MICROBIOL)

Publications in this journal

• Article: Phylogenetic analyses of phylum actinobacteria based on whole genome sequences.

  Mansi Verma, Devi Lal, Jaspreet Kaur, Anjali Saxena, Jasvinder Kaur, Shailly Anand, Rup Lal
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  ABSTRACT: Actinobacteria constitute one of the largest and ancient taxonomic phylum within the domain bacteria and are well known for their secondary metabolites. Considerable variation in the metabolic properties, genome size and GC content of the members of this phylum has been observed. Therefore, the placement of new or existing species based on 16S rRNA gene sometimes becomes problematic due to the low congruence level. In the present study, phylogeny of ninety actinobacterial genomes was reconstructed using single gene and whole genome based data. Where alignment-free phylogenetic method was found to be more robust, the concatenation of 94 proteins improved the resolution which all single gene based phylogenies failed to resolve. The comprehensive analysis of 94 conserved proteins resulted in a total of 42,447 informative sites, which is so far the largest meta-alignment obtained for this phylum. But the ultimate resolved phylogeny was obtained by generating a consensus tree by combining the information from single gene and genome based phylogenies. The present investigation clearly revealed that the consensus approach is a useful tool for phylogenetic inference and the taxonomic affiliations must be based on this approach. The consensus approach suggested that there is a need for taxonomic amendments of the orders Frankiales and Micrococcales.
  Research in Microbiology 04/2013;
• Article: Biosorption of heavy metals by lactic acid bacteria and identification of mercury binding protein.

  Hideki Kinoshita, Yui Sohma, Fumika Ohtake, Mitsuharu Ishida, Yasushi Kawai, Haruki Kitazawa, Tadao Saito, Kazuhiko Kimura
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  ABSTRACT: Heavy metals cause various health hazards. Using lactic acid bacteria (LAB), we tested the biosorption of heavy metals e.g. cadmium (Cd) (II), lead (Pb) (II), arsenic (As) (III), and mercury (Hg) (II). Cd (II) sorption was tested in 103 strains using atomic absorption spectrophotometery (AAS). Weissella viridescens MYU 205 (1×10(8) cells/ml) decreased Cd (II) levels in citrate buffer (pH 6.0) from one ppm to 0.459 ± 0.016 ppm, corresponding to 10.46 μg of Cd (II). After screening, 11 LAB strains were tested using various pH (pH 4.0, 5.0, 6.0, 7.0) showing the sorption was acid sensitive; and was cell concentration dependent, where the Cd (II) concentration decreased from one ppm to 0.042 (max) / 0.255 (min) ppm at 1×10(10) cells/ml. Additionally, the biosorption of Pb (II), As (III), and Hg (II) were tested using an inductively coupled plasma mass spectrometer (ICP-MS). The Hg (II) concentration was reduced the most followed by Pb (II) and As (III). Many of the bacterial cell surface proteins of W. viridescens MYU 205 showed binding to Hg (II) using the Hg (II) column assay. Having a CXXC motif, a ∼14 kDa protein may be one of the Hg (II) binding proteins. LAB biosorption may aid the detoxification of people exposed to heavy metals.
  Research in Microbiology 04/2013;
• Article: Plasmids as scribbling pads for operon formation and propagation.

  Vic Norris, Annabelle Merieau
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  ABSTRACT: Many bacterial genes are in operons and the process whereby operons are formed is therefore fundamental. To help elucidate this process, we propose in the Scribbling Pad hypothesis that bacteria have been constantly using plasmids for genetic experimentation and, in particular, for the construction of operons. This hypothesis simultaneously solves the problems of the creation of operons and the way operons are propagated. We cite results in the literature to support the hypothesis and make experimental predictions to test it.
  Research in Microbiology 04/2013;
• Article: Rice and bean AHL-mimic quorum-sensing signals specifically interfere with the capacity to form biofilms by plant-associated bacteria.

  Francisco Pérez-Montaño, Irene Jiménez-Guerrero, Rocío Contreras Sánchez-Matamoros, Francisco Javier López-Baena, Francisco Javier Ollero, Miguel Ángel Rodríguez-Carvajal, Ramón A Bellogín, M Rosario Espuny
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  ABSTRACT: Many bacteria regulate their gene expression in response to changes in their population density in a process called quorum sensing (QS), which involves communication between cells mediated by small diffusible signal molecules termed autoinducers. n-acyl-homoserine-lactones (AHLs) are the most common autoinducers in proteobacteria. QS-regulated genes are involved in complex interactions between bacteria of the same or different species and even with some eukaryotic organisms. Eukaryotes, including plants, can interfere with bacterial QS systems by synthesizing molecules that interfere with bacterial QS systems. In this work, the presence of AHL-mimic QS molecules in diverse Oryza sativa (rice) and Phaseolus vulgaris (bean) plant-samples were detected employing three biosensor strains. A more intensive analysis using biosensors carrying the lactonase enzyme showed that bean and rice seed-extract contain molecules that lack the typical lactone ring of AHLs. Interestingly, these molecules specifically alter the QS-regulated biofilm formation of two plant-associated bacteria, Sinorhizobium fredii SMH12 and Pantoea ananatis AMG501, suggesting that plants are able to enhance or to inhibit the bacterial QS systems depending on the bacterial strain. Further studies would contribute to a better understanding of plant-bacteria relationships at the molecular level.
  Research in Microbiology 04/2013;
• Article: Key issues in phage therapy: a report of a dedicated workshop at the Viruses of Microbes II Meeting.

  Isabelle Huys, Mario Vaneechoutte, Gilbert Verbeken, Laurent Debarbieux
  Research in Microbiology 04/2013;
• Article: A short-term mineral amendment impacts the mineral weathering bacterial communities in an acidic forest soil.

  C Lepleux, S Uroz, C Collignon, J-L Churin, M-P Turpault, P Frey-Klett
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  ABSTRACT: Mineral amendment (i.e. calcium, phosphorous, potassium and /or magnesium) is a management practice used in forestry to improve nutrient availability and recover soil fertility, especially in nutrient-poor forest ecosystems. However, whether this amendment can lead to modifications of the soil characteristics and an improvement in tree growth, and its impact on the soil bacterial communities, especially the mineral weathering bacterial communities, remains poorly documented. In this study, we investigated the short-term impact of a mineral amendment on the taxonomic and functional structure of the mineral weathering bacterial communities. To do this, a plantation of four-year old oak (Quercus petraea) trees amended with or without dolomite [CaMg(CO3)2] was established in the experimental forest site of Breuil-Chenue, which is characterized by an acidic soil and a low availability of calcium and magnesium. Three years after amendment, soil samples were used to isolate bacteria as well as to determine the soil characteristics and the metabolic potentials of these soil microbial communities. Based on a bioassay for quantifying the solubilisation of inorganic phosphorous, we demonstrate that the bacterial isolates coming from the non-amended bulk soil were significantly more efficient than those that were amended. No difference was observed between the bacterial isolates coming from the amended and non-amended rhizospheres. Notably, the taxonomic analyses revealed a dominance of bacterial isolates belonging to the Burkholderia genus in both samples. Overall, our results suggest that the bioavailability of nutritive cations into soil impacts the distribution and the efficacy of mineral weathering bacterial communities coming from the soil but not those coming from the rhizosphere.
  Research in Microbiology 04/2013;
• Article: Protein translocation across the inner membrane of Gram-negative bacteria: The Sec and Tat dependent protein transport pathways.

  Renuka Kudva, Kärt Denks, Patrick Kuhn, Andreas Vogt, Matthias Müller, Hans-Georg Koch
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  ABSTRACT: Gram negative bacteria possess a large variety of protein transport systems, by which proteins that are synthesised in the cytosol are exported to destinations in the cell envelope or entirely secreted into the extracellular environment. The inner membrane (IM) contains three major transport systems for the translocation and insertion of signal sequence containing proteins: the Sec translocon, the YidC insertase, and the Tat system. The heterotrimeric SecYEG translocon forms a narrow channel in the membrane that serves a dual function; it allows the translocation of unfolded proteins across the pore and the integration of α-helical proteins into the IM. The YidC insertase is a multi-spanning membrane protein that cooperates with the SecYEG translocon during the integration of membrane proteins but also functions as an independent insertase. Depending upon the type of protein cargo that needs to be transported, the Signal Recognition Particle (SRP), the SRP receptor, SecA and chaperones are required to coordinate translation with transport and to target and energise the different transport systems. The Tat system consists of three membrane proteins (TatA, TatB and TatC) which in a still unknown manner accomplish the transmembrane passage of completely folded proteins and protein complexes.
  Research in Microbiology 04/2013;
• Article: Autotransporter secretion: varying on a theme.

  Jan Grijpstra, Jesús Arenas, Lucy Rutten, Jan Tommassen
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  ABSTRACT: Autotransporters are widely distributed among Gram-negative bacteria. They can have a large variety of functions and many of them have a role in virulence. They are synthesized as large precursors with an N-terminal signal sequence that mediates transport across the inner membrane via the Sec machinery and a translocator domain that mediates the transport of the connected passenger domain across the outer membrane to the bacterial cell surface. Like integral outer membrane proteins, the translocator domain folds in a β-barrel structure and requires the Bam machinery for its insertion into the outer membrane. After transport across the outer membrane, the passenger may stay connected via the translocator domain to the bacterial cell surface or it is proteolytically released into the extracellular milieu. Based on the size of the translocator domain and its position relative to the passenger in the precursor, autotransporters are divided into four sub-categories. We review here the current knowledge of the biogenesis, structure and function of various autotransporters.
  Research in Microbiology 04/2013;
• Article: The targeting, docking and anti-proteolysis functions of the secretin chaperone PulS.

  Séverine Collin, Martin Krehenbrink, Ingrid Guilvout, Anthony P Pugsley
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  ABSTRACT: The Klebsiella oxytoca lipoprotein PulS might function as either or both a pilot and a docking factor in the outer membrane targeting and assembly of the Type II secretion system secretin PulD. In the piloting model, PulS binds to PulD monomers and targets them to the outer membrane via the lipoprotein sorting pathway components LolA and LolB. In this model, PulS also protects the PulD monomers from proteolysis during transit through the periplasm. In the docking model, PulS is targeted alone to the outer membrane, where it acts as a receptor for PulD monomers, allowing them to accumulate and assemble specifically in this membrane. PulS was shown to dissociate from and/or re-associate freely with PulD multimers in zwitterionic detergent, making it difficult to determine whether PulS remains associated with PulD dodecamers in the outer membrane by co-purification. However, PulD protomers in the dodecamer were shown to be stable in the absence of PulS, indicating that PulS is only required to protect the protease-susceptible monomer. DegP was identified as one of the proteases that could contribute to PulD degradation in the absence of PulS. Studies on the in vitro assembly and targeting of PulD into Escherichia coli membrane vesicles demonstrated its strong preference to insert into the inner membrane, as is the case in vivo in the absence of PulS. However, PulD could be targeted to outer membrane fragments in vitro if they were preloaded with PulS, indicating the technical feasibility of the docking model. We conclude that both modes of action might contribute to efficient outer membrane targeting of PulD in vivo, although the piloting function is likely to predominate.
  Research in Microbiology 04/2013;
• Article: Interplay between extracellular matrix components of Pseudomonas putida biofilms.

  Marta Martínez-Gil, José Miguel Quesada, María Isabel Ramos-González, María Isabel Soriano, Ricardo E de Cristóbal, Manuel Espinosa-Urgel
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  ABSTRACT: The extracellular matrix of bacterial biofilms has at least two key functions: to serve as a structural scaffold for the multicellular community, and to play a protective role against external stress. In this work, we report a compensatory effect whereby Pseudomonas putida reacts to the lack of either of the two main surface proteins involved in biofilm formation, LapA and LapF, by increasing expression and production of a species-specific EPS. Elevated levels of the second messenger molecule cyclic di-GMP alter the balance of extracellular matrix components, and the phenotypes of lapA and lapF mutants under these conditions are indicative of direct interactions taking place between large secreted proteins and exopolysaccharides. Our data suggest the existence of a mechanism by which bacteria would sense alterations in the composition of the extracellular matrix, leading to changes in expression of the different elements.
  Research in Microbiology 04/2013;
• Article: The Expanding Bacterial Type IV Secretion Lexicon.

  Minny Bhatty, Jenny A Laverde Gomez, Peter J Christie
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  ABSTRACT: The bacterial type IV secretion systems (T4SSs) comprise a biologically diverse group of translocation systems functioning to deliver DNA or protein substrates from donor to target cells generally by a mechanism dependent on establishment of direct cell-to-cell contact. Members of one T4SS subfamily, the conjugation systems, mediate the widespread and rapid dissemination of antibiotic resistance and virulence traits among bacterial pathogens. Members of a second subfamily, the effector translocators, are used by often medically-important pathogens to deliver effector proteins to eukaryotic target cells during the course of infection. Here we summarize our current understanding of the structural and functional diversity of T4SSs and of the evolutionary processes shaping this diversity. We compare mechanistic and architectural features of T4SSs from Gram-negative and -positive species. Finally, we introduce the concept of the 'minimized' T4SSs; these are systems composed of a conserved set of 5-6 subunits that are distributed among many Gram-positive and some Gram-negative species.
  Research in Microbiology 03/2013;
• Article: Two-partner secretion: as simple as it sounds?

  Françoise Jacob-Dubuisson, Jérémy Guérin, Stéphanie Baelen, Bernard Clantin
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  ABSTRACT: The two-partner secretion (TPS) pathway is a branch of type V secretion. TPS systems are dedicated to the secretion across the outer membrane of long proteins that form extended β-helices. They are composed of a 'TpsA' cargo protein and a 'TpsB' transporter, which belongs to the Omp85 superfamily. This basic design can be supplemented by additional components in some TPS systems. X-ray structures are available for the conserved TPS domain of several TpsA proteins and for one TpsB transporter. However, the molecular mechanisms of two-partner secretion remain to be deciphered, and in particular, the specific role(s) of the TPS domain and the conformational dynamics of the TpsB transporter. Deciphering the TPS pathway may reveal functional features of other transporters of the Omp85 superfamily.
  Research in Microbiology 03/2013;
• Article: Non classical secretion systems.

  Roland Lloubes, Alain Bernadac, Laetitia Houot, Stephanie Pommier
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  ABSTRACT: Bacteria use molecular machines or weapons to colonize, invade or fight other bacteria and eukaryotic cells. In addition to these various secretion systems, two different systems that release bacterial compounds have also been described. The first one corresponds to membrane vesicle formation and to long distance delivery of membrane or soluble components. The second system is dependent of the expression of the colicin lysis genes known for releasing cytoplasmic colicins as well as other soluble proteins. Both systems will be described thereafter.
  Research in Microbiology 03/2013;
• Article: The type VI secretion system - a widespread and versatile cell targeting system.

  Sarah J Coulthurst
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  ABSTRACT: The type VI secretion system (T6SS) is the most recently-described of the Gram-negative bacterial secretion systems and is widely distributed amongst diverse species. T6SSs are currently believed to be complex molecular machines which inject effector proteins into target cells and which incorporate a bacteriophage-like cell puncturing device. T6SSs have been implicated in eukaryotic cell targeting and virulence in a range of important pathogens. More recently, 'antibacterial' T6SSs have been reported, which are used to efficiently target competitor bacterial cells by the injection of antibacterial toxins. Although it is clear that T6SSs can be deployed as versatile weapons to compete with other bacteria or attack simple or higher eukaryotes, much remains to be determined about this intriguing system.
  Research in Microbiology 03/2013;
• Article: Oxygen regulation of alternative respiration in fungus Phycomyces blakesleeanus: connection with phosphate metabolism.

  Marina Stanić, Joanna Zakrzewska, Mirzeta Hadžibrahimović, Milan Zižić, Zoran Marković, Zeljko Vučinić, Miroslav Zivić
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  ABSTRACT: Environmental changes can often result in oxygen deficiency which influences cellular energy metabolism, but such effects have been insufficiently studied in fungi. The effects of oxygen deprivation on respiration and phosphate metabolites in P. blakesleeanus were investigated by oxygen electrode and (31)P NMR spectroscopy. Mycelium was incubated in hypoxic and anoxic conditions for 1.5, 3 and 5 h and then reoxygenated. Participation of alternative oxidase (AOX) in total respiration increased gradually in both treatments and after 5 h of anoxia exceeded a value 50% higher than in control. Shortly after reintroduction of oxygen into the system AOX level decreased close to the control level. Oxygen deprivation also caused a reversible decrease of polyphosphate/inorganic phosphate ratio (PPc/Pi), which was strongly correlated with the increase of AOX participation in total respiration. Unexpectedly, ATP content remained almost constant, probably due to the ability of PolyP to sustain energy and phosphate homeostasis of the cell under stress conditions. This was further substantiated by the effects of azide, a cytochrome c oxidase inhibitor, which also decreased PPc/Pi ratio, but to a smaller extent in oxygen deprived than control and reoxygenated specimens.
  Research in Microbiology 03/2013;
• Article: The type II secretion system - a dynamic fiber assembly nanomachine.

  Manuel Campos, David Cisneros, Mangayarkarasi Nivaskumar, Olivera Francetic
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  ABSTRACT: Type II secretion systems (T2SSs) share common origins and structure with archaeal flagella (archaella) and pili, bacterial competence systems and type IV pili. All of these systems use a conserved ATP-powered machinery to assemble helical fibers that are anchored in the plasma membrane. The T2SSs assemble pseudopili, periplasmic filaments that promote extracellular secretion of folded periplasmic proteins. Comparative analysis of T2SSs and related fiber assembly nanomachines might provide important clues on their functional specificities and dynamics. This review focuses on recent developments in the study of pseudopilus structure and biogenesis, and discusses mechanistic models of pseudopilus function in protein secretion.
  Research in Microbiology 03/2013;
• Article: Type I secretion systems - a story of appendices.

  Kerstin Kanonenberg, Christian K W Schwarz, Lutz Schmitt
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  ABSTRACT: Secretion is an essential task for prokaryotic organisms to interact with their surrounding environment. In particular, the production of extracellular proteins and peptides is important for many aspects of an organism's survival and adaptation to their ecological niche. In Gram-negative bacteria, six different protein secretion systems have been identified so far, named Type I to Type VI; differing greatly in their composition and mechanism of action (Economou et al., 2006). The two membranes present in Gram-negative bacteria are negotiated either by one-step transport mechanisms (Type I and Type III), where the unfolded substrate is translocated directly into the extracellular space, without any periplasmic intermediates, or by two-step mechanisms (Type II and Type V), where the substrate is first transported into the periplasm to allow folding before a second transport step across the outer membrane occurs. Here we focus on Type I secretion systems and summarise our current knowledge of these one-step-transport machineries with emphasis on the N-terminal extensions found in many Type I-specific ABC transporters. ABC transporters containing an N-terminal C39 peptidase domain cut off a leader peptide present in the substrate prior to secretion. The function of the second type of appendix, the C39 peptidase-like domain (CLD) is not yet completely understood. Recent results have shown that it is nonetheless essential for secretion and interacts specifically with the substrate of the transporter. The third group present does not contain any appendix. In light of this difference we compare the function of the appendix and the differences that might exist among the three families of T1SS.
  Research in Microbiology 03/2013;
• Article: Leaving home ain´t easy: Protein export systems in Gram-positive bacteria.

  Roland Freudl
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  ABSTRACT: Transport of proteins into or across biological membranes is catalyzed by membrane-bound transport machinery. In Gram-positive bacteria, the vast majority of proteins are exported out of the cytosol by the conserved general secretion (Sec) system or, alternatively, by the twin-arginine translocation (Tat) system, that closely resemble their well-studied counterparts in Gram-negative bacteria. Besides these common major export routes, additional unique protein export systems (such as accessory Sec2 systems and/or type VII/WXG100 secretion systems) exist in some Gram-positive bacteria that are specifically involved in the secretion of limited subsets of proteins.
  Research in Microbiology 03/2013;
• Article: Structural basis of eukaryotic cell targeting by type III secretion system (T3SS) effectors.

  Tommaso Tosi, Alexander Pflug, Karen F Discola, David Neves, Andréa Dessen
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  ABSTRACT: Type III secretion systems (T3SS) are macromolecular complexes that translocate a wide number of effector proteins into eukaryotic host cells. Once within the cytoplasm, many T3SS effectors mimic the structure and/or function of eukaryotic proteins in order to manipulate signaling cascades, and thus play pivotal roles in colonization, invasion, survival and virulence. Structural biology techniques have played key roles in the unraveling of bacterial strategies employed for mimicry and targeting. This review provides an overall view of our current understanding of structure and function of T3SS effectors, as well as of the different classes of eukaryotic proteins that are targeted and the consequences for the infected cell.
  Research in Microbiology 03/2013;
• Article: Generic and functional diversity in endophytic actinomycetes from wild Compositae plant species at South Sinai - Egypt.

  Sahar A El-Shatoury, Omnia A El-Kraly, Martha E Trujillo, Waleed M El-Kazzaz, El-Sayeda Gamal El-Din, Ahmed Dewedar
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  ABSTRACT: The diversity of culturable endophytic actinomycetes associated with wild Compositae plants is scantily explored. In this study, one hundred and thirty one endophytic actinobacteria were isolated from ten Compositae plant species collected from South Sinai in Egypt. Microscopic and chemotaxonomic investigation of the isolates indicated fourteen genera. Rare genera, such as Microtetraspora, and Intrasporangium, which have never been previously reported to be endophytic, were identified. Each plant species accommodated between three to eight genera of actinobacteria and unidentified strains were recovered from seven plant species. The generic diversity analysis of endophytic assemblages grouped the plant species into three main clusters, representing high, moderate and low endophytic diversity. The endophytes showed high functional diversity, based on forty four catabolic and plant growth promotion traits; providing some evidence that such traits could represent key criteria for successful residence of endophytes in the endosphere. Stress-tolerance traits were more predictive measure of functional diversity differences between the endophyte assemblages (Shannon's index, p = 0.01). The results indicate a potential prominent role of endophytes for their hosts and emphasize the potency of plant endosphere as a habitat for actinobacteria with promising future applications.
  Research in Microbiology 03/2013;