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Archives of Microbiology (v.193, #5)

Phylogeny and compatibility: plasmid classification in the genomics era by Jörn Petersen (pp. 313-321).

Whole genome sequences are present-day bonanzas for taxonomists. Comparative genomics provides a promising perspective to reveal the evolutionary relationship between organisms, but this strategy is not applicable for extrachromosomal elements due to their high recombination frequencies. Classification of plasmids is based on their compatibility, i.e., the ability to coexist within the same cell. Compatibility testing is a laborious experimental discipline of pairwise comparisons developed for a small set of replicons. Thus, novel approaches are urgently required to deal with the exponentially increasing amount of sequence data. In this minireview, a short overview about the functional role and distribution of plasmids as well as a summary of recent strategies to classify the replicons via phylogenetic analyses is given. Our own work essentially bases on genes of the replication module, i.e., the replicase and two conserved partitioning genes and we exemplified this approach for the four different plasmid types from Alphaproteobacteria. It is suitable for a reliable classification of these replicons and allows in silico predictions about their compatibility. The development of a general classification scheme for plasmids from all microbial lineages will ensure a systematic assessment of the upcoming data flood and help to understand the distribution of extrachromosomal elements.

Keywords: Plasmid classification; Replicase; Partitioning operon; Compatibility; Conjugation; Roseobacter clade

Ethanol induces calcium influx via the Cch1-Mid1 transporter in Saccharomyces cerevisiae by William E. Courchesne; Christopher Vlasek; Rachel Klukovich; Sara Coffee (pp. 323-334).

Yeast suffers from a variety of environmental stresses, such as osmotic pressure and ethanol produced during fermentation. Since calcium ions are protective for high concentrations of ethanol, we investigated whether Ca²⁺ flux occurs in response to ethanol stress. We find that exposure of yeast to ethanol induces a rise in the cytoplasmic concentration of Ca²⁺. The response is enhanced in cells shifted to high-osmotic media containing proline, galactose, sorbitol, or mannitol. Suspension of cells in proline and galactose-containing media increases the Ca²⁺ levels in the cytoplasm independent of ethanol exposure. The enhanced ability for ethanol to induce Ca²⁺ flux after the hypertonic shift is transient, decreasing rapidly over a period of seconds to minutes. There is partial recovery of the response after zymolyase treatment, suggesting that cell wall integrity affects the ethanol-induced Ca²⁺ flux. Acetate inhibits the Ca²⁺ accumulation elicited by the ethanol/osmotic stress. The Ca²⁺ flux is primarily via the Cch1 Ca²⁺ influx channel because strains carrying deletions of the cch1 and mid1 genes show greater than 90% reduction in Ca²⁺ flux. Furthermore, a functional Cch1 channel reduced growth inhibition by ethanol.

Keywords: Ethanol; Osmolarity; Calcium; Yeast

Effect of glucose on xylose utilization in Saccharomyces cerevisiae harboring the xylose reductase gene by Ji-Hye Han; Ju-Yong Park; Kye Sang Yoo; Hyun Woo Kang; Gi-Wook Choi; Bong-Woo Chung; Jiho Min (pp. 335-340).

We have constructed recombinant Saccharomyces cerevisiae JH1 harboring a xylose reductase gene (xyl1) isolated from Pichia stipitis. However, JH1 still utilizes glucose more easily than xylose. Therefore, in this study, we characterized the effect of a glucose supplement on xylose utilization, the expression level of xylose reductase as a recombinant gene in JH1, and the expression levels of two hexose transporters (Hxt4 and Hxt7) due to co-fermentation of different concentrations of glucose and xylose. Co-fermentation using 20 g/l of glucose increased xylose consumption up to 11.7 g/l, which was 7.9-fold that of xylose fermentation without a glucose supplement. In addition, we found xyl1 mRNA levels dramatically increased as cells grew under co-fermentation conditions with supplementary glucose; this result is consistent with a significant decrease in the xylose concentration 48 h after cultivation. In addition, the expression levels of Hxt4 and Hxt7 were strongly activated by the presence of glucose and xylose; in particular, Hxt7 showed a 2.9-fold increased expression relative to that of recombinant S. cerevisiae JHM with only a backbone vector, pYES2. The results of this study suggest that xylose utilization would be improved by activation of hexose transporters induced by glucose (rather than xylose) reductase expression.

Keywords: Saccharomyces cerevisiae ; Xylose reductase; Xylose uptake; Hexose transporter

Development of a fluorophore-ribosomal DNA restriction typing method for monitoring structural shifts of microbial communities by Tingting Wang; Xiaojun Zhang; Menghui Zhang; Linghua Wang; Liping Zhao (pp. 341-350).

DNA restriction fragment polymorphism technologies such as amplified ribosomal DNA restriction analysis (ARDRA) and terminal restriction fragment length polymorphism (T-RFLP) have been widely used in investigating microbial community structures. However, these methods are limited due to either the low resolution or sensitivity. In this study, a fluorophore-ribosomal DNA restriction typing (f-DRT) approach is developed for structural profiling of microbial communities. 16S rRNA genes are amplified from the community DNA and digested by a single restriction enzyme Msp I. All restriction fragments are end-labeled with a fluorescent nucleotide Cy5-dCTP via a one-step extension reaction and detected with an automated DNA sequencer. All 50 predicted restriction fragments between 100 and 600 bp were detected when twelve single 16S rRNA gene sequences were analyzed using f-DRT approach; 92% of these fragments were determined with accuracy of ±2 bp. In the defined model communities containing five components with different ratios, relative abundance of each component was correctly revealed by this method. The f-DRT analysis also showed structural shifts of intestinal microbiota in carcinogen-treated rats during the formation of precancerous lesions in the colon, as sensitive as multiple digestion-based T-RFLP analysis. This study provides a labor and cost-saving new method for monitoring structural shifts of microbial communities.

Keywords: rDNA; Restriction typing; Microbial community; Structural shifts

Modulation of a thermoregulated type VI secretion system by AHL-dependent Quorum Sensing in Yersinia pseudotuberculosis by Weipeng Zhang; Shengjuan Xu; Jing Li; Xihui Shen; Yao Wang; Zhiming Yuan (pp. 351-363).

The type VI secretion system (T6SS) is a novel secretion system found in many Gram-negative bacterial pathogens, which appears to be tightly regulated by different regulatory mechanisms. In the present study, we identified 4 T6SS clusters in Yersinia pseudotuberculosis and demonstrated that they were differentially thermoregulated. Among them, T6SS4 was preferentially expressed at 26°C, and its expression was growth phase dependent and subject to quorum sensing regulation. Both YpsI and YtbI AHL synthases contributed to the positive regulation of T6SS4, whereas YpsI synthase played the major role as T6SS4 expression was reduced strongly in the ypsI mutant strain but weakly in the ytbI mutant strain. Moreover, we provided evidence that exogenous addition of different synthetic AHLs complemented T6SS4 expression in different efficiencies in an ypsIytbI double mutant strain, suggesting C6-HSL had an antagonistic effect on T6SS4 expression. This is the first study demonstrating that the expression of T6SS is precisely regulated by temperature, growth phase, and AHL-dependent quorum sensing systems in Y. pseudotuberculosis.

Keywords: Yersinia pseudotuberculosis ; Type VI secretion system; Quorum sensing; N-acylhomoserine lactones

Ammonium and attachment of Rhodopirellula baltica by Carsten S. Frank; Philipp Langhammer; Bernhard Maximilian Fuchs; Jens Harder (pp. 365-372).

A dimorphic life cycle has been described for the planctomycete Rhodopirellula baltica SH1^T, with juvenile motile, free-swimming cells and adult sessile, attached-living cells. However, attachment as a response to environmental factors was not investigated. We studied the response of R. baltica to nitrogen limitation. In batch cultures, ammonium limitation coincided with a dominance of free-swimming cells and a low number of aggregates. Flow cytometry revealed a quantitative shift with increasing ammonium availability, from single cells towards attached cells in large aggregates. During growth of R. baltica on glucose and ammonium in chemostats, an ammonium addition caused a macroscopic change of the growth behaviour, from homogeneous growth in the liquid phase to a biofilm on the borosilicate glass wall of the chemostat vessel. Thus, an ammonium limitation—a carbon to nitrogen supply ratio of 30:1—sustained free-living growth without aggregate formation. A sudden increase in ammonium supply induced sessile growth of R. baltica. These observations reveal a response of Rhodopirellula baltica cells to ammonium: they abandon the free-swimming life, attach to particles and form biofilms.

Keywords: Ammonium; Planctomycetales ; Biofilm; Rhodopirellula ; Carbon/nitrogen ratio; Flow cytometry

Escherichia coli cold shock protein CsdA effects an increase in septation and the resultant formation of coccobacilli at low temperature by Ashley Pierce; Devyn Gillette; Pamela G. Jones (pp. 373-384).

Bacterial shape is controlled by peptidoglycan assembly along the lateral wall and at the septum site. In contrast to rods at 37°C, the wild-type strain formed coccobacilli at 12°C, indicating a prevailing shift toward septal peptidoglycan synthesis at low temperature. Escherichia coli cold shock protein CsdA is a DEAD-box RNA helicase with an extended variable region at the carboxyl terminus. The csdA null mutant formed elongated cells indicating that CsdA, directly or indirectly, effects an increase in septation and the resultant coccobacillus morphology. Lipoprotein NlpI is suggested for a role in cell division. The presence of a plasmid encoding CsdA or NlpI increased septation and coccobacillus morphology of the csdA null mutant cells. Plasmid-encoded CsdAΔ445 (lacking the C-terminal extension) in the mutant complemented the growth and resulted in the appearance of coccobacillus- and rod-shaped cells. In contrast, a plasmid encoding both NlpI and CsdAΔ445 in the wild-type or mutant resulted in inhibition of growth accompanied with the formation of elongated and misshapen cells. However, a plasmid encoding both NlpI and CsdA resulted in normal growth and coccobacilli. The data indicate that the addition of the C-terminal extension yields an increase in septation and the resultant increased formation of coccobacilli.

Keywords: CsdA; Cold shock response; Coccobacilli; DEAD-box RNA helicase

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Archives of Microbiology (v.193, #5)

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Archives of Microbiology (v.193, #5)