Ayako Takada

Involvement of RNase G in in vivo mRNA metabolism in Escherichia coli

Escherichia coli rng gene (previously called cafA) encodes a novel RNase, named RNase G, which is involved in the 5′ end‐processing of 16S rRNA. In rng mutant cells, a precursor form of 16S rRNA, 16.3S rRNA, is accumulated. Here we report a role of RNase G in the in vivo mRNA metabolism.

A decreased level of FtsZ is responsible for inviability of RNase E-deficient cells

The endoribonuclease RNase E, encoded by the essential gene rne, plays a major role in cellular RNA metabolism, i.e. maturation of functional RNAs such as rRNA and tRNA, degradation of many mRNAs and processing of the ftsZ mRNA which encodes the essential cell division protein FtsZ. RNase E function is somehow regulated by the RNA binding protein Hfq. We found that temperature‐sensitive colony formation of a rne‐1 mutant was partially suppressed by introduction of a hfq::cat mutation. Neither accumulation of rRNA and tRNAPhe precursors nor incomplete processing of ftsZ mRNA in the rne‐1 mutant was rescued by the hfq::cat mutation. However, the amount of FtsZ protein that was decreased in the rne‐1 mutant was recovered up to a level similar to that of wild‐type cells by the hfq::cat mutation. Overproduction of Hfq inhibited cell division because of decreased expression of FtsZ. Artificial expression of the FtsZ protein from a plasmid‐borne ftsZ gene partially suppressed the temperature‐sensitivity of the rne‐1 mutant. These results suggest that the decreased level of FtsZ is, at least in part, responsible for the inviability of RNase E‐deficient cells.

L-Glutamate Secretion by the N-Terminal Domain of the Corynebacterium glutamicum NCgl1221 Mechanosensitive Channel

The Corynebacterium glutamicum NCgl1221 mechanosensitive channel mediates L-glutamate secretion by sensing changes in membrane tension caused by treatments such as biotin limitation and penicillin. The NCgl1221 protein has an N-terminal domain (1-286 a.a.) homologous to the Escherichia coli MscS and a long C-terminal domain (287-533 a.a.) of unknown function. In order to investigate the role of the C-terminal domain in L-glutamate secretion, we constructed a series of C-terminally truncated mutants of NCgl1221. We found that the N-terminal domain, homologous to E. coli MscS, retained the ability to cause L-glutamate secretion in response to the treatment. Electrophysiological analysis confirmed that the N-terminal domain mediated L-glutamate secretion. 3D homology modeling has suggested that the N-terminal domain of NCgl1221 has an extra loop structure (221-232 a.a.) that is not found in most other MscS proteins. The mutant NCgl1221, deleted for this loop structure, lost the ability to secrete L-glutamate. In addition, we found that mutant NCgl1221 lacking the C-terminal extracytoplasmic domain (420-533 a.a.) produced L-glutamate without any inducing treatment. These results suggest that the N-terminal domain is necessary and sufficient for the excretion of L-glutamate in response to inducing treatment, and that the C-terminal extracytoplasmic domain has a negative regulatory role in L-glutamate production.

RNase E Is Required for Induction of the Glutamate-Dependent Acid Resistance System in Escherichia coli

The Escherichia coli RNase E is an essential endoribonuclease involved in processing and/or degradation of rRNAs, tRNAs, and non-coding small RNAs as well as many mRNAs. It is known that RNase E activity is somehow regulated by an RNA-binding protein Hfq, at least in some cases. We searched for proteins that showed changes in expression in both hfq::cat and rne-1 mutant cells as compared with the wild type, and found that a protein band of 49-kDa decreased in these mutant cells at 42 °C, the restrictive temperature for rne-1. N-terminal amino acid sequencing identified it as a mixture of GadA and GadB, two isozymes of glutamate decarboxylase involved in glutamate-dependent acid resistance. The rne-1 mutant as well as the hfq mutant showed decreased survival under acidic conditions (pH 2.5). Hfq is known to regulate the expression of GadA/B in RpoS- and GadY small RNA-dependent ways. We examined the expression of these two regulators in rne-1 mutant cells. In the mutant cells, the induction of GadY was defective at 42 °C, but the expression of RpoS was normal. These results indicate that RNase E is required for induction of the glutamate-dependent acid resistance system in a RpoS-independent manner.

Transcriptional Analysis of the Escherichia coli mreBCD Genes Responsible for Morphogenesis and Chromosome Segregation

The Escherichia coli mreB gene encodes an actin-like cytoskeletal protein and is required for rod shape formation of cells and chromosome segregation. Just downstream of mreB, the mreC and mreD genes are located. They are also required for rod shape formation, though their role in chromosome segregation is unclear. lacZ fusion analysis and Northern hybridization showed that the mreB, mreC, and mreD genes formed an operon. Most of the transcripts were expressed as a monocistronic mreB mRNA, and only 1–2% of the transcripts were expressed as a polycistronic mreBCD mRNA. Introduction of a frame-shift mutation in the mreB gene resulted in a significant decrease in the amount of polycistronic mreBCD mRNA but not in that of monocistronic mreB mRNA, suggesting that an attenuation-like regulation was involved in this transcriptional control. Primer extension analysis identified three transcriptional initiation sites. Three possible σD-dependent promoter-like sequences were found just upstream of these transcriptional initiation sites. lacZ fusion analysis confirmed that these three promoters contributed to the expression of mreBCD. On the basis of these findings, the essentiality of the mreB gene was confirmed.

Microfabrication of Si and GaAs by Plasma Etching Process Using Bacterial Cells as an Etching Mask Material

We demonstrated that bacterial cells can be used as a mask material for microfabrication of GaAs and Si by a Cl2 inductively coupled plasma (ICP) etching process. The etching rate of Escherichia coli cells was similar to that of electron beam resist or nanoimprint resist. We also demonstrated the degradation of bacterial cells by low-pressure plasma treatment using O2, Ar, air, and H2O for removal of bacterial cells as the etching mask material. Bacterial cells were efficiently degraded by ions in the low-pressure discharge plasma. The proposed process using bacterial cells can be expected to be applied to semiconductor dry etching processes.

High-Frequency Single-Cell Isolation of Bacteria Using Microenclosure Array with Multipillar Structure

We proposed and demonstrated the single-cell isolation of bacteria using a microenclosure array with a structure composed of many micropillars. We fabricated the microenclosure array on a semiconductor wafer by electron beam lithography and the dry etching technique. The capturing frequency for single cells of Escherichia coli was approximately 50% using a 4-µm-width microenclosure array. We think that the proposed novel technique is very simple and useful for the single-cell isolation of many kinds of bacteria using a microenclosure array of optimum size.

The role of Bgl2p in the transition to filamentous cells during biofilm formation by Candida albicans

The fungal pathogen Candida albicans undergoes a transition from yeast cells to filamentous cells that is related to its pathogenicity. The complex multicellular processes involved in biofilm formation by this fungus also include this transition. In this work, we investigated the morphological role of the Bgl2 protein (Bgl2p) in the transition to filamentous cells during biofilm formation by C. albicans. Bgl2p has been identified as a β‐1, 3‐glucosyltransferase, and transcription of the CaBGL2 gene is upregulated during biofilm formation. We used scanning electron microscopy to observe the microstructure of a bgl2 null mutant during biofilm formation and found a delay in the transition to filamentous cells in the premature phase (24 hours) of biofilm formation. Deletion of the CaBGL2 gene led to a decrease in the expression of CPH2 and TEC1, which encode transcription factors required for the transition to the filamentous form. These findings indicate that Bgl2p plays a role in the transition to filamentous cells during biofilm formation by C. albicans.

Effects of EGTA on cell surface structures of Corynebacterium glutamicum

The mycolic acid layer and S-layer of Corynebacterium glutamicum have been considered as permeability barriers against lytic agents. EGTA, a calcium chelator, inhibited C. glutamicum growth at relatively lower concentrations compared with other Gram-positive bacteria. We investigated the effect of EGTA on C. glutamicum cell surface structures. Simultaneous addition of EGTA and lysozyme resulted in cell lysis, whereas addition of these reagents separately had no such effect. Analysis of cell surface proteins showed that CspB, an S-layer protein, was released into the culture media and degraded to several sizes upon EGTA treatment. These findings suggest that EGTA treatment causes release and proteolysis of the CspB protein, resulting in increased cell surface permeability. FE-SEM visualization further confirmed alteration of cell surface structures in EGTA-treated cells. This is the first report suggesting the importance of calcium ions in cell surface integrity of C. glutamicum.

Microchannel-free collection and single-cell isolation of yeast cells in a suspension using liquid standing wave

We demonstrate a microchannel-free collection method at nodes of liquid standing waves by the vertical vibration of a suspension including yeast cells. The pattern formation of the collection of cells using standing waves in a suspension was investigated by varying the frequency and waveform of vibrations. The single-cell isolation of yeast cells was achieved using a microenclosure array set at the nodes. In addition, we succeeded in the microchannel-free collection of yeast cells in a suspension, where patterns were formed by tapping vibration. The proposed technique is very simple and we believe that it will be useful for single-cell analysis and investigation.