Phylogenetic analysis of fungal ABC transporters

Background: The superfamily of ABC proteins is among the largest known in nature. Its members are mainly, but not exclusively, involved in the transport of a broad range of substrates across biological membranes. Many contribute to multidrug resistance in microbial pathogens and cancer cells. The diversity of ABC proteins in fungi is comparable with those in multicellular animals, but so far fungal ABC proteins have barely been studied. Results: We performed a phylogenetic analysis of the ABC proteins extracted from the genomes of 27 fungal species from 18 orders representing 5 fungal phyla thereby covering the most important groups. Our analysis demonstrated that some of the subfamilies of ABC proteins remained highly conserved in fungi, while others have undergone a remarkable group-specific diversification. Members of the various fungal phyla also differed significantly in the number of ABC proteins found in their genomes, which is especially reduced in the yeast S. cerevisiae and S. pombe. Conclusions: Data obtained during our analysis should contribute to a better understanding of the diversity of the fungal ABC proteins and provide important clues about their possible biological functions.

Towards the development of Bacillus subtilis as a cell factory for membrane proteins and protein complexes

Background: The Gram-positive bacterium Bacillus subtilis is an important producer of high quality industrial enzymes and a few eukaryotic proteins. Most of these proteins are secreted into the growth medium, but successful examples of cytoplasmic protein production are also known. Therefore, one may anticipate that the high protein production potential of B. subtilis can be exploited for protein complexes and membrane proteins to facilitate their functional and structural analysis. The high quality of proteins produced with B. subtilis results from the action of cellular quality control systems that efficiently remove misfolded or incompletely synthesized proteins. Paradoxically, cellular quality control systems also represent bottlenecks for the production of various heterologous proteins at significant concentrations. Conclusion: While inactivation of quality control systems has the potential to improve protein production yields, this could be achieved at the expense of product quality. Mechanisms underlying degradation of secretory proteins are nowadays well understood and often controllable. It will therefore be a major challenge for future research to identify and modulate quality control systems of B. subtilis that limit the production of high quality protein complexes and membrane proteins, and to enhance those systems that facilitate assembly of these proteins.

Single-Cell Census of Mechanosensitive Channels in Living Bacteria

Bacteria are subjected to a host of different environmental stresses. One such insult occurs when cells encounter changes in the osmolarity of the surrounding media resulting in an osmotic shock. In recent years, a great deal has been learned about mechanosensitive (MS) channels which are thought to provide osmoprotection in these circumstances by opening emergency release valves in response to membrane tension. However, even the most elementary physiological parameters such as the number of MS channels per cell, how MS channel expression levels influence the physiological response of the cells, and how this mean number of channels varies from cell to cell remain unanswered. In this paper, we make a detailed quantitative study of the expression of the mechanosensitive channel of large conductance (MscL) in different media and at various stages in the growth history of bacterial cultures. Using both quantitative fluorescence microscopy and quantitative Western blots our study complements earlier electrophysiology-based estimates and results in the following key insights: i) the mean number of channels per cell is much higher than previously estimated, ii) measurement of the single-cell distributions of such channels reveals marked variability from cell to cell and iii) the mean number of channels varies under different environmental conditions. The regulation of MscL expression displays rich behaviors that depend strongly on culturing conditions and stress factors, which may give clues to the physiological role of MscL. The number of stress-induced MscL channels and the associated variability have far reaching implications for the in vivo response of the channels and for modeling of this response. As shown by numerous biophysical models, both the number of such channels and their variability can impact many physiological processes including osmoprotection, channel gating probability, and channel clustering

Towards the development of as a cell factory for membrane proteins and protein complexes-2

FtsA and ZipA are recruited next, independently from one another. Once both FtsA and ZipA have localized, the remaining proteins join the ring in the order indicated. Model for assembly of proteins into the septal ring during vegetative growth of . The assembly of late vegetative division proteins (FtsL, DivIB, DivIC and Pbp2B) is not linear and these components appear to assemble in a completely interdependent manner.<p><b>Copyright information:</b></p><p>Taken from "Towards the development of as a cell factory for membrane proteins and protein complexes"</p><p>http://www.microbialcellfactories.com/content/7/1/10</p><p>Microbial Cell Factories 2008;7():10-10.</p><p>Published online 4 Apr 2008</p><p>PMCID:PMC2323362.</p><p></p

Towards the development of as a cell factory for membrane proteins and protein complexes-0

Prises a peripheral motor domain SecA, the protein-conducting channel SecYEG, and the accessory proteins SecDF(yajC) and YidC. Membrane proteins are cotranslationally targeted to the Sec translocase as ribosome-bound nascent chains by the SRP and the SRP-receptor FtsY. FtsY associates with the SecY subunit of the Sec translocase, and associates with SRP in a GTP-dependent fashion. GTP hydrolysis at FtsY and SRP effects the release of the ribosome-nascent chain complex from SRP to the SecY subunit of the Sec translocase. Next, chain elongation at the ribosome is directly coupled to the SecY-mediated insertion of the nascent membrane protein into the cytoplasmic membrane. During membrane insertion, newly synthesized transmembrane segments of nascent membrane proteins contact YidC, which may facilitate the lateral release of these hydrophobic segments into the lipid bilayer and/or assist in their folding and assembly. Translocation of large polar extracellular regions through the SecYEG translocation pore is effected by SecA at the expense of ATP. YidC also acts as a Sec-independent membrane protein insertase for a number of small membrane proteins. These proteins are either targeted directly to YidC, or possibly utilize SRP and FtsY for targeting. How SRP discriminates between SecYEG- and YidC-dependent targeting of nascent membrane proteins is unknown. Abbreviation: PMF, proton motive force.<p><b>Copyright information:</b></p><p>Taken from "Towards the development of as a cell factory for membrane proteins and protein complexes"</p><p>http://www.microbialcellfactories.com/content/7/1/10</p><p>Microbial Cell Factories 2008;7():10-10.</p><p>Published online 4 Apr 2008</p><p>PMCID:PMC2323362.</p><p></p

Towards the development of as a cell factory for membrane proteins and protein complexes-3

Prises a peripheral motor domain SecA, the protein-conducting channel SecYEG, and the accessory proteins SecDF(yajC) and YidC. Membrane proteins are cotranslationally targeted to the Sec translocase as ribosome-bound nascent chains by the SRP and the SRP-receptor FtsY. FtsY associates with the SecY subunit of the Sec translocase, and associates with SRP in a GTP-dependent fashion. GTP hydrolysis at FtsY and SRP effects the release of the ribosome-nascent chain complex from SRP to the SecY subunit of the Sec translocase. Next, chain elongation at the ribosome is directly coupled to the SecY-mediated insertion of the nascent membrane protein into the cytoplasmic membrane. During membrane insertion, newly synthesized transmembrane segments of nascent membrane proteins contact YidC, which may facilitate the lateral release of these hydrophobic segments into the lipid bilayer and/or assist in their folding and assembly. Translocation of large polar extracellular regions through the SecYEG translocation pore is effected by SecA at the expense of ATP. YidC also acts as a Sec-independent membrane protein insertase for a number of small membrane proteins. These proteins are either targeted directly to YidC, or possibly utilize SRP and FtsY for targeting. How SRP discriminates between SecYEG- and YidC-dependent targeting of nascent membrane proteins is unknown. Abbreviation: PMF, proton motive force.<p><b>Copyright information:</b></p><p>Taken from "Towards the development of as a cell factory for membrane proteins and protein complexes"</p><p>http://www.microbialcellfactories.com/content/7/1/10</p><p>Microbial Cell Factories 2008;7():10-10.</p><p>Published online 4 Apr 2008</p><p>PMCID:PMC2323362.</p><p></p

Towards the development of as a cell factory for membrane proteins and protein complexes-1

The hexameric DivIVA oligomer. Further oligomerization of DivIVA "doggy-bones" leads to two-dimensional network formation. A tentative model for the two-dimensional DivIVA network [100].<p><b>Copyright information:</b></p><p>Taken from "Towards the development of as a cell factory for membrane proteins and protein complexes"</p><p>http://www.microbialcellfactories.com/content/7/1/10</p><p>Microbial Cell Factories 2008;7():10-10.</p><p>Published online 4 Apr 2008</p><p>PMCID:PMC2323362.</p><p></p

Modulation of Lactobacillus plantarum Gastrointestinal Robustness by Fermentation Conditions Enables Identification of Bacterial Robustness Markers.

Contains fulltext : 108700.pdf (publisher's version ) (Open Access)BACKGROUND: Lactic acid bacteria (LAB) are applied worldwide in the production of a variety of fermented food products. Additionally, specific Lactobacillus species are nowadays recognized for their health-promoting effects on the consumer. To optimally exert such beneficial effects, it is considered of great importance that these probiotic bacteria reach their target sites in the gut alive. METHODOLOGY/PRINCIPAL FINDINGS: In the accompanying manuscript by Bron et al. the probiotic model organism Lactobacillus plantarum WCFS1 was cultured under different fermentation conditions, which was complemented by the determination of the corresponding molecular responses by full-genome transcriptome analyses. Here, the gastrointestinal (GI) survival of the cultures produced was assessed in an in vitro assay. Variations in fermentation conditions led to dramatic differences in GI-tract survival (up to 7-log) and high robustness could be associated with low salt and low pH during the fermentations. Moreover, random forest correlation analyses allowed the identification of specific transcripts associated with robustness. Subsequently, the corresponding genes were targeted by genetic engineering, aiming to enhance robustness, which could be achieved for 3 of the genes that negatively correlated with robustness and where deletion derivatives displayed enhanced survival compared to the parental strain. Specifically, a role in GI-tract survival could be confirmed for the lp_1669-encoded AraC-family transcription regulator, involved in capsular polysaccharide remodeling, the penicillin-binding protein Pbp2A involved in peptidoglycan biosynthesis, and the Na(+)/H(+) antiporter NapA3. Moreover, additional physiological analysis established a role for Pbp2A and NapA3 in bile salt and salt tolerance, respectively. CONCLUSION: Transcriptome trait matching enabled the identification of biomarkers for bacterial (gut-)robustness, which is important for our molecular understanding of GI-tract survival and could facilitate the design of culture conditions aimed to enhance probiotic culture robustness