Proteomics, DNA arrays and the analysis of still unknown regulons and unknown proteins of Bacillus subtilis and pathogenic gram-positive bacteria

Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology

In this review, we present the use of proteomics to advance knowledge in the field of environmental biotechnology, including studies of bacterial physiology, metabolism and ecology. Bacteria are widely applied in environmental biotechnology for their ability to catalyze dehalogenation, methanogenesis, denitrification and sulfate reduction, among others. Their tolerance to radiation and toxic compounds is also of importance. Proteomics has an important role in helping uncover the pathways behind these cellular processes. Environmental samples are often highly complex, which makes proteome studies in this field especially challenging. Some of these challenges are the lack of genome sequences for the vast majority of environmental bacteria, difficulties in isolating bacteria and proteins from certain environments, and the presence of complex microbial communities. Despite these challenges, proteomics offers a unique dynamic view into cellular function. We present examples of environmental proteomics of model organisms, and then discuss metaproteomics (microbial community proteomics), which has the potential to provide insights into the function of a community without isolating organisms. Finally, the environmental proteomics literature is summarized as it pertains to the specific application areas of wastewater treatment, metabolic engineering, microbial ecology and environmental stress responses.

The analysis of Neisseria meningitidis proteomes: Reference maps and their applications

Neisseria meningitidis is an encapsulated Gram-negative bacterium responsible for significant morbidity and mortality worldwide. The availability of meningococcal genome sequences in combination with the rapid growth of proteomic techniques and other high-throughput methods, provided new approaches to the analysis of bacterial system biology. This review considers the meningococcal reference maps so far published as a starting point aimed to elucidate bacterial physiology and pathogenicity, paying particular attention to proteins with potential vaccine and diagnostic applications.

DNA microarray technology for the microbiologist: an overview

DNA microarrays have found widespread use as a flexible tool to investigate bacterial metabolism. Their main advantage is the comprehensive data they produce on the transcriptional response of the whole genome to an environmental or genetic stimulus. This allows the microbiologist to monitor metabolism and to define stimulons and regulons. Other fields of application are the identification of microorganisms or the comparison of genomes. The importance of this technology increases with the number of sequenced genomes and the falling prices for equipment and oligonucleotides. Knowledge of DNA microarrays is of rising relevance for many areas in microbiological research. Much literature has been published on various specific aspects of this technique that can be daunting to the casual user and beginner. This article offers a comprehensive outline of microarray technology for transcription analysis in microbiology. It shortly discusses the types of DNA microarrays available, the printing of custom arrays, common labeling strategies for targets, hybridization, scanning, normalization, and clustering of expression data.

Bacillus subtilis RghR (YvaN) represses rapG and rapH, which encode inhibitors of expression of the srfA operon

Rap proteins regulate the activity of response regulators including Spo0F, DegU and ComA. We found that overexpression of either RapG or RapH severely downregulated the expression of srfA, which belongs to the ComA regulon. Disruption of those genes, however, showed small effects on srfA expression. These observations suggested that Bacillus subtilis cells possess a repressor for rapG and rapH. To identify candidate repressors we developed a novel transcription factor array (TF array) assay, in which disruptions of 287 genes encoding regulatory proteins were independently transformed into a strain carrying rapH-lacZ and the resultant transformants were grown on agar plates containing Xgal to detect beta-galactosidase activity. We identified a yvaN disruptant which showed a rapH-overproducing phenotype. DNA microarray analysis of the yvaN mutant suggested that both rapG and rapH were overproduced, leading to inhibition of srfA expression. In a gel retardation assay, purified His-tagged YvaN specifically bound to promoter sequences of rapG and rapH. Further footprint and gel retardation analyses using various deleted probes uncovered critical sequences for YvaN binding. In addition, a lacZ fusion analysis confirmed the significance of YvaN binding for transcription regulation of rapG and rapH. Thus, YvaN was renamed RghR (rapG and rapH repressor). As the rapH gene is activated by ComK and RapH inhibits comK indirectly, this constitutes an autoregulatory loop modulated by RghR.

Evaluation of the role of sigma B in Mycobacterium smegmatis

The alternate sigma factor, sigB, is known to play a crucial role in maintaining the stationary phase in mycobacteria. In this communication, we have studied the proteomics of Mycobacterium smegmatis mc(2)155 and its two derivatives, one of which has a disrupted sigB gene and the other, PMVSigB, which contains a multicopy plasmid containing sigB. We have identified by two-dimensional gel analyses, several proteins that are over-expressed in PMVSigB compared to mc(2)155. These proteins are either stress proteins or participate actively in different metabolic pathways of the organisms. On the other hand, when sigB deleted mycobacteria were grown until the stationary phase and its two-dimensional protein profile was compared to that of mc(2)155, few DNA binding proteins were found to be up-regulated. We have shown recently that upon over-expressing sigB, the cell surface glycopeptidolipids of M. smegmatis are hyperglycosylated, a situation similar to what was observed for nutritionally starved bacteria. Gene expression profile through quantitative PCR presented here identified a Rhamnosyltransferase responsible for this hyperglycosylation.

Microarray-based analysis of the Staphylococcus aureus sigmaB regulon

Microarray-based analysis of the transcriptional profiles of the genetically distinct Staphylococcus aureus strains COL, GP268, and Newman indicate that a total of 251 open reading frames (ORFs) are influenced by sigmaB activity. While sigmaB was found to positively control 198 genes by a factor of > or =2 in at least two of the three genetic lineages analyzed, 53 ORFs were repressed in the presence of sigmaB. Gene products that were found to be influenced by sigmaB are putatively involved in all manner of cellular processes, including cell envelope biosynthesis and turnover, intermediary metabolism, and signaling pathways. Most of the genes and/or operons identified as upregulated by sigmaB were preceded by a nucleotide sequence that resembled the sigmaB consensus promoter sequence of Bacillus subtilis. A conspicuous number of virulence-associated genes were identified as regulated by sigmaB activity, with many adhesins upregulated and prominently represented in this group, while transcription of various exoproteins and toxins were repressed. The data presented here suggest that the sigmaB of S. aureus controls a large regulon and is an important modulator of virulence gene expression that is likely to act conversely to RNAIII, the effector molecule of the agr locus. We propose that this alternative transcription factor may be of importance for the invading pathogen to fine-tune its virulence factor production in response to changing host environments.

Optimization of a two-plasmid system for the identification of promoters recognized by RNA polymerase containing Staphylococcus aureus alternative sigma factor sigmaB

We optimized a previously established two-plasmid system for the identification of Staphylococcus aureus promoters that are recognized by the alternative transcription factor sigma(B). The method allowed the identification of 18 S. aureus sigma(B)-dependent promoters, 12 of which are reported here for the first time to be sigma(B)-dependent. S1-nuclease mapping of the respective transcriptional start points revealed that all the promoters contained sequences exhibiting high similarity to the consensus sequence of Bacillus subtilis sigma(B)-dependent promoters. The promoters governed expression of genes encoding proteins proposed to be involved in various cellular functions, including the stress response genes and virulence-associated clfA gene for fibrinogen-binding clumping factor. Comparison of the nucleotide sequences upstream of the identified transcription start points identified a sigma(B) consensus promoter (GttTaa-N(12-15)-gGGTAt) that is highly homologous to that of sigma(B) of B. subtilis.

The alternative sigma factor sigmaB of Bacillus cereus: response to stress and role in heat adaptation

A gene cluster encoding the alternative sigma factor sigma(B), three predicted regulators of sigma(B) (RsbV, RsbW, and RsbY), and one protein whose function is not known (Orf4) was identified in the genome sequence of the food pathogen Bacillus cereus ATCC 14579. Western blotting with polyclonal antibodies raised against sigma(B) revealed that there was 20.1-fold activation of sigma(B) after a heat shock from 30 to 42 degrees C. Osmotic upshock and ethanol exposure also upregulated sigma(B), albeit less than a heat shock. When the intracellular ATP concentration was decreased by exposure to carbonyl cyanide m-chlorophenylhydrazone (CCCP), only limited increases in sigma(B) levels were observed, revealing that stress due to ATP depletion is not an important factor in sigma(B) activation in B. cereus. Analysis of transcription of the sigB operon by Northern blotting and primer extension revealed the presence of a sigma(B)-dependent promoter upstream of the first open reading frame (rsbV) of the sigB operon, indicating that transcription of sigB is autoregulated. A second sigma(B)-dependent promoter was identified upstream of the last open reading frame (orf4) of the sigB operon. Production of virulence factors and the nonhemolytic enterotoxin Nhe in a sigB null mutant was the same as in the parent strain. However, sigma(B) was found to play a role in the protective heat shock response of B. cereus. The sigB null mutant was less protected against the lethal temperature of 50 degrees C by a preadaptation to 42 degrees C than the parent strain was, resulting in a more-than-100-fold-reduced survival of the mutant after 40 min at 50 degrees C.

Proteomic analysis of the synaptic plasma membrane fraction isolated from rat forebrain

Mass spectrometry (MS) in conjunction with liquid chromatography and gel separation techniques has been utilized to identify synaptic plasma membrane (SPM) proteins isolated from rat forebrain and digested with the protease trypsin. Initial results employing two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) separation of the SPM protein mixture have shown that several membrane proteins were under-represented due to solubilization problems in the dimension of isoelectric-point focusing. Given the complexity of the SPM, multiple stages of separation were necessary prior to mass spectrometric detection in order to facilitate protein identification. This particular study involved several approaches using one-dimensional (1D) sodium dodecyl sulfate (SDS)-PAGE, strong cation-exchange (SCX) chromatography and capillary reversed-phase high performance liquid chromatography (HPLC) techniques. In addition to these gel and HPLC separation stages, complementary information was obtained by using both matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) mass spectrometry. Data-dependent acquisition employing capillary HPLC-nanoESI/MS allowed for the detection of low-abundance tryptic peptides in the digested SPM fraction and identification of the corresponding proteins when product-ion information of a single or multiple peptides was used in protein database searching. The potential value of this subproteome methodology was exemplified by the identification of several proteins relevant to synaptic physiology which included various transporters, receptors, ion channels, and enzymes.

Proteomics of bacterial pathogens

The rapid growth of proteomics that has been built upon the available bacterial genome sequences has opened provided new approaches to the analysis of bacterial functional genomics. In the study of pathogenic bacteria the combined technologies of genomics, proteomics and bioinformatics has provided valuable tools for the study of complex phenomena determined by the action of multiple gene sets. The review considers some of the recent developments in the establishment of proteomic databases as well as attempts to define pathogenic determinants at the level of the proteome for some of the major human pathogens. Proteomics can also provide practical applications through the identification of immunogenic proteins that may be potential vaccine targets as well as in extending our understanding of antibiotic action. There is little doubt that proteomics has provided us with new and valuable information on bacterial pathogens and will continue to be an important source of information in the coming years.

A proteomic view of cell physiology of Bacillus subtilis--bringing the genome sequence to life

The genome sequence is the "blue-print of life", and the proteomic approach brings this genome sequence to life. Simple model systems are urgently required to "train" this transformation of the genome sequence into life: why not Bacillus subtilis, the model organism for gram-positive bacteria and of functional genomics? By combination of the highly sensitive 2D protein gel electrophoresis with the identification of the protein spots by microsequencing or mass spectrometry we established a 2D protein index of Bacillus subtilis. In order to depict the entire proteome of a B. subtilis cell, alkaline, cell-wall associated, or extracellular proteins were also included. The proteins of this database (see http://microbio2.biologie.uni-greifswald.de:8880/sub2d.htm) were allocated to proteins with house-keeping functions typical of growing cells and to proteins synthesized particularly in non-growing cells. A computer-aided evaluation of the 2D gels loaded with radioactively-labeled proteins from growing or stressed/starved cells proved to be a powerful tool for the analysis of global regulation of the expression of the entire genome. This is shown for the analysis of glycolysis/TCA cycle (house keeping proteins) and for the analysis of the heat stress stimulon. For the heat stress stimulon it is demonstrated how the proteomic approach can be used: (i) to define the structure of a stimulon, (ii) to dissect stimulons into regulons, (iii) to analyze the regulation, structure, and function of unknown regulons, (iv) to define overlapping reguIons or modulons, and finally (v) to explore complex adaptational networks. Furthermore, it will be demonstrated how the "dual channel pattern comparison" or "proteomics signature" (R. VanBogelen) can be used for a comprehensive understanding or prediction of the physiological state of growing or starving cell populations. This is shown for glucose-starved cells. In order to describe the structure and function of gene regulation groups it is generally recommended to complement the proteomics approach with DNA array technologies. Further studies will focus on the analysis of the global regulation of gene expression by the proteomic approach that cannot be addressed by the application of DNA array techniques: the phosphoproteome and its implications in signal transduction; the global control of protein stability; protein targeting and protein secretion.

The extracellular proteome of Bacillus subtilis under secretion stress conditions

The accumulation of malfolded proteins in the cell envelope of the Gram-positive eubacterium Bacillus subtilis was previously shown to provoke a so-called secretion stress response. In the present studies, proteomic approaches were employed to identify changes in the extracellular proteome of B. subtilis in response to secretion stress. The data shows that, irrespective of the way in which secretion stress is imposed on the cells, the levels of only two extracellular proteins, HtrA and YqxI, display major variations in a parallel manner. Whereas the extracellular level of the HtrA protease is determined through transcriptional regulation, the level of YqxI in the growth medium is determined post-transcriptionally in an HtrA-dependent manner. In the absence of secretion stress, the extracellular levels of HtrA and YqxI are low because of extracytoplasmic proteolysis. Finally, the protease active site of HtrA is dispensable for post-transcriptional YqxI regulation. It is known that Escherichia coli HtrA has combined protease and chaperone-like activities. As this protein shares a high degree of similarity with B. subtilis HtrA, it can be hypothesized that both activities are conserved in B. subtilis HtrA. Thus, a chaperone-like activity of B. subtilis HtrA could be involved in the appearance of YqxI on the extracellular proteome.

Proteomics in Vaccinology and Immunobiology: An Informatics Perspective of the Immunone

The postgenomic era, as manifest, inter alia, by proteomics, offers unparalleled opportunities for the efficient discovery of safe, efficacious, and novel subunit vaccines targeting a tranche of modern major diseases. A negative corollary of this opportunity is the risk of becoming overwhelmed by this embarrassment of riches. Informatics techniques, working to address issues of both data management and through prediction to shortcut the experimental process, can be of enormous benefit in leveraging the proteomic revolution. In this disquisition, we evaluate proteomic approaches to the discovery of subunit vaccines, focussing on viral, bacterial, fungal, and parasite systems. We also adumbrate the impact that proteomic analysis of host-pathogen interactions can have. Finally, we review relevant methods to the prediction of immunome, with special emphasis on quantitative methods, and the subcellular localization of proteins within bacteria.

Comparative proteomics of Staphylococcus aureus and the response of methicillin-resistant and methicillin-sensitive strains to Triton X-100

Proteomics is a powerful tool for analysing differences in gene expression between bacterial strains with alternate phenotypes. Staphylococcus aureus strains are grouped on the basis of their sensitivity to methicillin. Two-dimensional gel electrophoresis was combined with MS to compare the protein profiles of S. aureus strains COL (methicillin-resistant) and 8325 (methicillin-sensitive). Reference mapping via this approach identified 377 proteins that corresponded to 266 distinct ORFs. Amongst these identified proteins were 14 potential virulence factors. The production of 41 'hypothetical' proteins was confirmed, and eight of these appeared to be unique to S. aureus. Strain COL displayed 12 protein spots, which included alkaline-shock protein 23 (Asp23) and cold-shock proteins CspABC, which either were not present in strain 8325 or were present at a significantly lower intensity in this strain. Comparative maps were used to characterize the S. aureus response to treatment with Triton X-100 (TX-100), a detergent that has been shown to reduce methicillin resistance independently of an interaction with the mecA-encoded penicillin-binding protein 2a. In response to growth of the bacteria in the presence of TX-100, 44 protein spots showed altered levels of abundance, and 11 of these spots were found only in COL. The products of genes regulated by sigma(B) (the alternative sigma factor), including Asp23 and three proteins of unknown function, and SarA (a regulator of virulence genes) were shown to be present at significantly altered levels. SarA production was induced in TX-100-treated cultures. A protein of the sigma(B) operon, RsbV, was only detected in COL and its production was down-regulated in COL when the strain was treated with TX-100, whereas RsbW was present at reduced levels in both strains. Upon growth of both strains in the presence of TX-100, no effects on the production of the essential methicillin-resistance factor FemA were detected, whereas phosphoglucosamine mutase (GlmM) production was reduced in COL alone. This study suggests that proteins of the sigma(B) and sarA regulons, as well as other factors, are involved in methicillin resistance in S. aureus.

Effect of mild acid pH on the functioning of bacterial membranes in Vibrio cholerae

In this paper, we initiated the first two-dimensional electrophoresis map of Vibrio cholerae, the aetiological agent of cholera disease. In this pathogen the efficient adaptation to detrimental conditions plays an important role in its survival in both the aquatic reservoir and human intestine. By proteome analysis we investigated the effect of mild acid treatment on the physiology of V. cholerae. More than 50 proteins were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry and database searching. Amongst them, pH regulated proteins belong to various functional classes such as intermediary metabolism and bacterial envelope. Several proteins whose accumulation level was decreased in response to acidic pH are known to be involved in the organization and the functioning of membranes, including lipopolysaccharide. Consistent with this, we observed an increased susceptibility to hydrophobic drugs, a loss of motility and a reduction in the ability to form a biofilm in cells grown at pH 6. Our results suggest that V. cholerae is able to sense a moderate decrease in pH and to modify accordingly its structure and physiology.

Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis

The stringent response in Bacillus subtilis was characterized by using proteome and transcriptome approaches. Comparison of protein synthesis patterns of wild-type and relA mutant cells cultivated under conditions which provoke the stringent response revealed significant differences. According to their altered synthesis patterns in response to DL-norvaline, proteins were assigned to four distinct classes: (i) negative stringent control, i.e., strongly decreased protein synthesis in the wild type but not in the relA mutant (e.g., r-proteins); (ii) positive stringent control, i.e., induction of protein synthesis in the wild type only (e.g., YvyD and LeuD); (iii) proteins that were induced independently of RelA (e.g., YjcI); and (iv) proteins downregulated independently of RelA (e.g., glycolytic enzymes). Transcriptome studies based on DNA macroarray techniques were used to complement the proteome data, resulting in comparable induction and repression patterns of almost all corresponding genes. However, a comparison of both approaches revealed that only a subset of RelA-dependent genes or proteins was detectable by proteomics, demonstrating that the transcriptome approach allows a more comprehensive global gene expression profile analysis. The present study presents the first comprehensive description of the stringent response of a bacterial species and an almost complete map of protein-encoding genes affected by (p)ppGpp. The negative stringent control concerns reactions typical of growth and reproduction (ribosome synthesis, DNA synthesis, cell wall synthesis, etc.). Negatively controlled unknown y-genes may also code for proteins with a specific function during growth and reproduction (e.g., YlaG). On the other hand, many genes are induced in a RelA-dependent manner, including genes coding for already-known and as-yet-unknown proteins. A passive model is preferred to explain this positive control relying on the redistribution of the RNA polymerase under the influence of (p)ppGpp.

Applications of DNA microarrays in microbial systems

DNA microarray technology allows a parallel analysis of RNA abundance and DNA homology for thousands of genes in a single experiment. Over the past few years, this powerful technology has been used to explore transcriptional profiles and genome differences for a variety of microorganisms, greatly facilitating our understanding of microbial metabolism. With the increasing availability of complete microbial genomes, DNA microarrays are becoming a common tool in many areas of microbial research, including microbial physiology, pathogenesis, epidemiology, ecology, phylogeny, pathway engineering and fermentation optimization.

Global transcriptional response of Bacillus subtilis to heat shock

In response to heat stress, Bacillus subtilis activates the transcription of well over 100 different genes. Many of these genes are members of a general stress response regulon controlled by the secondary sigma factor, sigma(B), while others are under control of the HrcA or CtsR heat shock regulators. We have used DNA microarrays to monitor the global transcriptional response to heat shock. We find strong induction of known sigma(B)-dependent genes with a characteristic rapid induction followed by a return to near prestimulus levels. The HrcA and CtsR regulons are also induced, but with somewhat slower kinetics. Analysis of DNA sequences proximal to newly identified heat-induced genes leads us to propose ~70 additional members of the sigma(B) regulon. We have also identified numerous heat-induced genes that are not members of known heat shock regulons. Notably, we observe very strong induction of arginine biosynthesis and transport operons. Induction of several genes was confirmed by quantitative reverse transcriptase PCR. In addition, the transcriptional responses measured by microarray hybridization compare favorably with the numerous previous studies of heat shock in this organism. Since many different conditions elicit both specific and general stress responses, knowledge of the heat-induced general stress response reported here will be helpful for interpreting future microarray studies of other stress responses.

Bioaugmentation of soils by increasing microbial richness: missing links

It is generally assumed that increased microbial diversity corresponds to increased catabolic potential and, hence, to better removal of metabolites and pollutants. Yet, microbial diversity, more specifically richness of species in environmental samples and sites, is difficult to assess. It is proposed to interpret this diversity more in the framework of Pareto's law, i.e. 20% of the species govern 80% of the energy flux of the ecosystem. Ecological studies should attempt to delineate the main energy fluxes and that group of species playing quantitative key roles in the system. Consequently, bioaugmentation should aim at the rearrangement of the group of organisms dominantly involved in the overall energy flux, so that specific catabolic traits necessary for the clean up of pollutants are part of that active group. For soil ecosystems, the capacity of plant roots as creators of physical and chemical discontinuity should be used more strategically to bring about such rearrangements. Overall, this paper identifies a number of ecological concepts, such as the Pareto law, the Gompertz model and plant community-induced microbial competence, which may, given careful underpinning, open new perspectives for microbial ecology and biodegradation.

Toward a genome-scale understanding of group A Streptococcus pathogenesis

Recent significant contributions have been made to the understanding of Group A Streptococcus (GAS) pathogenesis. New regulatory pathways have been discovered, insight into the molecular basis of epidemics of serotype M1 disease has been obtained, the crystal structures of four toxins have been reported and a genome sequence of one GAS strain has been determined. Genome-scale approaches to the study of GAS pathogenesis are now rapidly emerging and will advance our fundamental understanding of the molecular basis of host-pathogen interactions.