Towards the proteome of the marine bacteriumRhodopirellula baltica: Mapping the soluble proteins

Fifteen years of physiological proteo(geno)mics with (marine) environmental bacteria

Environmental bacteria play a central role in the Earth's elemental cycles and represent a mostly untapped reservoir for novel metabolic capacities and biocatalysts. Over the last 15 years, the author's laboratory has focused on three major switches in the breakdown of organic carbon defined by the abundance and recalcitrance of the substrates: carbohydrates and amino acids by aerobic heterotrophs, fermentation end products by sulphate reducers and anaerobic degradation of aromatic compounds and hydrocarbons by denitrifiers and sulphate reducers. As these bacteria are novel isolates mostly not accessibly by molecular genetics, genomics combined with differential proteomics was early on applied to obtain molecular-functional insights into degradation pathways, catabolic and regulatory networks, as well as mechanisms and strategies for adapting to changing environmental conditions. This review provides some background on research motivations and briefly summarizes insights into studied model organisms, e.g. "Aromatoleum aromaticum" EbN1, Desulfobacula toluolica Tol2 and Phaeobacter inhibens DSM 17395.

Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica

Rhodopirellula baltica (R. baltica) is a Planctomycete, known to have intracellular membranes. Because of its unusual cell structure and ecological significance, we have conducted comprehensive analyses of its transmembrane transport proteins. The complete proteome of R. baltica was screened against the Transporter Classification Database (TCDB) to identify recognizable integral membrane transport proteins. 342 proteins were identified with a high degree of confidence, and these fell into several different classes. R. baltica encodes in its genome channels (12%), secondary carriers (33%), and primary active transport proteins (41%) in addition to classes represented in smaller numbers. Relative to most non-marine bacteria, R. baltica possesses a larger number of sodium-dependent symporters but fewer proton-dependent symporters, and it has dimethylsulfoxide (DMSO) and trimethyl-amine-oxide (TMAO) reductases, consistent with its Na(+)-rich marine environment. R. baltica also possesses a Na(+)-translocating NADH:quinone dehydrogenase (Na(+)-NDH), a Na(+) efflux decarboxylase, two Na(+)-exporting ABC pumps, two Na(+)-translocating F-type ATPases, two Na(+):H(+) antiporters and two K(+):H(+) antiporters. Flagellar motility probably depends on the sodium electrochemical gradient. Surprisingly, R. baltica also has a complete set of H(+)-translocating electron transport complexes similar to those present in α-proteobacteria and eukaryotic mitochondria. The transport proteins identified proved to be typical of the bacterial domain with little or no indication of the presence of eukaryotic-type transporters. However, novel functionally uncharacterized multispanning membrane proteins were identified, some of which are found only in Rhodopirellula species, but others of which are widely distributed in bacteria. The analyses lead to predictions regarding the physiology, ecology and evolution of R. baltica.

Proteomic responses of Roseobacter litoralis OCh149 to starvation and light regimen

Roseobacter litoralis OCh149 is a type strain of aerobic anoxygenic phototrophic bacteria in marine Roseobacter clade. Its full genome has been sequenced; however, proteomic research, which will give deeper insights into the environmental stimuli on gene expression networks, has yet to be performed. In the present study, a proteomic approach was employed to analyze the status of R. litoralis OCh149 in carbon starvation during the stationary phase and its responses to a dark/light regimen (12 h:12 h) in both exponential and stationary phases. LC-MS/MS-based analysis of highly abundant proteins under carbon starvation revealed that proteins involved in transport, the transcription/translation process and carbohydrate metabolism were the major functional categories, while poly-β-hydroxyalkanoate (PHA), previously accumulated in cells, was remobilized after stress. Glucose, as the sole carbon source in the defined medium, was broken down by Entner-Doudoroff and reductive pentose phosphate (PP) pathways. Carbohydrate catabolism-related proteins were down-regulated under light regardless of the growth phase, probably due to inhibition of respiration by light. In contrast, responses of amino acid metabolisms to light regimen varied among different proteins during growth phases depending on cellular requirements for proliferation, growth or survival. Fluorescence induction and relaxation measurements suggested that functional absorption cross-sections of the photosynthetic complexes decreased during the dark period and always recovered to about the previous level during the light period. Although the photosynthetic genes in R. litoralis OCh149 are located on the plasmid, these data indicate the regulatory mechanism of photoheterotroph metabolism by both carbon and light availability.

An overview of 2D DIGE analysis of marine (environmental) bacteria

Microbes are the "unseen majority" of living organisms on Earth and main drivers of the biogeochemical cycles in marine and most other environments. Their significance for an intact biosphere is bringing environmental bacteria increasingly into the focus of genome-based science. Proteomics is playing a prominent role for providing a molecular understanding of how these microbes work and for identifying the key biocatalysts involved in the major biogeochemical processes. This overview describes the major insights obtained from two-dimensional difference gel electrophoresis (2D DIGE) analyses of specific degradation pathways, complex metabolic networks, cellular processes, and regulatory patterns in the marine aerobic heterotrophs Rhodopirellula baltica SH1 (Planctomycetes) and Phaeobacter gallaeciensis DSM 17395 (Roseobacter clade) and the anaerobic aromatic compound degrader Aromatoleum aromaticum EbN1 (Betaproteobacteria).

Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function

Planctomycetes form a distinct phylum of the domain Bacteria and possess unusual features such as intracellular compartmentalization and a lack of peptidoglycan in their cell walls. Remarkably, cells of the genus Gemmata even contain a membrane-bound nucleoid analogous to the eukaryotic nucleus. Moreover, the so-called 'anammox' planctomycetes have a unique anaerobic, autotrophic metabolism that includes the ability to oxidize ammonium; this process is dependent on a characteristic membrane-bound cell compartment called the anammoxosome, which might be a functional analogue of the eukaryotic mitochondrion. The compartmentalization of planctomycetes challenges our hypotheses regarding the origins of eukaryotic organelles. Furthermore, the recent discovery of both an endocytosis-like ability and proteins homologous to eukaryotic clathrin in a planctomycete marks this phylum as one to watch for future research on the origin and evolution of the eukaryotic cell.

Life cycle analysis of the model organism Rhodopirellula baltica SH 1(T) by transcriptome studies

The marine organism Rhodopirellula baltica is a representative of the globally distributed phylum Planctomycetes whose members exhibit an intriguing lifestyle and cell morphology. The analysis of R. baltica's genome has revealed many biotechnologically promising features including a set of unique sulfatases and C1‐metabolism genes. Salt resistance and the potential for adhesion in the adult phase of the cell cycle were observed during cultivation. To promote the understanding of this model organism and to specify the functions of potentially useful genes, gene expression throughout a growth curve was monitored using a whole genome microarray approach. Transcriptional profiling suggests that a large number of hypothetical proteins are active within the cell cycle and in the formation of the different cell morphologies. Numerous genes with potential biotechnological applications were found to be differentially regulated, revealing further characteristics of their functions and regulation mechanisms. More specifically, the experiments shed light on the expression patterns of genes belonging to the organism's general stress response, those involved in the reorganization of its genome and those effecting morphological changes. These transcriptomic results contribute to a better understanding of thus far unknown molecular elements of cell biology. Further, they pave the way for the biotechnological exploitation of R. baltica's distinctive metabolic features as a step towards sourcing the phylum Planctomycetes at large.

Growth phase-dependent global protein and metabolite profiles of Phaeobacter gallaeciensis strain DSM 17395, a member of the marine Roseobacter-clade

The marine heterotrophic roseobacter Phaeobacter gallaeciensis DSM 17395 was grown with glucose in defined mineral medium. Relative abundance changes of global protein (2-D DIGE) and metabolite (GC-MS) profiles were determined across five different time points of growth. In total, 215 proteins were identified and 147 metabolites detected (101 structurally identified), among which 60 proteins and 87 metabolites displayed changed abundances upon entry into stationary growth phase. Glucose breakdown to pyruvate apparently proceeds via the Entner-Doudoroff (ED) pathway, since phosphofructokinase of the Embden-Meyerhof-Parnas pathway is missing and the key metabolite of the ED-pathway, 2-keto-3-desoxygluconate, was detected. The absence of pfk in other genome-sequenced roseobacters suggests that the use of the ED pathway is an important physiological property among these heterotrophic marine bacteria. Upon entry into stationary growth phase (due to glucose starvation), sulfur assimilation (including cysteine biosynthesis) and parts of cell envelope synthesis (e.g. the lipid precursor 1-monooleoylglycerol) were down-regulated and cadaverine formation up-regulated. In contrast, central carbon catabolism remained essentially unchanged, pointing to a metabolic "stand-by" modus as an ecophysiological adaptation strategy. Stationary phase response of P. gallaeciensis differs markedly from that of standard organisms such as Escherichia coli, as evident e.g. by the absence of an rpoS gene.

Transcriptional response of the model planctomycete Rhodopirellula baltica SH1(T) to changing environmental conditions

BACKGROUND

The marine model organism Rhodopirellula baltica SH1(T) was the first Planctomycete to have its genome completely sequenced. The genome analysis predicted a complex lifestyle and a variety of genetic opportunities to adapt to the marine environment. Its adaptation to environmental stressors was studied by transcriptional profiling using a whole genome microarray.

RESULTS

Stress responses to salinity and temperature shifts were monitored in time series experiments. Chemostat cultures grown in mineral medium at 28 degrees C were compared to cultures that were shifted to either elevated (37 degrees C) or reduced (6 degrees C) temperatures as well as high salinity (59.5 per thousand) and observed over 300 min. Heat shock showed the induction of several known chaperone genes. Cold shock altered the expression of genes in lipid metabolism and stress proteins. High salinity resulted in the modulation of genes coding for compatible solutes, ion transporters and morphology. In summary, over 3000 of the 7325 genes were affected by temperature and/or salinity changes.

CONCLUSION

Transcriptional profiling confirmed that R. baltica is highly responsive to its environment. The distinct responses identified here have provided new insights into the complex adaptation machinery of this environmentally relevant marine bacterium. Our transcriptome study and previous proteome data suggest a set of genes of unknown functions that are most probably involved in the global stress response. This work lays the foundation for further bioinformatic and genetic studies which will lead to a comprehensive understanding of the biology of a marine Planctomycete.

A comprehensive proteome map of the Haemophilus parasuis serovar 5

Haemophilus parasuis is the causative agent of Glässer's disease of pigs, a disease associated with fibrinous polyserositis, polyarthritis and meningitis. Systematic reference maps of outer membrane, intracellular and extracellular proteome fractions of the clinical isolate H. parasuis SH0165 were examined by 2-DE coupled with MALDI-TOF MS. A total of 539 proteins spots were successfully identified, corresponding to 317 different proteins that were classified into functional categories. The majority of these proteins were linked to housekeeping functions in amino acid transport and metabolism, secondary metabolites biosynthesis, transport and catabolism and post-translational modification, protein turnover and chaperones. A significant number of outer membrane proteins were identified, such as Wza, Omp2, Omp5, D15 and PalA, which were supposed to play important roles in basic physiology of H. parasuis. In addition, several virulence-associated proteins involved in type I (TolC), type III (DsbA and DsbC) and type V (Autotransporter adhesins) secretion systems, and solute-binding proteins participating in iron-uptake systems were also identified in the present study.

Proteome analysis of Streptococcus suis serotype 2

Outbreaks in humans, caused by Streptococcus suis serotype 2 (SS2), were reported in 1998 and 2005 in China. However, the mechanism of SS2-associated infection remains unclear. For the first time, a 2-D gel approach combined with MS was used to establish a comprehensive 2-D reference map for aiding our understanding of the pathogenicity of SS2. The identification of 694 out of 834 processed spots revealed 373 proteins. Most of the identified proteins were located in the cytoplasm and were involved in energy metabolism, protein synthesis, and cellular processes. Proteins that were abundant in the 2-DE gels could be linked mainly to housekeeping functions in carbohydrate metabolism, protein quality control and translation. 2-DE of secretory proteins was performed using IPG strips of pH 4-7. Among the 102 protein spots processed, 87 spots representing 77 proteins were successfully identified. Some virulence-associated proteins of SS2 were found, including arginine deiminase, ornithine carbamoyl-transferase, carbamate kinase, muramidase-released protein precursor, extracellular factor, and suilysin. Enolase and endopeptidase have been proposed as putative virulence-associated factors in this study. The 2-D reference map might provide a powerful tool for analyzing the virulence factor and the regulatory network involved in the pathogenicity of this microorganism.

Proteome analysis ofRickettsia felis highlights the expression profile of intracellular bacteria

The proteome of Rickettsia felis, an obligate intracellular bacterium responsible for spotted fever, was analyzed using two complementary proteomic approaches: 2-DE coupled with MALDI-TOF, and SDS-PAGE with nanoLC-MS/MS. This strategy allowed identification of 165 proteins and helped to answer some questions raised by the genome sequence of this bacterium. We successfully identified potential virulence factors including two putative adhesins, four proteins of the type IV secretion system, four Sca autotransporters, four components of ABC transporters, some R. felis-specific proteins, and one antitoxin of the toxin-antitoxin system. Notably, the antitoxin was the first to be identified in intracellular bacteria. Only one protein containing rickettsia palindromic repeats was found, whereas none of the split genes, transposases, or tetratricopeptide/ankyrin repeats were detectably expressed. Comparison of the protein expression profiles of R. felis and 23 other bacterial species according to functional categories showed that intracellular bacteria express more proteins related to translation, especially ribosomal proteins. However, the remaining bacteria express more proteins related to energy production and carbohydrate/amino acid metabolism. In conclusion, this study reveals R. felis virulence factor expression and highlights the unique protein expression profile of intracellular bacteria.

The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance

In the rRNA-based tree of life four bacterial phyla, comprising the Planctomycetes, Verrucomicrobia, Chlamydiae and Lentisphaerae, form together with the candidate phyla Poribacteria and OP3 a monophyletic group referred to as the PVC superphylum. This assemblage contains organisms that possess dramatically different lifestyles and which colonize sharply contrasting habitats. Some members of this group are among the most successful human pathogens, others are abundant soil microbes, and others still are of major importance for the marine nitrogen cycle and hold much promise for sustainable wastewater treatment. Recent comparative genomic and metagenomic analyses of a few representatives of this group revealed many unusual features and generated unexpected hypotheses regarding their physiology, some of which have already been confirmed experimentally. Furthermore, the availability of these genome sequences offered new insights into the evolutionary history of this peculiar group of microbes with major medical, ecological and biotechnological relevance.

Mass Spectrometric Identification of Proteins in Complex Post-Genomic Projects

The rapidly developing proteomics technologies help to advance the global understanding of physiological and cellular processes. The lifestyle of a study organism determines the type and complexity of a given proteomic project. The complexity of this study is characterized by a broad collection of pathway-specific subproteomes, reflecting the metabolic versatility as well as the regulatory potential of the aromatic-degrading, denitrifying bacterium 'Aromatoleum' sp. strain EbN1. Differences in protein profiles were determined using a gel-based approach. Protein identification was based on a progressive application of MALDI-TOF-MS, MALDI-TOF-MS/MS and LC-ESI-MS/MS. This progression was result-driven and automated by software control. The identification rate was increased by the assembly of a project-specific list of background signals that was used for internal calibration of the MS spectra, and by the combination of two search engines using a dedicated MetaScoring algorithm. In total, intelligent bioinformatics could increase the identification yield from 53 to 70% of the analyzed 5,050 gel spots; a total of 556 different proteins were identified. MS identification was highly reproducible: most proteins were identified more than twice from parallel 2DE gels with an average sequence coverage of >50% and rather restrictive score thresholds (Mascot >or=95, ProFound >or=2.2, MetaScore >or=97). The MS technologies and bioinformatics tools that were implemented and integrated to handle this complex proteomic project are presented. In addition, we describe the basic principles and current developments of the applied technologies and provide an overview over the current state of microbial proteome research.

Growth phase dependent regulation of protein composition in Rhodopirellula baltica

Growth phase dependent changes of protein composition in the marine bacterium Rhodopirellula baltica were quantitatively monitored by applying the two-dimensional difference gel electrophoresis (2D DIGE) technology. The number of regulated proteins (fold changes in protein abundance > absolute value(2)) increased from early (10) to late stationary growth phase (179), with fold changes reaching maximal values of 40. About 110 of these regulated protein spots were analysed by MALDI-TOF-MS and identified by mapping of peptide masses. Results indicate an opposing regulation of tricarboxylic acid cycle and oxidative pentose phosphate cycle, a downregulation of several enzymes involved in amino acid biosynthesis and an upregulation of the alternative sigma factor sigmaH in stationary phase. Interestingly, 26 proteins of unknown function were up- or downregulated in the stationary phase. Several proteins were specifically regulated during growth on solid surface (agar plates). These proteins could possibly be involved in the development of the different R. baltica morphotypes, i.e. motile swarmer cells and sessile cell aggregates (so-called rosettes).