Confirmation of the expression of a large set of conserved hypothetical proteins in Shewanella oneidensis MR-1

Proteogenomics of rare taxonomic phyla: A prospective treasure trove of protein coding genes

Sustainable innovations in sequencing technologies have resulted in a torrent of microbial genome sequencing projects. However, the prokaryotic genomes sequenced so far are unequally distributed along their phylogenetic tree; few phyla contain the majority, the rest only a few representatives. Accurate genome annotation lags far behind genome sequencing. While automated computational prediction, aided by comparative genomics, remains a popular choice for genome annotation, substantial fraction of these annotations are erroneous. Proteogenomics utilizes protein level experimental observations to annotate protein coding genes on a genome wide scale. Benefits of proteogenomics include discovery and correction of gene annotations regardless of their phylogenetic conservation. This not only allows detection of common, conserved proteins but also the discovery of protein products of rare genes that may be horizontally transferred or taxonomy specific. Chances of encountering such genes are more in rare phyla that comprise a small number of complete genome sequences. We collated all bacterial and archaeal proteogenomic studies carried out to date and reviewed them in the context of genome sequencing projects. Here, we present a comprehensive list of microbial proteogenomic studies, their taxonomic distribution, and also urge for targeted proteogenomics of underexplored taxa to build an extensive reference of protein coding genes.

Systematic characterization of hypothetical proteins in Synechocystis sp. PCC 6803 reveals proteins functionally relevant to stress responses

We described here a global detection and functional inference of hypothetical proteins involved in stress response in Synechocystis sp. PCC 6803. In the study, we first applied an iTRAQ-LC-MS/MS based quantitative proteomics to the Synechocystis cells grown under five stress conditions. The analysis detected a total of 807 hypothetical proteins with high confidence. Among them, 480 were differentially regulated. We then applied a Weighted Gene Co-expression Network Analysis approach to construct transcriptional networks for Synechocystis under nutrient limitation and osmotic stress conditions using transcriptome datasets. The analysis showed that 305 and 467 coding genes of hypothetical proteins were functionally relevant to nutrient limitation and osmotic stress, respectively. A comparison of responsive hypothetical proteins to all stress conditions allowed identification of 22 hypothetical proteins commonly responsive to all stresses, suggesting they may be part of the core stress responses in Synechocystis. Finally, functional inference of these core stress responsive proteins using both sequence similarity and non-similarity approaches was conducted. The study provided new insights into the stress response networks in Synechocystis, and also demonstrated that a combination of experimental "OMICS" and bioinformatics methodologies could improve functional annotation for hypothetical proteins.

Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions

Shewanellae are facultative γ-proteobacteria whose remarkable respiratory versatility has resulted in interest in their utility for bioremediation of heavy metals and radionuclides and for energy generation in microbial fuel cells. Extensive experimental efforts over the last several years and the availability of 21 sequenced Shewanella genomes made it possible to collect and integrate a wealth of information on the genus into one public resource providing new avenues for making biological discoveries and for developing a system level understanding of the cellular processes. The Shewanella knowledgebase was established in 2005 to provide a framework for integrated genome-based studies on Shewanella ecophysiology. The present version of the knowledgebase provides access to a diverse set of experimental and genomic data along with tools for curation of genome annotations and visualization and integration of genomic data with experimental data. As a demonstration of the utility of this resource, we examined a single microarray data set from Shewanella oneidensis MR-1 for new insights into regulatory processes. The integrated analysis of the data predicted a new type of bacterial transcriptional regulation involving co-transcription of the intergenic region with the downstream gene and suggested a biological role for co-transcription that likely prevents the binding of a regulator of the upstream gene to the regulator binding site located in the intergenic region.

Database URL:http://shewanella-knowledgebase.org:8080/Shewanella/ or http://spruce.ornl.gov:8080/Shewanella/

A perfect genome annotation is within reach with the proteomics and genomics alliance

High-throughput identification of proteins and their accurate partial sequencing by shotgun nanoLC-MS/MS are now feasible for any cellular model at a full genomic scale. Proteogenomics is the integration of these data with the genome. Mining microbial proteomes allows validation of predicted orphan genes and correction of genome annotation errors such as discovery of unannotated genes, reversal of reading frames and identification of translational start sites, stop codon read-throughs or programmed frameshifts. Recent advances have been achieved in database searches, N-terminal oriented proteomics and homology-driven proteogenomics. From now on, proteogenomics on newly sequenced model genomes can be carried out at the earliest stage of the genome project as already exemplified by Mycoplasma mobile and Deinococcus deserti genomes. The proteomics and genomics alliance produces almost complete and accurate gene catalogues for small microbial genomes, a comprehensiveness which is essential for efficient systems biology.

Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation

Hypothetical (HyP) and conserved HyP genes account for >30% of sequenced bacterial genomes. For the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, 347 of the 3634 genes were annotated as conserved HyP (9.5%) along with 887 HyP genes (24.4%). Given the large fraction of the genome, it is plausible that some of these genes serve critical cellular roles. The study goals were to determine which genes were expressed and provide a more functionally based annotation. To accomplish this, expression profiles of 1234 HyP and conserved genes were used from transcriptomic datasets of 11 environmental stresses, complemented with shotgun LC–MS/MS and AMT tag proteomic data. Genes were divided into putatively polycistronic operons and those predicted to be monocistronic, then classified by basal expression levels and grouped according to changes in expression for one or multiple stresses. One thousand two hundred and twelve of these genes were transcribed with 786 producing detectable proteins. There was no evidence for expression of 17 predicted genes. Except for the latter, monocistronic gene annotation was expanded using the above criteria along with matching Clusters of Orthologous Groups. Polycistronic genes were annotated in the same manner with inferences from their proximity to more confidently annotated genes. Two targeted deletion mutants were used as test cases to determine the relevance of the inferred functional annotations.

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.

Characterization of strategies for obtaining confident identifications in bottom-up proteomics measurements using hybrid FTMS instruments

Hybrid FTMS instruments, such as the LTQ-FT and LTQ-Orbitrap, are capable of generating high duty cycle linear ion trap MS/MS data along with high resolution information without compromising the overall throughput of measurements. Combined with online LC separations, these instruments provide powerful capabilities for proteomics research. In the present work, we explore three alternative strategies for high throughput proteomics measurements using hybrid FTMS instruments. Our accurate mass and time tag (AMT tag) strategy enables identification of thousands of peptides in a single LC-FTMS analysis by comparing accurate molecular mass and LC elution time information from the analysis to a reference database. An alternative strategy considered here, termed accurate precursor mass filter (APMF), employs linear ion trap (low resolution) MS/MS identifications generated by an appropriate search engine, such as SEQUEST, refined with high resolution precursor ion data obtained from FTMS mass spectra. The APMF results can be additionally filtered using the LC elution time information from the AMT tag database, which constitutes a precursor mass and time filter (PMTF), the third approach implemented in this study. Both the APMF and the PMTF approaches are evaluated for coverage and confidence of peptide identifications and contrasted with the AMT tag strategy. The commonly used decoy database method and an alternative method based on mass accuracy histograms were used to reliably quantify identification confidence, revealing that both methods yielded similar results. Comparison of the AMT, APMF and PMTF approaches indicates that the AMT tag approach is preferential for studies desiring a highest achievable number of identified peptides. In contrast, the APMF approach does not require an AMT tag database and provides a moderate level of peptide coverage combined with acceptable confidence values of approximately 99%. The PMTF approach yielded a significantly better peptide identification confidence, >99.9%, that essentially excluded any false peptide identifications. Since AMT tag databases that exclude incorrect identifications are desirable, this study points to the value of a multipass APMF approach to generate AMT tag databases, which are then validated using the PMTF approach. The resulting compact, high quality databases can then be used for subsequent high-throughput, high peptide coverage AMT tag studies.

Application of pressurized solvents for ultrafast trypsin hydrolysis in proteomics: proteomics on the fly

A new method for rapid proteolytic digestion of proteins under high pressure that uses pressure cycling technology in the range of 5-35 kpsi was demonstrated for proteomic analysis. Successful in-solution digestions of single proteins and complex protein mixtures were achieved in 60 s and then analyzed by reversed phase liquid chromatography-electrospray ionization ion trap-mass spectrometry. Method performance in terms of the number of Shewanella oneidensis peptides and proteins identified in a shotgun approach was evaluated relative to a traditional "overnight" sample preparation method. Advantages of the new method include greatly simplified sample processing, easy implementation, no cross contamination among samples, and cost effectiveness.

Comparative bacterial proteomics: analysis of the core genome concept

While comparative bacterial genomic studies commonly predict a set of genes indicative of common ancestry, experimental validation of the existence of this core genome requires extensive measurement and is typically not undertaken. Enabled by an extensive proteome database developed over six years, we have experimentally verified the expression of proteins predicted from genomic ortholog comparisons among 17 environmental and pathogenic bacteria. More exclusive relationships were observed among the expressed protein content of phenotypically related bacteria, which is indicative of the specific lifestyles associated with these organisms. Although genomic studies can establish relative orthologous relationships among a set of bacteria and propose a set of ancestral genes, our proteomics study establishes expressed lifestyle differences among conserved genes and proposes a set of expressed ancestral traits.

Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation

While bacterial genome annotations have significantly improved in recent years, techniques for bacterial proteome annotation (including post-translational chemical modifications, signal peptides, proteolytic events, etc.) are still in their infancy. At the same time, the number of sequenced bacterial genomes is rising sharply, far outpacing our ability to validate the predicted genes, let alone annotate bacterial proteomes. In this study, we use tandem mass spectrometry (MS/MS) to annotate the proteome of Shewanella oneidensis MR-1, an important microbe for bioremediation. In particular, we provide the first comprehensive map of post-translational modifications in a bacterial genome, including a large number of chemical modifications, signal peptide cleavages, and cleavages of N-terminal methionine residues. We also detect multiple genes that were missed or assigned incorrect start positions by gene prediction programs, and suggest corrections to improve the gene annotation. This study demonstrates that complementing every genome sequencing project by an MS/MS project would significantly improve both genome and proteome annotations for a reasonable cost.

Dosage-Dependent Proteome Response of Shewanella oneidensis MR-1 to Acute Chromate Challenge

Proteome alterations in the metal-reducing bacterium Shewanella oneidensis MR-1 in response to different acute dose challenges (0.3, 0.5, or 1 mM) of the toxic metal chromate [Cr(VI)] were characterized with multidimensional HPLC-MS/MS. Proteome measurements were performed and compared on both quadrupole ion traps as well as linear trapping quadrupole mass spectrometers. We have found that the implementation of multidimensional liquid chromatography on-line with the rapid scanning, high throughput linear trapping quadrupole platform resulted in a dramatic increase in the number of measured peptides and, thus, the number of identified proteins. A total of 2406 functionally diverse, nonredundant proteins were identified in this study, representing a relatively deep proteome coverage for this organism. The core molecular response to chromate challenge under all three concentrations consisted predominantly of proteins with annotated functions in transport and binding (e.g., components of the TonB1 iron transport system, TonB-dependent receptors, and sulfate transporters) as well as a functionally undefined DNA-binding response regulator (SO2426) that might play a role in mediating metal stress responses. In addition, proteins annotated as a cytochrome c, a putative azoreductase, and various proteins involved in general stress protection were up-regulated at the higher Cr(VI) doses (0.5 and 1 mM) only. Proteins down-regulated in response to metal treatment were distributed across diverse functional categories, with energy metabolism proteins dominating. The results presented in this work demonstrate the dynamic dosage response of S. oneidensis to sub-toxic levels of chromate.

LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris

High efficiency capillary liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to examine the proteins extracted from Desulfovibrio vulgaris cells across six treatment conditions. While our previous study provided a proteomic overview of the cellular metabolism based on proteins with known functions [W. Zhang, M.A. Gritsenko, R.J. Moore, D.E. Culley, L. Nie, K. Petritis, E.F. Strittmatter, D.G. Camp II, R.D. Smith, F.J. Brockman, A proteomic view of the metabolism in Desulfovibrio vulgaris determined by liquid chromatography coupled with tandem mass spectrometry, Proteomics 6 (2006) 4286-4299], this study describes the global detection and functional inference for hypothetical D. vulgaris proteins. Using criteria that a given peptide of a protein is identified from at least two out of three independent LC-MS/MS measurements and that for any protein at least two different peptides are identified among the three measurements, 129 open reading frames (ORFs) originally annotated as hypothetical proteins were found to encode expressed proteins. Functional inference for the conserved hypothetical proteins was performed by a combination of several non-homology based methods: genomic context analysis, phylogenomic profiling, and analysis of a combination of experimental information, including peptide detection in cells grown under specific culture conditions and cellular location of the proteins. Using this approach we were able to assign possible functions to 20 conserved hypothetical proteins. This study demonstrated that a combination of proteomics and bioinformatics methodologies can provide verification of the expression of hypothetical proteins and improve genome annotation.