SWISS‐2DPAGE: A database of two‐dimensional gel electrophoresis images

Appel, Ron D.; Sanchez, Jean‐Charles; Bairoch, Amos Marc; Golaz, Olivier; Miu, M.; Vargas, Javier; Hochstrasser, Denis F.

doi:10.1002/elps.11501401185

Cited by 109 publications

(50 citation statements)

References 41 publications

(5 reference statements)

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“…In bacteria, from which archaea probably acquired dnaK , we were able to see a similar phenomenon searching on RegulonDB [59] for iTSS and SWISS-2DPAGE [61] for 2Dgel/MS data. In E. coli there is an iTSS (TSS_31 cluster) inside dnaK CDS ( locus b0014) which defines an intraORF that has no 5ʹ UTR, starts from an ATG codon and would translate a 37.0 kDa MW isoform with pI of 4.84.…”

Section: Resultsmentioning

confidence: 75%

“…The database registers a putative intraRNA (TSS_3889 cluster) that would translate a 30.1 kDa product starting at an ATG codon 6 nt downstream of the iTSS, with predicted pI of 5.79 and acidity-correct apparent MW of 32.7 kDa. We searched the two-dimensional gel electrophoresis image database SWISS-2DPAGE [61] for duplicated EF-G spots placed in accordance with the isoform prediction and retrieved the spot ID 2D-001WR8 (32.1 kDa, pI 5.78). Efforts to purify E. coli EF-G forty-five years ago revealed two isoforms [62] that were washed away in successive purification rounds.…”

Section: Resultsmentioning

confidence: 99%

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Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

et al. 2018

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Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same locus. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon Halobacterium salinarum. In the present work we used differential RNA-seq (dRNA-seq) in H. salinarum NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for kef1, acs3 and orc4 genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas vesicle protein gene gvpC1. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone dnaK and the aerobic respiration related cydA in both H. salinarum and Escherichia coli. Also, intraRNA translation evidence in H. salinarum, E. coli and yeast of a universal elongation factor (aEF-2, fusA and eEF-2) suggests that this is an ancient phenomenon present in all domains of life.

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Section: Resultsmentioning

confidence: 75%

Section: Resultsmentioning

confidence: 99%

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

et al. 2018

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“…The gels have 306 and 338 spots, respectively. The synthetic gel ofplasma was compared with a gel obtained from a pool ofplasma ofhealthy subjects (run in triplicate) and with that in the SWISS-2DPAGE database (Swiss Institute of Bioinfonnatics) which collects data on proteins identified by two-dimensional polyacrylamide gel electrophoresis (14). All three were quite similar.…”

Section: Methodsmentioning

confidence: 99%

Synthetic Gel of Carotid Artery Plaque

Terzuoli

Felici

Ciari

et al. 2007

Int J Immunopathol Pharmacol

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Atherosclerosis is a complex disease that affects medium and large arteries, leading to the formation and progression of plaque. In this process the proteins play an essential role and as a consequence, proteomic-based strategies examining the protein content of cells or tissues could offer a useful approach for the study of plaque proteins. Due to the heterogeneous cell composition of plaque, proteome analysis of whole lesions is difficult, besides being also complicated by the presence of plasma proteins that cannot be completely eliminated. A good way to study variations in protein expression among series of gels is to construct a synthetic gel. This type of gel is obtained by averaging the positions, shapes and optical densities of spots in a given set of gels. To be included in the synthetic gel, spots must be found in at least three gels. To obtain a profile representative of the proteome of atherosclerotic plaque, canceling its high variability, we constructed a synthetic gel using an average of ten carotid plaque samples. We then compared it with an equivalent synthetic gel constructed using ten plasma samples from the same carotid surgery patients. For the comparison of two synthetic gels (plasma/plaque) we could discriminate plasma proteins from plaque proteins. Besides analysis of spots common to plasma, the synthetic gel is useful to detect spots exclusive to plaque, thus simplifying a very complex mixture.Atherosclerosis is a chronic disease that affects medium and large arteries. The process originates from the interaction between cells of the arterial wall, lipoproteins and inflammatory cells (1), leading to the development of complex lesions or plaque that protrude into the arterial lumen. Mediators of inflammation are not only instrumental in the formation of plaque, but may also be involved in the rapid progression of atheromatous lesions, leading to plaque fissuring and intraluminal thrombosis. Several gene products including lipoprotein receptors, adhesion molecules, growth factors, cytokines, matrix metalloproteinases and proteins associated with cell death are also involved (2-3). This suggests that proteins play an essential role in the formation and progression of plaque.The use ofproteomic-based strategies, examining the protein content of cells or tissues, offers a useful approach for the study of plaque proteins (4). Proteins obtained from fragments of tissue with atherosclerotic lesions were recently studied in vitro (5-6), revealing an increase in transport proteins (Apo AIV, haptoglobin, transferrin, actin), signal transduction proteins (serum amyloid protein P) and a decrease in shock protein 27. The only proteins detected directly in coronary and carotid

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“…2-D gel image database (SWISS-2DPAGE) was established in 1993, with the premise of having an internet-accessible resource where all the spots on high quality 2-D gels of an organism's proteome were clearly annotated and identified (Appel et al, 1993 Regula et al, 2000;Cordwell et al, 2002;Liao et al, 2003;Coelho et al, 2004;Eymann et al, 2004;Folio et al, 2004;Rosen et al, 2004;Encheva et al, 2005;Wang et al, 2005;Encheva et al, 2006). Through concerted and exhaustive efforts, it is often possible to resolve and identify more than a thousand protein spots in a comprehensive 2-D reference map.…”

Section: Whole Cell Proteomementioning

confidence: 99%

Two-dimensional gel electrophoresis in bacterial proteomics

et al. 2012

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Two-dimensional gel electrophoresis (2-DE) is a gel-based technique widely used for analyzing the protein composition of biological samples. It is capable of resolving complex mixtures containing more than a thousand protein components into individual protein spots through the coupling of two orthogonal biophysical separation techniques: isoelectric focusing (first dimension) and polyacrylamide gel electrophoresis (second dimension). 2-DE is ideally suited for analyzing the entire expressed protein complement of a bacterial cell: its proteome. Its relative simplicity and good reproducibility have led to 2-DE being widely used for exploring proteomics within a wide range of environmental and medically-relevant bacteria. Here we give a broad overview of the basic principles and historical development of gel-based proteomics, and how this powerful approach can be applied for studying bacterial biology and physiology. We highlight specific 2-DE applications that can be used to analyze when, where and how much proteins are expressed. The links between proteomics, genomics and mass spectrometry are discussed. We explore how proteomics involving tandem mass spectrometry can be used to analyze (post-translational) protein modifications or to identify proteins of unknown origin by de novo peptide sequencing. The use of proteome fractionation techniques and non-gel-based proteomic approaches are also discussed. We highlight how the analysis of proteins secreted by bacterial cells (secretomes or exoproteomes) can be used to study infection processes or the immune response. This review is aimed at non-specialists who wish to gain a concise, comprehensive and contemporary overview of the nature and applications of bacterial proteomics.

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SWISS‐2DPAGE: A database of two‐dimensional gel electrophoresis images

Cited by 109 publications

References 41 publications

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea

Synthetic Gel of Carotid Artery Plaque

Two-dimensional gel electrophoresis in bacterial proteomics

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