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Meireles DDA, Yokomizo CH, Silva FP, Venâncio TM, Degenhardt MFDS, Oliveira CLPD, Netto LES. Functional diversity of YbbN/CnoX proteins: Insights from a comparative analysis of three thioredoxin-like oxidoreductases from Pseudomonas aeruginosa, Xylella fastidiosa and Escherichia coli. Redox Biol 2024; 72:103128. [PMID: 38554523 PMCID: PMC10998233 DOI: 10.1016/j.redox.2024.103128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/26/2024] [Accepted: 03/17/2024] [Indexed: 04/01/2024] Open
Abstract
YbbN/CnoX are proteins that display a Thioredoxin (Trx) domain linked to a tetratricopeptide domain. YbbN from Escherichia coli (EcYbbN) displays a co-chaperone (holdase) activity that is induced by HOCl. Here, we compared EcYbbN with YbbN proteins from Xylella fastidiosa (XfYbbN) and from Pseudomonas aeruginosa (PaYbbN). EcYbbN presents a redox active Cys residue at Trx domain (Cys63), 24 residues away from SQHC motif (SQHC[N24]C) that can form mixed disulfides with target proteins. In contrast, XfYbbN and PaYbbN present two Cys residues in the CXXC (CAPC) motif, while only PaYbbN shows the Cys residue equivalent to Cys63 of EcYbbN. Our phylogenetic analysis revealed that most of the YbbN proteins are in the bacteria domain of life and that their members can be divided into four groups according to the conserved Cys residues. EcYbbN (SQHC[N24]C), XfYbbN (CAPC[N24]V) and PaYbbN (CAPC[N24]C) are representatives of three sub-families. In contrast to EcYbbN, both XfYbbN and PaYbbN: (1) reduced an artificial disulfide (DTNB) and (2) supported the peroxidase activity of Peroxiredoxin Q from X. fastidiosa, suggesting that these proteins might function similarly to the canonical Trx enzymes. Indeed, XfYbbN was reduced by XfTrx reductase with a high catalytic efficiency (kcat/Km = 1.27 x 107 M-1 s-1), similar to the canonical XfTrx (XfTsnC). Furthermore, EcYbbN and XfYbbN, but not PaYbbN displayed HOCl-induced holdase activity. Remarkably, EcYbbN gained disulfide reductase activity while lost the HOCl-activated chaperone function, when the SQHC was replaced by CQHC. In contrast, the XfYbbN CAPA mutant lost the disulfide reductase activity, while kept its HOCl-induced chaperone function. In all cases, the induction of the holdase activity was accompanied by YbbN oligomerization. Finally, we showed that deletion of ybbN gene did not render in P. aeruginosa more sensitive stressful treatments. Therefore, YbbN/CnoX proteins display distinct properties, depending on the presence of the three conserved Cys residues.
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Affiliation(s)
- Diogo de Abreu Meireles
- Laboratório de Fisiologia e Bioquímica de Microrganismos, (LFBM), Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, RJ, Brazil.
| | - César Henrique Yokomizo
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Francisnei Pedrosa Silva
- Laboratório de Química e Função de Peptídeos e Proteínas (LQFPP), Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, RJ, Brazil
| | - Thiago Motta Venâncio
- Laboratório de Química e Função de Peptídeos e Proteínas (LQFPP), Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos do Goytacazes, RJ, Brazil
| | | | | | - Luis Eduardo Soares Netto
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de Sao Paulo, Sao Paulo, SP, Brazil.
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Izquierdo-Fiallo K, Muñoz-Villagrán C, Orellana O, Sjoberg R, Levicán G. Comparative genomics of the proteostasis network in extreme acidophiles. PLoS One 2023; 18:e0291164. [PMID: 37682893 PMCID: PMC10490939 DOI: 10.1371/journal.pone.0291164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Extreme acidophiles thrive in harsh environments characterized by acidic pH, high concentrations of dissolved metals and high osmolarity. Most of these microorganisms are chemolithoautotrophs that obtain energy from low redox potential sources, such as the oxidation of ferrous ions. Under these conditions, the mechanisms that maintain homeostasis of proteins (proteostasis), as the main organic components of the cells, are of utmost importance. Thus, the analysis of protein chaperones is critical for understanding how these organisms deal with proteostasis under such environmental conditions. In this work, using a bioinformatics approach, we performed a comparative genomic analysis of the genes encoding classical, periplasmic and stress chaperones, and the protease systems. The analysis included 35 genomes from iron- or sulfur-oxidizing autotrophic, heterotrophic, and mixotrophic acidophilic bacteria. The results showed that classical ATP-dependent chaperones, mostly folding chaperones, are widely distributed, although they are sub-represented in some groups. Acidophilic bacteria showed redundancy of genes coding for the ATP-independent holdase chaperones RidA and Hsp20. In addition, a systematically high redundancy of genes encoding periplasmic chaperones like HtrA and YidC was also detected. In the same way, the proteolytic ATPase complexes ClpPX and Lon presented redundancy and broad distribution. The presence of genes that encoded protein variants was noticeable. In addition, genes for chaperones and protease systems were clustered within the genomes, suggesting common regulation of these activities. Finally, some genes were differentially distributed between bacteria as a function of the autotrophic or heterotrophic character of their metabolism. These results suggest that acidophiles possess an abundant and flexible proteostasis network that protects proteins in organisms living in energy-limiting and extreme environmental conditions. Therefore, our results provide a means for understanding the diversity and significance of proteostasis mechanisms in extreme acidophilic bacteria.
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Affiliation(s)
- Katherin Izquierdo-Fiallo
- Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile (USACH), Santiago, Chile
| | - Claudia Muñoz-Villagrán
- Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile (USACH), Santiago, Chile
| | - Omar Orellana
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Rachid Sjoberg
- Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile (USACH), Santiago, Chile
| | - Gloria Levicán
- Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile (USACH), Santiago, Chile
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Dupuy E, Collet JF. Fort CnoX: Protecting Bacterial Proteins From Misfolding and Oxidative Damage. Front Mol Biosci 2021; 8:681932. [PMID: 34017858 PMCID: PMC8129009 DOI: 10.3389/fmolb.2021.681932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/13/2021] [Indexed: 11/13/2022] Open
Abstract
How proteins fold and are protected from stress-induced aggregation is a long-standing mystery and a crucial question in biology. Here, we present the current knowledge on the chaperedoxin CnoX, a novel type of protein folding factor that combines holdase chaperone activity with a redox protective function. Focusing on Escherichia coli CnoX, we explain the essential role played by this protein under HOCl (bleach) stress, discussing how it protects its substrates from both aggregation and irreversible oxidation, which could otherwise interfere with refolding. Finally, we highlight the unique ability of CnoX, apparently conserved during evolution, to cooperate with the GroEL/ES folding machinery.
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Affiliation(s)
- Emile Dupuy
- WELBIO, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Jean-François Collet
- WELBIO, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain, Brussels, Belgium
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4
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Abstract
Neutrophils kill invading microbes and therefore represent the first line of defense of the innate immune response. Activated neutrophils assemble NADPH oxidase to convert substantial amounts of molecular oxygen into superoxide, which, after dismutation into peroxide, serves as the substrate for the generation of the potent antimicrobial hypochlorous acid (HOCl) in the phagosomal space. In this minireview, we explore the most recent insights into physiological consequences of HOCl stress. Not surprisingly, Gram-negative bacteria have evolved diverse posttranslational defense mechanisms to protect their proteins, the main targets of HOCl, from HOCl-mediated damage. We discuss the idea that oxidation of conserved cysteine residues and partial unfolding of its structure convert the heat shock protein Hsp33 into a highly active chaperone holdase that binds unfolded proteins and prevents their aggregation. We examine two novel members of the Escherichia coli chaperone holdase family, RidA and CnoX, whose thiol-independent activation mechanism differs from that of Hsp33 and requires N-chlorination of positively charged amino acids during HOCl exposure. Furthermore, we summarize the latest findings with respect to another bacterial defense strategy employed in response to HOCl stress, which involves the accumulation of the universally conserved biopolymer inorganic polyphosphate. We then discuss sophisticated adaptive strategies that bacteria have developed to enhance their survival during HOCl stress. Understanding bacterial defense and survival strategies against one of the most powerful neutrophilic oxidants may provide novel insights into treatment options that potentially compromise the ability of pathogens to resist HOCl stress and therefore may increase the efficacy of the innate immune response.
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Goemans CV, Vertommen D, Agrebi R, Collet JF. CnoX Is a Chaperedoxin: A Holdase that Protects Its Substrates from Irreversible Oxidation. Mol Cell 2018; 70:614-627.e7. [PMID: 29754824 DOI: 10.1016/j.molcel.2018.04.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/22/2018] [Accepted: 04/03/2018] [Indexed: 02/01/2023]
Abstract
Bleach (HOCl) is a powerful oxidant that kills bacteria in part by causing protein aggregation. It inactivates ATP-dependent chaperones, rendering cellular proteins mostly dependent on holdases. Here we identified Escherichia coli CnoX (YbbN) as a folding factor that, when activated by bleach via chlorination, functions as an efficient holdase, protecting the substrates of the major folding systems GroEL/ES and DnaK/J/GrpE. Remarkably, CnoX uniquely combines this function with the ability to prevent the irreversible oxidation of its substrates. This dual activity makes CnoX the founding member of a family of proteins, the "chaperedoxins." Because CnoX displays a thioredoxin fold and a tetratricopeptide (TPR) domain, two structural motifs conserved in all organisms, this investigation sets the stage for the discovery of additional chaperedoxins in bacteria and eukaryotes that could cooperate with proteins from both the Hsp60 and Hsp70 families.
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Affiliation(s)
- Camille V Goemans
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Didier Vertommen
- de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Rym Agrebi
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Jean-François Collet
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium.
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6
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Du H, Kim S, Hur YS, Lee MS, Lee SH, Cheon CI. A cytosolic thioredoxin acts as a molecular chaperone for peroxisome matrix proteins as well as antioxidant in peroxisome. Mol Cells 2015; 38:187-94. [PMID: 26013260 PMCID: PMC4332030 DOI: 10.14348/molcells.2015.2255] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 12/17/2014] [Accepted: 12/18/2014] [Indexed: 12/14/2022] Open
Abstract
Thioredoxin (TRX) is a disulfide reductase present ubiquitously in all taxa and plays an important role as a regulator of cellular redox state. Recently, a redox-independent, chaperone function has also been reported for some thioredoxins. We previously identified nodulin-35, the subunit of soybean uricase, as an interacting target of a cytosolic soybean thioredoxin, GmTRX. Here we report the further characterization of the interaction, which turns out to be independent of the disulfide reductase function and results in the co-localization of GmTRX and nodulin-35 in peroxisomes, suggesting a possible function of GmTRX in peroxisomes. In addition, the chaperone function of GmTRX was demonstrated in in vitro molecular chaperone activity assays including the thermal denaturation assay and malate dehydrogenase aggregation assay. Our results demonstrate that the target of GmTRX is not only confined to the nodulin-35, but many other peroxisomal proteins, including catalase (AtCAT), transthyretin-like protein 1 (AtTTL1), and acyl-coenzyme A oxidase 4 (AtACX4), also interact with the GmTRX. Together with an increased uricase activity of nodulin-35 and reduced ROS accumulation observed in the presence of GmTRX in our results, especially under heat shock and oxidative stress conditions, it appears that GmTRX represents a novel thioredoxin that is co-localized to the peroxisomes, possibly providing functional integrity to peroxisomal proteins.
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Affiliation(s)
- Hui Du
- Department of Biological Science, Sookmyung Women’s University, Seoul 140-742, Korea
| | - Sunghan Kim
- Department of Plant Science, Seoul National University, Seoul 151-742, Korea
| | - Yoon-Sun Hur
- Department of Biological Science, Sookmyung Women’s University, Seoul 140-742, Korea
| | - Myung-Sok Lee
- Department of Biological Science, Sookmyung Women’s University, Seoul 140-742, Korea
| | - Suk-Ha Lee
- Department of Plant Science, Seoul National University, Seoul 151-742, Korea
| | - Choong-Ill Cheon
- Department of Biological Science, Sookmyung Women’s University, Seoul 140-742, Korea
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7
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Giaouris E, Samoilis G, Chorianopoulos N, Ercolini D, Nychas GJ. Differential protein expression patterns between planktonic and biofilm cells of Salmonella enterica serovar Enteritidis PT4 on stainless steel surface. Int J Food Microbiol 2013; 162:105-13. [PMID: 23376784 DOI: 10.1016/j.ijfoodmicro.2012.12.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 12/27/2012] [Accepted: 12/28/2012] [Indexed: 10/27/2022]
Abstract
In the present study, the proteome of a strain of S. enterica serovar Enteritidis PT4, grown either as biofilm on stainless steel surface or as free-floating (planktonic) in Brain Heart (BH) broth, was investigated in order to detect the strong differences in whole-cell protein expression patterns between the two growth styles. The proteins extracted from both types of cells were subjected to 2-D PAGE, followed by in-gel tryptic digestion, extraction, subsequent MALDI-TOF mass spectrometry (MS) analysis and finally database searches for protein identification. Using this approach, 30 proteins were identified as differentially expressed between the two growth modes on an "on-off" basis, that is, proteins that were detected in one case but not in the other. In particular, 20 and 10 proteins were identified in biofilm and planktonic-grown cells, respectively. The group of proteins whose expression was visible only during biofilm growth included proteins involved in global regulation and stress response (ArcA, BtuE, Dps, OsmY, SspA, TrxA, YbbN and YhbO), nutrient transport (Crr, DppA, Fur and SufC), degradation and energy metabolism (GcvT, GpmA, RibB), detoxification (SseA and YibF), DNA metabolism (SSB), curli production (CsgF), and murein synthesis (MipA). To summarize, this study demonstrates that biofilm growth of S. Enteritidis causes distinct changes in protein expression and offers valuable new data regarding some of the proteins presumably involved in this process. The putative role of these proteins in the maintenance of a biofilm community in Salmonella and other bacteria is discussed.
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Affiliation(s)
- Efstathios Giaouris
- Department of Food Science and Nutrition, University of the Aegean, Mitropoliti Ioakeim 2, Myrina, 81400 Lemnos, Greece.
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Sanz-Barrio R, Fernández-San Millán A, Carballeda J, Corral-Martínez P, Seguí-Simarro JM, Farran I. Chaperone-like properties of tobacco plastid thioredoxins f and m. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:365-79. [PMID: 21948853 PMCID: PMC3245471 DOI: 10.1093/jxb/err282] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 06/27/2011] [Accepted: 08/12/2011] [Indexed: 05/19/2023]
Abstract
Thioredoxins (Trxs) are ubiquitous disulphide reductases that play important roles in the redox regulation of many cellular processes. However, some redox-independent functions, such as chaperone activity, have also been attributed to Trxs in recent years. The focus of our study is on the putative chaperone function of the well-described plastid Trxs f and m. To that end, the cDNA of both Trxs, designated as NtTrxf and NtTrxm, was isolated from Nicotiana tabacum plants. It was found that bacterially expressed tobacco Trx f and Trx m, in addition to their disulphide reductase activity, possessed chaperone-like properties. In vitro, Trx f and Trx m could both facilitate the reactivation of the cysteine-free form of chemically denatured glucose-6 phosphate dehydrogenase (foldase chaperone activity) and prevent heat-induced malate dehydrogenase aggregation (holdase chaperone activity). Our results led us to infer that the disulphide reductase and foldase chaperone functions prevail when the proteins occur as monomers and the well-conserved non-active cysteine present in Trx f is critical for both functions. By contrast, the holdase chaperone activity of both Trxs depended on their oligomeric status: the proteins were functional only when they were associated with high molecular mass protein complexes. Because the oligomeric status of both Trxs was induced by salt and temperature, our data suggest that plastid Trxs could operate as molecular holdase chaperones upon oxidative stress, acting as a type of small stress protein.
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Affiliation(s)
- Ruth Sanz-Barrio
- Instituto de Agrobiotecnología, Universidad Pública de Navarra-CSIC-Gobierno de Navarra, Campus Arrosadía, E-31006 Pamplona, Spain
| | - Alicia Fernández-San Millán
- Instituto de Agrobiotecnología, Universidad Pública de Navarra-CSIC-Gobierno de Navarra, Campus Arrosadía, E-31006 Pamplona, Spain
| | - Jon Carballeda
- Instituto de Agrobiotecnología, Universidad Pública de Navarra-CSIC-Gobierno de Navarra, Campus Arrosadía, E-31006 Pamplona, Spain
| | - Patricia Corral-Martínez
- Instituto para la Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universidad Politécnica de Valencia, Ciudad Politécnica de la Innovación, Edificio 8E - Escalera I, Camino de Vera s/n, E-46022 Valencia, Spain
| | - José M. Seguí-Simarro
- Instituto para la Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universidad Politécnica de Valencia, Ciudad Politécnica de la Innovación, Edificio 8E - Escalera I, Camino de Vera s/n, E-46022 Valencia, Spain
| | - Inmaculada Farran
- Instituto de Agrobiotecnología, Universidad Pública de Navarra-CSIC-Gobierno de Navarra, Campus Arrosadía, E-31006 Pamplona, Spain
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Smock RG, Blackburn ME, Gierasch LM. Conserved, disordered C terminus of DnaK enhances cellular survival upon stress and DnaK in vitro chaperone activity. J Biol Chem 2011; 286:31821-9. [PMID: 21768118 DOI: 10.1074/jbc.m111.265835] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The 70-kDa heat shock proteins (Hsp70s) function as molecular chaperones through the allosteric coupling of their nucleotide- and substrate-binding domains, the structures of which are highly conserved. In contrast, the roles of the poorly structured, variable length C-terminal regions present on Hsp70s remain unclear. In many eukaryotic Hsp70s, the extreme C-terminal EEVD tetrapeptide sequence associates with co-chaperones via binding to tetratricopeptide repeat domains. It is not known whether this is the only function for this region in eukaryotic Hsp70s and what roles this region performs in Hsp70s that do not form complexes with tetratricopeptide repeat domains. We compared C-terminal sequences of 730 Hsp70 family members and identified a novel conservation pattern in a diverse subset of 165 bacterial and organellar Hsp70s. Mutation of conserved C-terminal sequence in DnaK, the predominant Hsp70 in Escherichia coli, results in significant impairment of its protein refolding activity in vitro without affecting interdomain allostery, interaction with co-chaperones DnaJ and GrpE, or the binding of a peptide substrate, defying classical explanations for the chaperoning mechanism of Hsp70. Moreover, mutation of specific conserved sites within the DnaK C terminus reduces the capacity of the cell to withstand stresses on protein folding caused by elevated temperature or the absence of other chaperones. These features of the C-terminal region support a model in which it acts as a disordered tether linked to a conserved, weak substrate-binding motif and that this enhances chaperone function by transiently interacting with folding clients.
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Affiliation(s)
- Robert G Smock
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA
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Lin J, Wilson MA. Escherichia coli thioredoxin-like protein YbbN contains an atypical tetratricopeptide repeat motif and is a negative regulator of GroEL. J Biol Chem 2011; 286:19459-69. [PMID: 21498507 PMCID: PMC3103325 DOI: 10.1074/jbc.m111.238741] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 04/13/2011] [Indexed: 11/06/2022] Open
Abstract
Many proteins contain a thioredoxin (Trx)-like domain fused with one or more partner domains that diversify protein function by the modular construction of new molecules. The Escherichia coli protein YbbN is a Trx-like protein that contains a C-terminal domain with low homology to tetratricopeptide repeat motifs. YbbN has been proposed to act as a chaperone or co-chaperone that aids in heat stress response and DNA synthesis. We report the crystal structure of YbbN, which is an elongated molecule with a mobile Trx domain and four atypical tetratricopeptide repeat motifs. The Trx domain lacks a canonical CXXC active site architecture and is not a functional oxidoreductase. A variety of proteins in E. coli interact with YbbN, including multiple ribosomal protein subunits and a strong interaction with GroEL. YbbN acts as a mild inhibitor of GroESL chaperonin function and ATPase activity, suggesting that it is a negative regulator of the GroESL system. Combined with previous observations that YbbN enhances the DnaK-DnaJ-GrpE chaperone system, we propose that YbbN coordinately regulates the activities of these two prokaryotic chaperones, thereby helping to direct client protein traffic initially to DnaK. Therefore, YbbN may play a role in integrating the activities of different chaperone pathways in E. coli and related bacteria.
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Affiliation(s)
- Jiusheng Lin
- From the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0664
| | - Mark A. Wilson
- From the Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0664
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11
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Mykytczuk NCS, Trevors JT, Foote SJ, Leduc LG, Ferroni GD, Twine SM. Proteomic insights into cold adaptation of psychrotrophic and mesophilic Acidithiobacillus ferrooxidans strains. Antonie Van Leeuwenhoek 2011; 100:259-77. [DOI: 10.1007/s10482-011-9584-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Accepted: 04/29/2011] [Indexed: 11/29/2022]
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12
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Dekker C, Willison KR, Taylor WR. On the evolutionary origin of the chaperonins. Proteins 2011; 79:1172-92. [DOI: 10.1002/prot.22952] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 10/06/2010] [Accepted: 10/29/2010] [Indexed: 11/09/2022]
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13
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Carranza P, Grunau A, Schneider T, Hartmann I, Lehner A, Stephan R, Gehrig P, Grossmann J, Groebel K, Hoelzle LE, Eberl L, Riedel K. A gel-free quantitative proteomics approach to investigate temperature adaptation of the food-borne pathogen Cronobacter turicensis
3032. Proteomics 2010; 10:3248-61. [DOI: 10.1002/pmic.200900460] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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14
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Scharl T, Striedner G, Pötschacher F, Leisch F, Bayer K. Interactive visualization of clusters in microarray data: an efficient tool for improved metabolic analysis of E. coli. Microb Cell Fact 2009; 8:37. [PMID: 19604371 PMCID: PMC2717919 DOI: 10.1186/1475-2859-8-37] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Accepted: 07/15/2009] [Indexed: 11/25/2022] Open
Abstract
Background Interpretation of comprehensive DNA microarray data sets is a challenging task for biologists and process engineers where scientific assistance of statistics and bioinformatics is essential. Interdisciplinary cooperation and concerted development of software-tools for simplified and accelerated data analysis and interpretation is the key to overcome the bottleneck in data-analysis workflows. This approach is exemplified by gcExplorer an interactive visualization toolbox based on cluster analysis. Clustering is an important tool in gene expression data analysis to find groups of co-expressed genes which can finally suggest functional pathways and interactions between genes. The visualization of gene clusters gives practitioners an understanding of the cluster structure of their data and makes it easier to interpret the cluster results. Results In this study the interactive visualization toolbox gcExplorer is applied to the interpretation of E. coli microarray data. The data sets derive from two fedbatch experiments conducted in order to investigate the impact of different induction strategies on the host metabolism and product yield. The software enables direct graphical comparison of these two experiments. The identification of potentially interesting gene candidates or functional groups is substantially accelerated and eased. Conclusion It was shown that gcExplorer is a very helpful tool to gain a general overview of microarray experiments. Interesting gene expression patterns can easily be found, compared among different experiments and combined with information about gene function from publicly available databases.
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Affiliation(s)
- Theresa Scharl
- Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria.
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