1
|
Impact of Growth Rate on the Protein-mRNA Ratio in Pseudomonas aeruginosa. mBio 2023; 14:e0306722. [PMID: 36475772 PMCID: PMC9973009 DOI: 10.1128/mbio.03067-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Our understanding of how bacterial pathogens colonize and persist during human infection has been hampered by the limited characterization of bacterial physiology during infection and a research bias toward in vitro, fast-growing bacteria. Recent research has begun to address these gaps in knowledge by directly quantifying bacterial mRNA levels during human infection, with the goal of assessing microbial community function at the infection site. However, mRNA levels are not always predictive of protein levels, which are the primary functional units of a cell. Here, we used carefully controlled chemostat experiments to examine the relationship between mRNA and protein levels across four growth rates in the bacterial pathogen Pseudomonas aeruginosa. We found a genome-wide positive correlation between mRNA and protein abundances across all growth rates, with genes required for P. aeruginosa viability having stronger correlations than nonessential genes. We developed a statistical method to identify genes whose mRNA abundances poorly predict protein abundances and calculated an RNA-to-protein (RTP) conversion factor to improve mRNA predictions of protein levels. The application of the RTP conversion factor to publicly available transcriptome data sets was highly robust, enabling the more accurate prediction of P. aeruginosa protein levels across strains and growth conditions. Finally, the RTP conversion factor was applied to P. aeruginosa human cystic fibrosis (CF) infection transcriptomes to provide greater insights into the functionality of this bacterium in the CF lung. This study addresses a critical problem in infection microbiology by providing a framework for enhancing the functional interpretation of bacterial human infection transcriptome data. IMPORTANCE Our understanding of bacterial physiology during human infection is limited by the difficulty in assessing bacterial function at the infection site. Recent studies have begun to address this question by quantifying bacterial mRNA levels in human-derived samples using transcriptomics. One challenge for these studies is the poor predictivity of mRNA for protein levels for some genes. Here, we addressed this challenge by measuring the transcriptomes and proteomes of P. aeruginosa grown at four growth rates. Our results revealed that the growth rate does not impact the genome-wide correlation of mRNA and protein levels. We used statistical methods to identify the genes for which mRNA and protein were poorly correlated and developed an RNA-to-protein (RTP) conversion factor that improved the predictivity of protein levels across strains and growth conditions. Our results provide new insights into mRNA-protein correlations and tools to enhance our understanding of bacterial physiology from transcriptome data.
Collapse
|
2
|
Wu B, Qiao J, Wang X, Liu M, Xu S, Sun D. Factors affecting the rapid changes of protein under short-term heat stress. BMC Genomics 2021; 22:263. [PMID: 33849452 PMCID: PMC8042900 DOI: 10.1186/s12864-021-07560-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/26/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Protein content determines the state of cells. The variation in protein abundance is crucial when organisms are in the early stages of heat stress, but the reasons affecting their changes are largely unknown. RESULTS We quantified 47,535 mRNAs and 3742 proteins in the filling grains of wheat in two different thermal environments. The impact of mRNA abundance and sequence features involved in protein translation and degradation on protein expression was evaluated by regression analysis. Transcription, codon usage and amino acid frequency were the main drivers of changes in protein expression under heat stress, and their combined contribution explains 58.2 and 66.4% of the protein variation at 30 and 40 °C (20 °C as control), respectively. Transcription contributes more to alterations in protein content at 40 °C (31%) than at 30 °C (6%). Furthermore, the usage of codon AAG may be closely related to the rapid alteration of proteins under heat stress. The contributions of AAG were 24 and 13% at 30 and 40 °C, respectively. CONCLUSION In this study, we analyzed the factors affecting the changes in protein expression in the early stage of heat stress and evaluated their influence.
Collapse
Affiliation(s)
- Bingjin Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jianwen Qiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xiaoming Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Manshuang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Daojie Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| |
Collapse
|
3
|
The Role of Replication Clamp-Loader Protein HolC of Escherichia coli in Overcoming Replication/Transcription Conflicts. mBio 2021; 12:mBio.00184-21. [PMID: 33688004 PMCID: PMC8092217 DOI: 10.1128/mbio.00184-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Escherichia coli, DNA replication is catalyzed by an assembly of proteins, the DNA polymerase III holoenzyme. This complex includes the polymerase and proofreading subunits, the processivity clamp, and clamp loader complex. The holC gene encodes an accessory protein (known as χ) to the core clamp loader complex and is the only protein of the holoenzyme that binds to single-strand DNA binding protein, SSB. HolC is not essential for viability, although mutants show growth impairment, genetic instability, and sensitivity to DNA damaging agents. In this study, we isolate spontaneous suppressor mutants in a ΔholC strain and identify these by whole-genome sequencing. Some suppressors are alleles of RNA polymerase, suggesting that transcription is problematic for holC mutant strains, or alleles of sspA, encoding stringent starvation protein. Using a conditional holC plasmid, we examine factors affecting transcription elongation and termination for synergistic or suppressive effects on holC mutant phenotypes. Alleles of RpoA (α), RpoB (β), and RpoC (β') RNA polymerase holoenzyme can partially suppress loss of HolC. In contrast, mutations in transcription factors DksA and NusA enhanced the inviability of holC mutants. HolC mutants showed enhanced sensitivity to bicyclomycin, a specific inhibitor of Rho-dependent termination. Bicyclomycin also reverses suppression of holC by rpoA, rpoC, and sspA An inversion of the highly expressed rrnA operon exacerbates the growth defects of holC mutants. We propose that transcription complexes block replication in holC mutants and that Rho-dependent transcriptional termination and DksA function are particularly important to sustain viability and chromosome integrity.IMPORTANCE Transcription elongation complexes present an impediment to DNA replication. We provide evidence that one component of the replication clamp loader complex, HolC, of Escherichia coli is required to overcome these blocks. This genetic study of transcription factor effects on holC growth defects implicates Rho-dependent transcriptional termination and DksA function as critical. It also implicates, for the first time, a role of SspA, stringent starvation protein, in avoidance or tolerance of replication/replication conflicts. We speculate that HolC helps avoid or resolve collisions between replication and transcription complexes, which become toxic in HolC's absence.
Collapse
|
4
|
Nobori T, Wang Y, Wu J, Stolze SC, Tsuda Y, Finkemeier I, Nakagami H, Tsuda K. Multidimensional gene regulatory landscape of a bacterial pathogen in plants. NATURE PLANTS 2020; 6:883-896. [PMID: 32541952 DOI: 10.1038/s41477-020-0690-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/08/2020] [Indexed: 05/25/2023]
Abstract
Understanding the gene regulation of plant pathogens is crucial for pest control and thus global food security. An integrated understanding of bacterial gene regulation in the host is dependent on multi-omic datasets, but these are largely lacking. Here, we simultaneously characterized the transcriptome and proteome of a bacterial pathogen in plants. We found a number of bacterial processes affected by plant immunity at the transcriptome and proteome levels. For instance, salicylic acid-mediated plant immunity suppressed the accumulation of proteins comprising the tip component of the bacterial type III secretion system. Interestingly, there were instances of concordant and discordant regulation of bacterial messenger RNAs and proteins. Gene co-expression analysis uncovered previously unknown gene regulatory modules underlying virulence. This study provides molecular insights into the multiple layers of gene regulation that contribute to bacterial growth in planta, and elucidates the role of plant immunity in affecting pathogen responses.
Collapse
Affiliation(s)
- Tatsuya Nobori
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Yiming Wang
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- College of Plant Protection, Nanjing Agriculture University, Nanjing, China
| | - Jingni Wu
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Sara Christina Stolze
- Protein Mass Spectrometry Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Yayoi Tsuda
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Iris Finkemeier
- Protein Mass Spectrometry Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Plant Biology and Biotechnology, University of Muenster, Münster, Germany
| | - Hirofumi Nakagami
- Protein Mass Spectrometry Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kenichi Tsuda
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
| |
Collapse
|
5
|
Moreira MH, Barros GC, Requião RD, Rossetto S, Domitrovic T, Palhano FL. From reporters to endogenous genes: the impact of the first five codons on translation efficiency in Escherichia coli. RNA Biol 2019; 16:1806-1816. [PMID: 31470761 PMCID: PMC6844562 DOI: 10.1080/15476286.2019.1661213] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 08/23/2019] [Indexed: 12/29/2022] Open
Abstract
Translation initiation is a critical step in the regulation of protein synthesis, and it is subjected to different control mechanisms, such as 5' UTR secondary structure and initiation codon context, that can influence the rates at which initiation and consequentially translation occur. For some genes, translation elongation also affects the rate of protein synthesis. With a GFP library containing nearly all possible combinations of nucleotides from the 3rd to the 5th codon positions in the protein coding region of the mRNA, it was previously demonstrated that some nucleotide combinations increased GFP expression up to four orders of magnitude. While it is clear that the codon region from positions 3 to 5 can influence protein expression levels of artificial constructs, its impact on endogenous proteins is still unknown. Through bioinformatics analysis, we identified the nucleotide combinations of the GFP library in Escherichia coli genes and examined the correlation between the expected levels of translation according to the GFP data with the experimental measures of protein expression. We observed that E. coli genes were enriched with the nucleotide compositions that enhanced protein expression in the GFP library, but surprisingly, it seemed to affect the translation efficiency only marginally. Nevertheless, our data indicate that different enterobacteria present similar nucleotide composition enrichment as E. coli, suggesting an evolutionary pressure towards the conservation of short translational enhancer sequences.
Collapse
Affiliation(s)
- Mariana H. Moreira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Géssica C. Barros
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rodrigo D. Requião
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Silvana Rossetto
- Departamento de Ciência da Computação, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tatiana Domitrovic
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernando L. Palhano
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
6
|
Abstract
In the self-assembly process which drives the formation of cellular membranes, micelles, and capsids, a collection of separated subunits spontaneously binds together to form functional and more ordered structures. In this work, we study the statistical physics of self-assembly in a simpler scenario: the formation of dimers from a system of monomers. The properties of the model allow us to frame the microstate counting as a combinatorial problem whose solution leads to an exact partition function. From the associated equilibrium conditions, we find that such dimer systems come in two types: "search-limited" and "combinatorics-limited," only the former of which has states where partial assembly can be dominated by correct contacts. Using estimates of biophysical quantities in systems of single-stranded DNA dimerization, transcription factor and DNA interactions, and protein-protein interactions, we find that all of these systems appear to be of the search-limited type, i.e., their fully correct dimerization regimes are more limited by the ability of monomers to find one another in the constituent volume than by the combinatorial disadvantage of correct dimers. We derive the parameter requirements for fully correct dimerization and find that rather than the ratio of particle number and volume (i.e., number density) being the relevant quantity, it is the product of particle diversity and volume that is constrained. Ultimately, this work contributes to an understanding of self-assembly by using the simple case of a system of dimers to analytically study the combinatorics of assembly.
Collapse
Affiliation(s)
- Mobolaji Williams
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| |
Collapse
|
7
|
Gene expression and protein synthesis of esterase from Streptococcus mutans are affected by biodegradation by-product from methacrylate resin composites and adhesives. Acta Biomater 2018; 81:158-168. [PMID: 30268915 DOI: 10.1016/j.actbio.2018.09.050] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 09/14/2018] [Accepted: 09/26/2018] [Indexed: 11/22/2022]
Abstract
An esterase from S. mutans UA159, SMU_118c, was shown to hydrolyze methacrylate resin-based dental monomers. OBJECTIVE To investigate the association of SMU_118c to the whole cellular hydrolytic activity of S. mutans toward polymerized resin composites, and to examine how the bacterium adapts its hydrolytic activity in response to environmental stresses triggered by the presence of a resin composites and adhesives biodegradation by-product (BBP). MATERIALS AND METHODS Biofilms of S. mutans UA159 parent wild strain, SMU_118c knockout strain (ΔSMU_118c), and SMU_118c complemented strain (ΔSMU_118cC) were incubated with photo-polymerized resin composite. High performance liquid chromatography was used to quantify the amount of a universal 2,2-Bis[4-(2-hydroxy-3-methacryloxypropoxy)phenyl]propane (bisGMA)-derived BBP, bishydroxy-propoxy-phenyl-propane (bisHPPP) in the media. Fluorescence in situ hybridization (FISH) and quantitative proteomic analysis were used to measure SMU_118c gene expression and production of SMU_118c protein, respectively, from biofilms of S. mutans UA159 wild strain that were cultured with bisHPPP. RESULTS The levels of bisHPPP released from composite were similar for ΔSMU_118c and media control, and these were significantly lower compared to the parent wild-strain UA159 and complemented strain (ΔSMU_118cC) (p < 0.05). Gene expression of SMU_118c and productions of SMU_118c protein were higher for bisHPPP incubated biofilms (p < 0.05). SIGNIFICANCE This study suggests that SMU_118c is a dominant esterase in S. mutans and capable of catalyzing the hydrolysis of the resinous matrix of polymerized composites and adhesives. In turn, the bacterial response to BBP was to increase the expression of the esterase gene and enhance esterase production, potentially accelerating the biodegradation of the restoration, adhesive and restoration-tooth interface, ultimately contributing to premature restoration failure. STATEMENT OF SIGNIFICANCE We recently reported (Huang et al., 2018) on the isolation and initial characterization of a specific esterase (SMU_118c) from S. mutans that show degradative activity toward the hydrolysis of dental monomers. The current study further characterize this enzyme and shows that SMU_118c is a dominant degradative esterase activity in the cariogenic bacterium S. mutans and is capable of catalyzing the hydrolysis of the resinous matrix of polymerized composites and adhesives. In turn, the bacterial response to biodegradation by-products from composites and adhesives was to increase the expression of the esterase gene and enhance esterase production, accelerating the biodegradation of the restoration, adhesive and the restoration-tooth interface, potentially contributing to the pathogenesis of recurrent caries around resin composite restorations.
Collapse
|
8
|
Matsumoto M, Nakayama KI. The promise of targeted proteomics for quantitative network biology. Curr Opin Biotechnol 2018; 54:88-97. [PMID: 29550704 DOI: 10.1016/j.copbio.2018.02.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 02/21/2018] [Accepted: 02/27/2018] [Indexed: 12/20/2022]
Abstract
Proteomics is a powerful tool for obtaining information on a large number of proteins with regard to their expression levels, interactions with other molecules, and posttranslational modifications. Whereas nontargeted, discovery proteomics uncovers differences in the proteomic landscape under different conditions, targeted proteomics has been developed to overcome the limitations of this approach with regard to quantitation. In addition to technical advances in instruments and informatics tools, the advent of the synthetic proteome composed of synthetic peptides or recombinant proteins has advanced the adoption of targeted proteomics across a wide range of research fields. Targeted proteomics can now be applied to measurement of the dynamics of any proteins of interest under a variety of conditions as well as to estimation of the absolute abundance or stoichiometry of proteins in a given network. Multiplexed targeted proteomics assays of high reproducibility and accuracy can provide insight at the quantitative level into entire networks that govern biological phenomena or diseases. Such assays will establish a new paradigm for data-driven science.
Collapse
Affiliation(s)
- Masaki Matsumoto
- Department of Molecular and Cellular Biology and Division of Proteomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology and Division of Proteomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.
| |
Collapse
|
9
|
Response induced in Mycoplasma gallisepticum under heat shock might be relevant to infection process. Sci Rep 2017; 7:11330. [PMID: 28900116 PMCID: PMC5595898 DOI: 10.1038/s41598-017-09237-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 07/25/2017] [Indexed: 12/26/2022] Open
Abstract
Despite the fact the term "proteome" was proposed to characterize a set of proteins in one of mycoplasma species, proteome response to various exposures in this bacteria are still obscure. Commonly, authors studying proteomic response on perturbation models in mycoplasmas use single approach and do not confirm their findings by alternative methods. Consequently, the results of proteomic analysis should be validated by complementary techniques. In this study we utilized three complementary approaches (SWATH, MRM, 2D-DIGE) to assess response of Mycoplasma gallisepticum under heat stress on proteomic level and combined these findings with metabolic response and the results of transcriptional profiling. We divide response into two modes - one is directly related to heat stress and other is triggered during heat stress, but not directly relevant to it. The latter includes accumulation of ATP and shedding of antigens. Both of these phenomena may be relevant to evasion of host's immune system and dissemination during mycoplasmosis in vivo.
Collapse
|
10
|
Speda J, Jonsson BH, Carlsson U, Karlsson M. Metaproteomics-guided selection of targeted enzymes for bioprospecting of mixed microbial communities. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:128. [PMID: 28523076 PMCID: PMC5434538 DOI: 10.1186/s13068-017-0815-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/08/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND Hitherto, the main goal of metaproteomic analyses has been to characterize the functional role of particular microorganisms in the microbial ecology of various microbial communities. Recently, it has been suggested that metaproteomics could be used for bioprospecting microbial communities to query for the most active enzymes to improve the selection process of industrially relevant enzymes. In the present study, to reduce the complexity of metaproteomic samples for targeted bioprospecting of novel enzymes, a microbial community capable of producing cellulases was maintained on a chemically defined medium in an enzyme suppressed metabolic steady state. From this state, it was possible to specifically and distinctively induce the desired cellulolytic activity. The extracellular fraction of the protein complement of the induced sample could thereby be purified and compared to a non-induced sample of the same community by differential gel electrophoresis to discriminate between constitutively expressed proteins and proteins upregulated in response to the inducing substance. RESULTS Using the applied approach, downstream analysis by mass spectrometry could be limited to only proteins recognized as upregulated in the cellulase-induced sample. Of 39 selected proteins, the majority were found to be linked to the need to degrade, take up, and metabolize cellulose. In addition, 28 (72%) of the proteins were non-cytosolic and 17 (44%) were annotated as carbohydrate-active enzymes. The results demonstrated both the applicability of the proposed approach for identifying extracellular proteins and guiding the selection of proteins toward those specifically upregulated and targeted by the enzyme inducing substance. Further, because identification of interesting proteins was based on the regulation of enzyme expression in response to a need to hydrolyze and utilize a specific substance, other unexpected enzyme activities were able to be identified. CONCLUSIONS The described approach created the conditions necessary to be able to select relevant extracellular enzymes that were extracted from the enzyme-induced microbial community. However, for the purpose of bioprospecting for enzymes to clone, produce, and characterize for practical applications, it was concluded that identification against public databases was not sufficient to identify the correct gene or protein sequence for cloning of the identified novel enzymes.
Collapse
Affiliation(s)
- Jutta Speda
- Molecular Biotechnology, Dept. of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
| | - Bengt-Harald Jonsson
- Molecular Biotechnology, Dept. of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
| | - Uno Carlsson
- Biochemistry, Dept. of Physics, Chemistry and Biology, Linköping University, 58183 Linköping, Sweden
| | - Martin Karlsson
- Molecular Biotechnology, Dept. of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
- InZymes Biotech AB, Gjuterigatan 1B, 582 73 Linköping, Sweden
| |
Collapse
|
11
|
Liang M, Zhou X, Xu C. Systems biology in biofuel. PHYSICAL SCIENCES REVIEWS 2016. [DOI: 10.1515/psr-2016-0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
12
|
Meyer MM. The role of mRNA structure in bacterial translational regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27301829 DOI: 10.1002/wrna.1370] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 01/08/2023]
Abstract
The characteristics of bacterial messenger RNAs (mRNAs) that influence translation efficiency provide many convenient handles for regulation of gene expression, especially when coupled with the processes of transcription termination and mRNA degradation. An mRNA's structure, especially near the site of initiation, has profound consequences for how readily it is translated. This property allows bacterial gene expression to be altered by changes to mRNA structure induced by temperature, or interactions with a wide variety of cellular components including small molecules, other RNAs (such as sRNAs and tRNAs), and RNA-binding proteins. This review discusses the links between mRNA structure and translation efficiency, and how mRNA structure is manipulated by conditions and signals within the cell to regulate gene expression. The range of RNA regulators discussed follows a continuum from very complex tertiary structures such as riboswitch aptamers and ribosomal protein-binding sites to thermosensors and mRNA:sRNA interactions that involve only base-pairing interactions. Furthermore, the high degrees of diversity observed for both mRNA structures and the mechanisms by which inhibition of translation occur have significant consequences for understanding the evolution of bacterial translational regulation. WIREs RNA 2017, 8:e1370. doi: 10.1002/wrna.1370 For further resources related to this article, please visit the WIREs website.
Collapse
|
13
|
Naveen V, Hsiao CD. NrdR Transcription Regulation: Global Proteome Analysis and Its Role in Escherichia coli Viability and Virulence. PLoS One 2016; 11:e0157165. [PMID: 27275780 PMCID: PMC4898720 DOI: 10.1371/journal.pone.0157165] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 05/25/2016] [Indexed: 12/16/2022] Open
Abstract
Bacterial ribonucleotide reductases (RNRs) play an important role in the synthesis of dNTPs and their expression is regulated by the transcription factors, NrdR and Fur. Recent transcriptomic studies using deletion mutants have indicated a role for NrdR in bacterial chemotaxis and in the maintenance of topoisomerase levels. However, NrdR deletion alone has no effect on bacterial growth or virulence in infected flies or in human blood cells. Furthermore, transcriptomic studies are limited to the deletion strain alone, and so are inadequate for drawing biological implications when the NrdR repressor is active or abundant. Therefore, further examination is warranted of changes in the cellular proteome in response to both NrdR overexpression, as well as deletion, to better understand its functional relevance as a bacterial transcription repressor. Here, we profile bacterial fate under conditions of overexpression and deletion of NrdR in E. coli. Biochemical assays show auxiliary zinc enhances the DNA binding activity of NrdR. We also demonstrate at the physiological level that increased nrdR expression causes a significant reduction in bacterial growth and fitness even at normal temperatures, and causes lethality at elevated temperatures. Corroborating these direct effects, global proteome analysis following NrdR overexpression showed a significant decrease in global protein expression. In parallel, studies on complementary expression of downregulated essential genes polA, eno and thiL showed partial rescue of the fitness defect caused by NrdR overexpression. Deletion of downregulated non-essential genes ygfK and trxA upon NrdR overexpression resulted in diminished bacterial growth and fitness suggesting an additional role for NrdR in regulating other genes. Moreover, in comparison with NrdR deletion, E. coli cells overexpressing NrdR showed significantly diminished adherence to human epithelial cells, reflecting decreased bacterial virulence. These results suggest that elevated expression of NrdR could be a suitable means to retard bacterial growth and virulence, as its elevated expression reduces bacterial fitness and impairs host cell adhesion.
Collapse
Affiliation(s)
- Vankadari Naveen
- Molecular Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Chwan-Deng Hsiao
- Molecular Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan
- * E-mail:
| |
Collapse
|
14
|
Laparra JM, Alfonso-García A, Alegría A, Barberá R, Cilla A. 7keto-stigmasterol and 7keto-cholesterol induce differential proteome changes to intestinal epitelial (Caco-2) cells. Food Chem Toxicol 2015; 84:29-36. [PMID: 26140950 DOI: 10.1016/j.fct.2015.06.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 06/22/2015] [Accepted: 06/25/2015] [Indexed: 12/11/2022]
Abstract
Recent studies have expanded the appreciation of the roles of oxysterols triggering inflammatory, immune cytotoxic and apoptotic processes, but have not been considered for proteome analysis. A comparative proteomic study in intestinal epithelial cell cultures incubated (60 μM/24 h) with 7keto-cholesterol or 7keto-stigmasterol was performed. The influence of both compounds was studied following the nLC-TripleTOF analysis. Findings were compared to results for control cultures. In the principal component analysis (PCA) of proteome patterns, two components were extracted accounting for 99.8% of the variance in the protein expression. PCA analysis clearly discriminated between the perturbations in the proteome of cell cultures incubated with 7keto-cholesterol and 7keto-stigmasterol. These proteins participate in mitochondrial function, lipid homeostasis, inflammation and immunity and cell proliferation. Remarkable differences between proteome patterns in cell cultures exposed to 7keto-cholesterol and 7keto-stigmasterol affect macrophage migration inhibitory factor, apolipoprotein E, Bcl-2-associated transcription factor and cellular retinoic acid-binding protein. Besides, exposure to 7keto-stigmasterol increased the concentration of ubiquitin-conjugating enzyme E2 and the mitochondrial superoxide dismutase protein. Such findings raise new questions about safety studies and the regulatory potential of oxysterols in the differentiation and function of intestinal and associated immune cells, their response to environmental stimuli and impairment of absorption processes.
Collapse
Affiliation(s)
- J M Laparra
- Institute of Food Engineering for Development, Politechnical University of Valencia, Avda. Cami de Vera s/n, 46022 Valencia, Spain.
| | - A Alfonso-García
- Nutrition and Food Chemistry, Faculty of Pharmacy, University of Valencia, Avda. Vicente Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain
| | - A Alegría
- Nutrition and Food Chemistry, Faculty of Pharmacy, University of Valencia, Avda. Vicente Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain
| | - R Barberá
- Nutrition and Food Chemistry, Faculty of Pharmacy, University of Valencia, Avda. Vicente Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain
| | - A Cilla
- Nutrition and Food Chemistry, Faculty of Pharmacy, University of Valencia, Avda. Vicente Andrés Estellés s/n, Burjassot, 46100 Valencia, Spain
| |
Collapse
|
15
|
Comparative Secretome Analysis of Trichoderma reesei and Aspergillus niger during Growth on Sugarcane Biomass. PLoS One 2015; 10:e0129275. [PMID: 26053961 PMCID: PMC4460134 DOI: 10.1371/journal.pone.0129275] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 05/06/2015] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Our dependence on fossil fuel sources and concern about the environment has generated a worldwide interest in establishing new sources of fuel and energy. Thus, the use of ethanol as a fuel is advantageous because it is an inexhaustible energy source and has minimal environmental impact. Currently, Brazil is the world's second largest producer of ethanol, which is produced from sugarcane juice fermentation. However, several studies suggest that Brazil could double its production per hectare by using sugarcane bagasse and straw, known as second-generation (2G) bioethanol. Nevertheless, the use of this biomass presents a challenge because the plant cell wall structure, which is composed of complex sugars (cellulose and hemicelluloses), must be broken down into fermentable sugar, such as glucose and xylose. To achieve this goal, several types of hydrolytic enzymes are necessary, and these enzymes represent the majority of the cost associated with 2G bioethanol processing. Reducing the cost of the saccharification process can be achieved via a comprehensive understanding of the hydrolytic mechanisms and enzyme secretion of polysaccharide-hydrolyzing microorganisms. In many natural habitats, several microorganisms degrade lignocellulosic biomass through a set of enzymes that act synergistically. In this study, two fungal species, Aspergillus niger and Trichoderma reesei, were grown on sugarcane biomass with two levels of cell wall complexity, culm in natura and pretreated bagasse. The production of enzymes related to biomass degradation was monitored using secretome analyses after 6, 12 and 24 hours. Concurrently, we analyzed the sugars in the supernatant. RESULTS Analyzing the concentration of monosaccharides in the supernatant, we observed that both species are able to disassemble the polysaccharides of sugarcane cell walls since 6 hours post-inoculation. The sugars from the polysaccharides such as arabinoxylan and β-glucan (that compose the most external part of the cell wall in sugarcane) are likely the first to be released and assimilated by both species of fungi. At all time points tested, A. niger produced more enzymes (quantitatively and qualitatively) than T. reesei. However, the most important enzymes related to biomass degradation, including cellobiohydrolases, endoglucanases, β-glucosidases, β-xylosidases, endoxylanases, xyloglucanases, and α-arabinofuranosidases, were identified in both secretomes. We also noticed that the both fungi produce more enzymes when grown in culm as a single carbon source. CONCLUSION Our work provides a detailed qualitative and semi-quantitative secretome analysis of A. niger and T. reesei grown on sugarcane biomass. Our data indicate that a combination of enzymes from both fungi is an interesting option to increase saccharification efficiency. In other words, these two fungal species might be combined for their usage in industrial processes.
Collapse
|
16
|
Duval M, Simonetti A, Caldelari I, Marzi S. Multiple ways to regulate translation initiation in bacteria: Mechanisms, regulatory circuits, dynamics. Biochimie 2015; 114:18-29. [PMID: 25792421 DOI: 10.1016/j.biochi.2015.03.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/08/2015] [Indexed: 11/15/2022]
Abstract
To adapt their metabolism rapidly and constantly in response to environmental variations, bacteria often target the translation initiation process, during which the ribosome assembles on the mRNA. Here, we review different mechanisms of regulation mediated by cis-acting elements, sRNAs and proteins, showing, when possible, their intimate connection with the translational apparatus. Indeed the ribosome itself could play a direct role in several regulatory mechanisms. Different features of the regulatory signals (sequences, structures and their positions on the mRNA) are contributing to the large variety of regulatory mechanisms. Ribosome heterogeneity, variation of individual cells responses and the spatial and temporal organization of the translation process add more layers of complexity. This hampers to define manageable set of rules for bacterial translation initiation control.
Collapse
Affiliation(s)
- Mélodie Duval
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| | - Angelita Simonetti
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| | - Isabelle Caldelari
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| | - Stefano Marzi
- Architecture et Réactivité de l'ARN, Université de Strasbourg, IBMC-CNRS, F-67084 Strasbourg, France
| |
Collapse
|
17
|
Venkataramanan KP, Min L, Hou S, Jones SW, Ralston MT, Lee KH, Papoutsakis ET. Complex and extensive post-transcriptional regulation revealed by integrative proteomic and transcriptomic analysis of metabolite stress response in Clostridium acetobutylicum. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:81. [PMID: 26269711 PMCID: PMC4533764 DOI: 10.1186/s13068-015-0260-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 04/30/2015] [Indexed: 05/16/2023]
Abstract
BACKGROUND Clostridium acetobutylicum is a model organism for both clostridial biology and solvent production. The organism is exposed to its own toxic metabolites butyrate and butanol, which trigger an adaptive stress response. Integrative analysis of proteomic and RNAseq data may provide novel insights into post-transcriptional regulation. RESULTS The identified iTRAQ-based quantitative stress proteome is made up of 616 proteins with a 15 % genome coverage. The differentially expressed proteome correlated poorly with the corresponding differential RNAseq transcriptome. Up to 31 % of the differentially expressed proteins under stress displayed patterns opposite to those of the transcriptome, thus suggesting significant post-transcriptional regulation. The differential proteome of the translation machinery suggests that cells employ a different subset of ribosomal proteins under stress. Several highly upregulated proteins but with low mRNA levels possessed mRNAs with long 5'UTRs and strong RBS scores, thus supporting the argument that regulatory elements on the long 5'UTRs control their translation. For example, the oxidative stress response rubrerythrin was upregulated only at the protein level up to 40-fold without significant mRNA changes. We also identified many leaderless transcripts, several displaying different transcriptional start sites, thus suggesting mRNA-trimming mechanisms under stress. Downregulation of Rho and partner proteins pointed to changes in transcriptional elongation and termination under stress. CONCLUSIONS The integrative proteomic-transcriptomic analysis demonstrated complex expression patterns of a large fraction of the proteome. Such patterns could not have been detected with one or the other omic analyses. Our analysis proposes the involvement of specific molecular mechanisms of post-transcriptional regulation to explain the observed complex stress response.
Collapse
Affiliation(s)
- Keerthi P. Venkataramanan
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA
| | - Lie Min
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA
| | - Shuyu Hou
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA
| | - Shawn W. Jones
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA
| | - Matthew T. Ralston
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />15 Innovation Way, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711 USA
| | - Kelvin H. Lee
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA
| | - E. Terry Papoutsakis
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA
| |
Collapse
|
18
|
Nuñez PA, Romero H, Farber MD, Rocha EPC. Natural selection for operons depends on genome size. Genome Biol Evol 2014; 5:2242-54. [PMID: 24201372 PMCID: PMC3845653 DOI: 10.1093/gbe/evt174] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In prokaryotes, genome size is associated with metabolic versatility, regulatory complexity, effective population size, and horizontal transfer rates. We therefore analyzed the covariation of genome size and operon conservation to assess the evolutionary models of operon formation and maintenance. In agreement with previous results, intraoperonic pairs of essential and of highly expressed genes are more conserved. Interestingly, intraoperonic pairs of genes are also more conserved when they encode proteins at similar cell concentrations, suggesting a role of cotranscription in diminishing the cost of waste and shortfall in gene expression. Larger genomes have fewer and smaller operons that are also less conserved. Importantly, lower conservation in larger genomes was observed for all classes of operons in terms of gene expression, essentiality, and balanced protein concentration. We reached very similar conclusions in independent analyses of three major bacterial clades (α- and β-Proteobacteria and Firmicutes). Operon conservation is inversely correlated to the abundance of transcription factors in the genome when controlled for genome size. This suggests a negative association between the complexity of genetic networks and operon conservation. These results show that genome size and/or its proxies are key determinants of the intensity of natural selection for operon organization. Our data fit better the evolutionary models based on the advantage of coregulation than those based on genetic linkage or stochastic gene expression. We suggest that larger genomes with highly complex genetic networks and many transcription factors endure weaker selection for operons than smaller genomes with fewer alternative tools for genetic regulation.
Collapse
Affiliation(s)
- Pablo A Nuñez
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (CICVyA-INTA), Buenos Aires, Argentina
| | | | | | | |
Collapse
|
19
|
Pelchovich G, Nadejda S, Dana A, Tuller T, Bravo IG, Gophna U. Ribosomal mutations affecting the translation of genes that use non-optimal codons. FEBS J 2014; 281:3701-18. [PMID: 24966114 DOI: 10.1111/febs.12892] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 06/10/2014] [Accepted: 06/23/2014] [Indexed: 01/26/2023]
Abstract
Genes that are laterally acquired by a new host species often contain codons that are non-optimal to the tRNA repertoire of the new host, which may lead to insufficient translational levels. Inefficient translation can be overcome by different mechanisms, such as incremental amelioration of the coding sequence, compensatory mutations in the regulatory sequences leading to increased transcription or increase in gene copy number. However, there is also a possibility that ribosomal mutations can improve the expression of such genes. To test this hypothesis, we examined the effects of point mutations in the endogenous ribosomal proteins S12 and S5 in Escherichia coli, which are known to be involved in the decoding of the mRNA, on the efficiency of translation of exogenous genes that use non-optimal codons, in vivo. We show that an S12 mutant in E. coli is able to express exogenous genes, with non-optimal codons, to higher levels than the wild-type, and explore the mechanisms underlying this phenomenon in this mutant. Our results suggest that the transient emergence of mutants that allow efficient expression of exogenous genes with non-optimal codons could also increase the chances of fixation of laterally transferred genes.
Collapse
Affiliation(s)
- Gidi Pelchovich
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | | | | | | | | | | |
Collapse
|
20
|
Huang S, Chen L, Te R, Qiao J, Wang J, Zhang W. Complementary iTRAQ proteomics and RNA-seq transcriptomics reveal multiple levels of regulation in response to nitrogen starvation in Synechocystis sp. PCC 6803. MOLECULAR BIOSYSTEMS 2014; 9:2565-74. [PMID: 23942477 DOI: 10.1039/c3mb70188c] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sequential adaptation to environmental stress needs complex regulation at different cellular levels in cyanobacteria. To uncover the regulatory mechanism in response to nitrogen starvation, we investigated the genome-wide correlation between protein abundance and gene expression in a model cyanobacterium Synechocystis sp. PCC 6803 using complementary quantitative iTRAQ proteomics and RNA-seq transcriptomics. Consistent with the cell growth inhibition, proteomic analysis indicated phase-dependent down-regulation of proteins related to nitrogen metabolism, ribosome complexes, glycolysis pathway and tricarboxylic acid (TCA) cycles by nitrogen starvation. Transcriptomic analysis also showed that genes related to "Photosynthesis", "Protein synthesis" and "Energy metabolism" were significantly down-regulated by nitrogen starvation. Interestingly, the concordance between protein abundances and their corresponding mRNAs exhibited a functional categories-dependent pattern, with some categories, such as "Protein synthesis" and "Energy metabolism", having a relatively high correlation, while others even with numerous discordant changes in protein-mRNA pairs, indicated divergent regulation of transcriptional and post-transcriptional processes. In particular, an increased abundance of proteins related to "Photosynthesis" upon nitrogen starvation was found to be reversely correlated with the down-regulation of their corresponding mRNAs. In addition, two metabolic modules highly correlated with nitrogen starvation were identified by a co-expression network analysis, and were found to contain mostly photosynthetic proteins and hypothetical proteins, respectively. We further confirmed the involvement of the photosynthetic genes in nitrogen starvation tolerance by constructing and analyzing the psbV gene deletion mutant.
Collapse
Affiliation(s)
- Siqiang Huang
- School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, P.R. China.
| | | | | | | | | | | |
Collapse
|
21
|
Tomescu OA, Mattanovich D, Thallinger GG. Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data. BMC SYSTEMS BIOLOGY 2014; 8 Suppl 2:S4. [PMID: 25033389 PMCID: PMC4101701 DOI: 10.1186/1752-0509-8-s2-s4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Background Technological improvements have shifted the focus from data generation to data analysis. The availability of large amounts of data from transcriptomics, protemics and metabolomics experiments raise new questions concerning suitable integrative analysis methods. We compare three integrative analysis techniques (co-inertia analysis, generalized singular value decomposition and integrative biclustering) by applying them to gene and protein abundance data from the six life cycle stages of Plasmodium falciparum. Co-inertia analysis is an analysis method used to visualize and explore gene and protein data. The generalized singular value decomposition has shown its potential in the analysis of two transcriptome data sets. Integrative Biclustering applies biclustering to gene and protein data. Results Using CIA, we visualize the six life cycle stages of Plasmodium falciparum, as well as GO terms in a 2D plane and interpret the spatial configuration. With GSVD, we decompose the transcriptomic and proteomic data sets into matrices with biologically meaningful interpretations and explore the processes captured by the data sets. IBC identifies groups of genes, proteins, GO Terms and life cycle stages of Plasmodium falciparum. We show method-specific results as well as a network view of the life cycle stages based on the results common to all three methods. Additionally, by combining the results of the three methods, we create a three-fold validated network of life cycle stage specific GO terms: Sporozoites are associated with transcription and transport; merozoites with entry into host cell as well as biosynthetic and metabolic processes; rings with oxidation-reduction processes; trophozoites with glycolysis and energy production; schizonts with antigenic variation and immune response; gametocyctes with DNA packaging and mitochondrial transport. Furthermore, the network connectivity underlines the separation of the intraerythrocytic cycle from the gametocyte and sporozoite stages. Conclusion Using integrative analysis techniques, we can integrate knowledge from different levels and obtain a wider view of the system under study. The overlap between method-specific and common results is considerable, even if the basic mathematical assumptions are very different. The three-fold validated network of life cycle stage characteristics of Plasmodium falciparum could identify a large amount of the known associations from literature in only one study.
Collapse
|
22
|
Agrawal GK, Sarkar A, Righetti PG, Pedreschi R, Carpentier S, Wang T, Barkla BJ, Kohli A, Ndimba BK, Bykova NV, Rampitsch C, Zolla L, Rafudeen MS, Cramer R, Bindschedler LV, Tsakirpaloglou N, Ndimba RJ, Farrant JM, Renaut J, Job D, Kikuchi S, Rakwal R. A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues. MASS SPECTROMETRY REVIEWS 2013; 32:335-65. [PMID: 23315723 DOI: 10.1002/mas.21365] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 09/10/2012] [Accepted: 09/10/2012] [Indexed: 05/21/2023]
Abstract
Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.
Collapse
Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry, PO Box 13265, Kathmandu, Nepal.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Breaking on through to the other side: protein export through the bacterial Sec system. Biochem J 2013; 449:25-37. [PMID: 23216251 DOI: 10.1042/bj20121227] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
More than one-third of cellular proteomes traffic into and across membranes. Bacteria have invented several sophisticated secretion systems that guide various proteins to extracytoplasmic locations and in some cases inject them directly into hosts. Of these, the Sec system is ubiquitous, essential and by far the best understood. Secretory polypeptides are sorted from cytoplasmic ones initially due to characteristic signal peptides. Then they are targeted to the plasma membrane by chaperones/pilots. The translocase, a dynamic nanomachine, lies at the centre of this process and acts as a protein-conducting channel with a unique property; allowing both forward transfer of secretory proteins but also lateral release into the lipid bilayer with high fidelity and efficiency. This process, tightly orchestrated at the expense of energy, ensures fundamental cell processes such as membrane biogenesis, cell division, motility, nutrient uptake and environmental sensing. In the present review, we examine this fascinating process, summarizing current knowledge on the structure, function and mechanics of the Sec pathway.
Collapse
|
24
|
Sharma R, Dill BD, Chourey K, Shah M, VerBerkmoes NC, Hettich RL. Coupling a detergent lysis/cleanup methodology with intact protein fractionation for enhanced proteome characterization. J Proteome Res 2012; 11:6008-18. [PMID: 23126408 DOI: 10.1021/pr300709k] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The expanding use of surfactants for proteome sample preparations has prompted the need to systematically optimize the application and removal of these MS-deleterious agents prior to proteome measurements. Here we compare four detergent cleanup methods (trichloroacetic acid (TCA) precipitation, chloroform/methanol/water (CMW) extraction, a commercial detergent removal spin column method (DRS) and filter-aided sample preparation (FASP)) to provide efficiency benchmarks with respect to protein, peptide, and spectral identifications in each case. Our results show that for protein-limited samples, FASP outperforms the other three cleanup methods, while at high protein amounts, all the methods are comparable. This information was used to investigate and contrast molecular weight-based fractionated with unfractionated lysates from three increasingly complex samples ( Escherichia coli K-12, a five microbial isolate mixture, and a natural microbial community groundwater sample), all of which were prepared with an SDS-FASP approach. The additional fractionation step enhanced the number of protein identifications by 8% to 25% over the unfractionated approach across the three samples.
Collapse
Affiliation(s)
- Ritin Sharma
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville-Tennessee 37996, United States
| | | | | | | | | | | |
Collapse
|
25
|
Recombinant E. coli expressing Vitreoscilla haemoglobin prefers aerobic metabolism under microaerobic conditions: A proteome-level study. J Biosci 2012; 37:617-33. [DOI: 10.1007/s12038-012-9245-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
26
|
Characterizing the Escherichia coli O157:H7 proteome including protein associations with higher order assemblies. PLoS One 2011; 6:e26554. [PMID: 22087229 PMCID: PMC3210124 DOI: 10.1371/journal.pone.0026554] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 09/28/2011] [Indexed: 11/19/2022] Open
Abstract
Background The recent outbreak of severe infections with Shiga toxin (Stx) producing Escherichia coli (STEC) serotype O104:H4 highlights the need to understand horizontal gene transfer among E. coli strains, identify novel virulence factors and elucidate their pathogenesis. Quantitative shotgun proteomics can contribute to such objectives, allowing insights into the part of the genome translated into proteins and the connectivity of biochemical pathways and higher order assemblies of proteins at the subcellular level. Methodology/Principal Findings We examined protein profiles in cell lysate fractions of STEC strain 86-24 (serotype O157:H7), following growth in cell culture or bacterial isolation from intestines of infected piglets, in the context of functionally and structurally characterized biochemical pathways of E. coli. Protein solubilization in the presence of Triton X-100, EDTA and high salt was followed by size exclusion chromatography into the approximate Mr ranges greater than 280 kDa, 280-80 kDa and 80-10 kDa. Peptide mixtures resulting from these and the insoluble fraction were analyzed by quantitative 2D-LC-nESI-MS/MS. Of the 2521 proteins identified at a 1% false discovery rate, representing 47% of all predicted E. coli O157:H7 gene products, the majority of integral membrane proteins were enriched in the high Mr fraction. Hundreds of proteins were enriched in a Mr range higher than that predicted for a monomer supporting their participation in protein complexes. The insoluble STEC fraction revealed enrichment of aggregation-prone proteins, including many that are part of large structure/function entities such as the ribosome, cytoskeleton and O-antigen biosynthesis cluster. Significance Nearly all E. coli O157:H7 proteins encoded by prophage regions were expressed at low abundance levels or not detected. Comparative quantitative analyses of proteins from distinct cell lysate fractions allowed us to associate uncharacterized proteins with membrane attachment, potential participation in stable protein complexes, and susceptibility to aggregation as part of larger structural assemblies.
Collapse
|
27
|
Ahn JH, Keum JW, Kim DM. Expression screening of fusion partners from an E. coli genome for soluble expression of recombinant proteins in a cell-free protein synthesis system. PLoS One 2011; 6:e26875. [PMID: 22073212 PMCID: PMC3206877 DOI: 10.1371/journal.pone.0026875] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Accepted: 10/05/2011] [Indexed: 12/04/2022] Open
Abstract
While access to soluble recombinant proteins is essential for a number of proteome studies, preparation of purified functional proteins is often limited by the protein solubility. In this study, potent solubility-enhancing fusion partners were screened from the repertoire of endogenous E. coli proteins. Based on the presumed correlation between the intracellular abundance and folding efficiency of proteins, PCR-amplified ORFs of a series of highly abundant E. coli proteins were fused with aggregation-prone heterologous proteins and then directly expressed for quantitative estimation of the expression efficiency of soluble translation products. Through two-step screening procedures involving the expression of 552 fusion constructs targeted against a series of cytokine proteins, we were able to discover a number of endogenous E. coli proteins that dramatically enhanced the soluble expression of the target proteins. This strategy of cell-free expression screening can be extended to quantitative, global analysis of genomic resources for various purposes.
Collapse
Affiliation(s)
- Jin-Ho Ahn
- Department of Fine Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Jung-Won Keum
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
| | - Dong-Myung Kim
- Department of Fine Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, Republic of Korea
- * E-mail:
| |
Collapse
|
28
|
Stefanopoulou M, Kokoschka M, Sheldrick WS, Wolters DA. Cell response of Escherichia coli
to cisplatin-induced stress. Proteomics 2011; 11:4174-88. [DOI: 10.1002/pmic.201100203] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 07/19/2011] [Accepted: 08/04/2011] [Indexed: 11/08/2022]
|
29
|
Liang L, Tan X, Juarez S, Villaverde H, Pablo J, Nakajima-Sasaki R, Gotuzzo E, Saito M, Hermanson G, Molina D, Felgner S, Morrow WJW, Liang X, Gilman RH, Davies DH, Tsolis RM, Vinetz JM, Felgner PL. Systems biology approach predicts antibody signature associated with Brucella melitensis infection in humans. J Proteome Res 2011; 10:4813-24. [PMID: 21863892 PMCID: PMC3189706 DOI: 10.1021/pr200619r] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A complete understanding of the factors that determine selection of antigens recognized by the humoral immune response following infectious agent challenge is lacking. Here we illustrate a systems biology approach to identify the antibody signature associated with Brucella melitensis (Bm) infection in humans and predict proteomic features of serodiagnostic antigens. By taking advantage of a full proteome microarray expressing previously cloned 1406 and newly cloned 1640 Bm genes, we were able to identify 122 immunodominant antigens and 33 serodiagnostic antigens. The reactive antigens were then classified according to annotated functional features (COGs), computationally predicted features (e.g., subcellular localization, physical properties), and protein expression estimated by mass spectrometry (MS). Enrichment analyses indicated that membrane association and secretion were significant enriching features of the reactive antigens, as were proteins predicted to have a signal peptide, a single transmembrane domain, and outer membrane or periplasmic location. These features accounted for 67% of the serodiagnostic antigens. An overlay of the seroreactive antigen set with proteomic data sets generated by MS identified an additional 24%, suggesting that protein expression in bacteria is an additional determinant in the induction of Brucella-specific antibodies. This analysis indicates that one-third of the proteome contains enriching features that account for 91% of the antigens recognized, and after B. melitensis infection the immune system develops significant antibody titers against 10% of the proteins with these enriching features. This systems biology approach provides an empirical basis for understanding the breadth and specificity of the immune response to B. melitensis and a new framework for comparing the humoral responses against other microorganisms.
Collapse
Affiliation(s)
- Li Liang
- Department of Medicine, Division of Infectious Diseases, University of California, Irvine, California 92697, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Fischer A, Yang SJ, Bayer AS, Vaezzadeh AR, Herzig S, Stenz L, Girard M, Sakoulas G, Scherl A, Yeaman MR, Proctor RA, Schrenzel J, François P. Daptomycin resistance mechanisms in clinically derived Staphylococcus aureus strains assessed by a combined transcriptomics and proteomics approach. J Antimicrob Chemother 2011; 66:1696-711. [PMID: 21622973 DOI: 10.1093/jac/dkr195] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVES The development of daptomycin resistance in Staphylococcus aureus is associated with clinical treatment failures. The mechanism(s) of such resistance have not been clearly defined. METHODS We studied an isogenic daptomycin-susceptible (DAP(S)) and daptomycin-resistant (DAP(R)) S. aureus strain pair (616; 701) from a patient with relapsing endocarditis during daptomycin treatment, using comparative transcriptomic and proteomic techniques. RESULTS Minor differences in the genome content were found between strains by DNA hybridization. Transcriptomic analyses identified a number of genes differentially expressed in important functional categories: cell division; metabolism of bacterial envelopes; and global regulation. Of note, the DAP(R) isolate exhibited reduced expression of the major cell wall autolysis gene coincident with the up-regulation of genes involved in cell wall teichoic acid production. Using quantitative (q)RT-PCR on the gene cadre putatively involved in cationic peptide resistance, we formulated a putative regulatory network compatible with microarray data sets, mainly implicating bacterial envelopes. Of interest, qRT-PCR of this same gene cadre from two distinct isogenic DAP(S)/DAP(R) clinical strain pairs revealed evidence of other strain-dependent networks operative in the DAP(R) phenotype. Comparative proteomics of 616 versus 701 revealed a differential abundance of proteins in various functional categories, including cell wall-associated targets and biofilm formation proteins. Phenotypically, strains 616 and 701 showed major differences in their ability to develop bacterial biofilms in the presence of the antibacterial lipid, oleic acid. CONCLUSIONS Compatible with previous in vitro observations, in vivo-acquired DAP(R) in S. aureus is a complex, multistep phenomenon involving: (i) strain-dependent phenotypes; (ii) transcriptome adaptation; and (iii) modification of the lipid and protein contents of cellular envelopes.
Collapse
Affiliation(s)
- Adrien Fischer
- Genomic Research Laboratory, University Hospitals of Geneva and University of Geneva, Geneva, Switzerland.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Simões T, Charro N, Blonder J, Faria D, Couto FM, Chan KC, Waybright T, Isaaq HJ, Veenstra TD, Penque D. Molecular profiling of the human nasal epithelium: A proteomics approach. J Proteomics 2011; 75:56-69. [PMID: 21621024 PMCID: PMC7185466 DOI: 10.1016/j.jprot.2011.05.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 05/05/2011] [Indexed: 12/25/2022]
Abstract
A comprehensive proteomic profiling of nasal epithelium (NE) is described. This study relies on simple subcellular fractionation used to obtain soluble- and membrane-enriched fractions followed by 2-dimensional liquid chromatography (2D-LC) separation and tandem mass spectrometry (MS/MS). The cells were collected using a brushing technique applied on NE of clinically evaluated volunteers. Subsequently, the soluble- and the membrane-protein enriched fractions were prepared and analyzed in parallel using 2D-LC-MS/MS. In a set of 1482 identified proteins, 947 (63.9%) proteins were found to be associated to membrane fraction. Grand average hydropathy value index (GRAVY) analysis, the transmembrane protein mapping and annotations of primary location deposited in the Human Protein Reference Database (HPRD) confirmed an enrichment of hydrophobic proteins on this dataset. Ingenuity Pathway Analysis (IPA) of soluble fraction revealed an enrichment of molecular and cellular functions associated with cell death, protein folding and drug metabolism while in membrane fraction showed an enrichment of functions associated with molecular transport, protein trafficking and cell-to-cell signaling and interaction. The IPA showed similar enrichment of functions associated with cellular growth and proliferation in both soluble and membrane subproteomes. This finding was in agreement with protein content analysis using exponentially modified protein abundance index (emPAI). A comparison of our data with previously published studies focusing on respiratory tract epithelium revealed similarities related to identification of proteins associated with physical barrier function and immunological defence. In summary, we extended the NE molecular profile by identifying and characterizing proteins associated to pivotal functions of a respiratory epithelium, including the control of fluid volume and ionic composition at the airways' surface, physical barrier maintenance, detoxification and immunological defence. The extent of similarities supports the applicability of a less invasive analysis of NE to assess prognosis and treatment response of lung diseases such as asthma, cystic fibrosis and chronic obstructive pulmonary disease.
Collapse
Affiliation(s)
- Tânia Simões
- Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr. Ricardo Jorge, INSA I.P., Portugal
| | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Tuller T, Girshovich Y, Sella Y, Kreimer A, Freilich S, Kupiec M, Gophna U, Ruppin E. Association between translation efficiency and horizontal gene transfer within microbial communities. Nucleic Acids Res 2011; 39:4743-55. [PMID: 21343180 PMCID: PMC3113575 DOI: 10.1093/nar/gkr054] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Horizontal gene transfer (HGT) is a major force in microbial evolution. Previous studies have suggested that a variety of factors, including restricted recombination and toxicity of foreign gene products, may act as barriers to the successful integration of horizontally transferred genes. This study identifies an additional central barrier to HGT-the lack of co-adaptation between the codon usage of the transferred gene and the tRNA pool of the recipient organism. Analyzing the genomic sequences of more than 190 microorganisms and the HGT events that have occurred between them, we show that the number of genes that were horizontally transferred between organisms is positively correlated with the similarity between their tRNA pools. Those genes that are better adapted to the tRNA pools of the target genomes tend to undergo more frequent HGT. At the community (or environment) level, organisms that share a common ecological niche tend to have similar tRNA pools. These results remain significant after controlling for diverse ecological and evolutionary parameters. Our analysis demonstrates that there are bi-directional associations between the similarity in the tRNA pools of organisms and the number of HGT events occurring between them. Similar tRNA pools between a donor and a host tend to increase the probability that a horizontally acquired gene will become fixed in its new genome. Our results also suggest that frequent HGT may be a homogenizing force that increases the similarity in the tRNA pools of organisms within the same community.
Collapse
Affiliation(s)
- Tamir Tuller
- Faculty of Mathematics and Computer Science, Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Blavatnik School of Computer Science, School of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | | | | | | | | | | | | | | |
Collapse
|
33
|
Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME JOURNAL 2010; 5:999-1013. [PMID: 21151004 DOI: 10.1038/ismej.2010.189] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As part of an ongoing survey of microbial community gene expression in the ocean, we sequenced and compared ∼38 Mbp of community transcriptomes and ∼157 Mbp of community genomes from four bacterioplankton samples, along a defined depth profile at Station ALOHA in North Pacific subtropical gyre (NPSG). Taxonomic analysis suggested that the samples were dominated by three taxa: Prochlorales, Consistiales and Cenarchaeales, which comprised 36-69% and 29-63% of the annotated sequences in the four DNA and four cDNA libraries, respectively. The relative abundance of these taxonomic groups was sometimes very different in the DNA and cDNA libraries, suggesting differential relative transcriptional activities per cell. For example, the 125 m sample genomic library was dominated by Pelagibacter (∼36% of sequence reads), which contributed fewer sequences to the community transcriptome (∼11%). Functional characterization of highly expressed genes suggested taxon-specific contributions to specific biogeochemical processes. Examples included Roseobacter relatives involved in aerobic anoxygenic phototrophy at 75 m, and an unexpected contribution of low abundance Crenarchaea to ammonia oxidation at 125 m. Read recruitment using reference microbial genomes indicated depth-specific partitioning of coexisting microbial populations, highlighted by a transcriptionally active high-light-like Prochlorococcus population in the bottom of the photic zone. Additionally, nutrient-uptake genes dominated Pelagibacter transcripts, with apparent enrichment for certain transporter types (for example, the C4-dicarboxylate transport system) over others (for example, phosphate transporters). In total, the data support the utility of coupled DNA and cDNA analyses for describing taxonomic and functional attributes of microbial communities in their natural habitats.
Collapse
|
34
|
Wegener KM, Singh AK, Jacobs JM, Elvitigala T, Welsh EA, Keren N, Gritsenko MA, Ghosh BK, Camp DG, Smith RD, Pakrasi HB. Global proteomics reveal an atypical strategy for carbon/nitrogen assimilation by a cyanobacterium under diverse environmental perturbations. Mol Cell Proteomics 2010; 9:2678-89. [PMID: 20858728 DOI: 10.1074/mcp.m110.000109] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Cyanobacteria, the only prokaryotes capable of oxygenic photosynthesis, are present in diverse ecological niches and play crucial roles in global carbon and nitrogen cycles. To proliferate in nature, cyanobacteria utilize a host of stress responses to accommodate periodic changes in environmental conditions. A detailed knowledge of the composition of, as well as the dynamic changes in, the proteome is necessary to gain fundamental insights into such stress responses. Toward this goal, we have performed a large-scale proteomic analysis of the widely studied model cyanobacterium Synechocystis sp. PCC 6803 under 33 different environmental conditions. The resulting high-quality dataset consists of 22,318 unique peptides corresponding to 1955 proteins, a coverage of 53% of the predicted proteome. Quantitative determination of protein abundances has led to the identification of 1198 differentially regulated proteins. Notably, our analysis revealed that a common stress response under various environmental perturbations, irrespective of amplitude and duration, is the activation of atypical pathways for the acquisition of carbon and nitrogen from urea and arginine. In particular, arginine is catabolized via putrescine to produce succinate and glutamate, sources of carbon and nitrogen, respectively. This study provides the most comprehensive functional and quantitative analysis of the Synechocystis proteome to date, and shows that a significant stress response of cyanobacteria involves an uncommon mode of acquisition of carbon and nitrogen.
Collapse
|
35
|
Battchikova N, Vainonen JP, Vorontsova N, Keranen M, Carmel D, Aro EM. Dynamic changes in the proteome of Synechocystis 6803 in response to CO(2) limitation revealed by quantitative proteomics. J Proteome Res 2010; 9:5896-912. [PMID: 20795750 DOI: 10.1021/pr100651w] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyanobacteria developed efficient carbon concentrating mechanisms which significantly improve the photosynthetic performance and survival of cells under limiting CO(2) conditions. Dynamic changes of the Synechocystis proteome to CO(2) limitation were investigated using shotgun LC-MS/MS approach with isobaric tag for relative and absolute quantification (iTRAQ) technique. Synechocystis cells grown at high (3%) CO(2) were shifted to air-level CO(2) followed by protein extraction after 6, 24, and 72 h. About 19% of the cyanobacterial proteome was identified and the expression changes were quantified for 17% of theoretical ORFs. For 76 proteins, up- or down-regulation was found to be significant (more than 1.5 or less than 0.7). Major changes were observed in proteins participating in inorganic carbon uptake, CO(2) fixation, nitrogen transport and assimilation, as well as in the protection of the photosynthetic machinery from excess of light. Further, a number of hypothetical proteins with unknown functions were discovered. In general, the cells appear to acclimate to low CO(2) without a significant stress since the stress-related molecular chaperones were down-regulated and only a minor decline was detected for proteins of phycobilisomes, photosynthetic complexes, and translation machinery. The results of iTRAQ experiment were validated by the Western blot analysis for selected proteins.
Collapse
Affiliation(s)
- Natalia Battchikova
- Department of Biochemistry and Food Chemistry, Molecular Plant Biology, University of Turku, Finland.
| | | | | | | | | | | |
Collapse
|
36
|
Sanchez A, Perez-Riverol Y, González LJ, Noda J, Betancourt L, Ramos Y, Gil J, Vera R, Padrón G, Besada V. Evaluation of Phenylthiocarbamoyl-Derivatized Peptides by Electrospray Ionization Mass Spectrometry: Selective Isolation and Analysis of Modified Multiply Charged Peptides for Liquid Chromatography−Tandem Mass Spectrometry Experiments. Anal Chem 2010; 82:8492-501. [DOI: 10.1021/ac1012738] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aniel Sanchez
- Proteomics Department and Bioinformatic Department, Physical-Chemistry Division, Biomedical Research, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Havana, Cuba
| | - Yasset Perez-Riverol
- Proteomics Department and Bioinformatic Department, Physical-Chemistry Division, Biomedical Research, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Havana, Cuba
| | - Luis Javier González
- Proteomics Department and Bioinformatic Department, Physical-Chemistry Division, Biomedical Research, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Havana, Cuba
| | - Jesus Noda
- Proteomics Department and Bioinformatic Department, Physical-Chemistry Division, Biomedical Research, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Havana, Cuba
| | - Lazaro Betancourt
- Proteomics Department and Bioinformatic Department, Physical-Chemistry Division, Biomedical Research, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Havana, Cuba
| | - Yassel Ramos
- Proteomics Department and Bioinformatic Department, Physical-Chemistry Division, Biomedical Research, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Havana, Cuba
| | - Jeovanis Gil
- Proteomics Department and Bioinformatic Department, Physical-Chemistry Division, Biomedical Research, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Havana, Cuba
| | - Roberto Vera
- Proteomics Department and Bioinformatic Department, Physical-Chemistry Division, Biomedical Research, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Havana, Cuba
| | - Gabriel Padrón
- Proteomics Department and Bioinformatic Department, Physical-Chemistry Division, Biomedical Research, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Havana, Cuba
| | - Vladimir Besada
- Proteomics Department and Bioinformatic Department, Physical-Chemistry Division, Biomedical Research, Center for Genetic Engineering and Biotechnology, P.O. Box 6162, Havana, Cuba
| |
Collapse
|
37
|
Müller SA, Kohajda T, Findeiss S, Stadler PF, Washietl S, Kellis M, von Bergen M, Kalkhof S. Optimization of parameters for coverage of low molecular weight proteins. Anal Bioanal Chem 2010; 398:2867-81. [PMID: 20803007 PMCID: PMC2990009 DOI: 10.1007/s00216-010-4093-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 07/26/2010] [Accepted: 08/03/2010] [Indexed: 11/16/2022]
Abstract
Proteins with molecular weights of <25 kDa are involved in major biological processes such as ribosome formation, stress adaption (e.g., temperature reduction) and cell cycle control. Despite their importance, the coverage of smaller proteins in standard proteome studies is rather sparse. Here we investigated biochemical and mass spectrometric parameters that influence coverage and validity of identification. The underrepresentation of low molecular weight (LMW) proteins may be attributed to the low numbers of proteolytic peptides formed by tryptic digestion as well as their tendency to be lost in protein separation and concentration/desalting procedures. In a systematic investigation of the LMW proteome of Escherichia coli, a total of 455 LMW proteins (27% of the 1672 listed in the SwissProt protein database) were identified, corresponding to a coverage of 62% of the known cytosolic LMW proteins. Of these proteins, 93 had not yet been functionally classified, and five had not previously been confirmed at the protein level. In this study, the influences of protein extraction (either urea or TFA), proteolytic digestion (solely, and the combined usage of trypsin and AspN as endoproteases) and protein separation (gel- or non-gel-based) were investigated. Compared to the standard procedure based solely on the use of urea lysis buffer, in-gel separation and tryptic digestion, the complementary use of TFA for extraction or endoprotease AspN for proteolysis permits the identification of an extra 72 (32%) and 51 proteins (23%), respectively. Regarding mass spectrometry analysis with an LTQ Orbitrap mass spectrometer, collision-induced fragmentation (CID and HCD) and electron transfer dissociation using the linear ion trap (IT) or the Orbitrap as the analyzer were compared. IT-CID was found to yield the best identification rate, whereas IT-ETD provided almost comparable results in terms of LMW proteome coverage. The high overlap between the proteins identified with IT-CID and IT-ETD allowed the validation of 75% of the identified proteins using this orthogonal fragmentation technique. Furthermore, a new approach to evaluating and improving the completeness of protein databases that utilizes the program RNAcode was introduced and examined.
Collapse
Affiliation(s)
- Stephan A Müller
- Department of Proteomics, UFZ, Helmholtz-Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Iwasaki M, Miwa S, Ikegami T, Tomita M, Tanaka N, Ishihama Y. One-dimensional capillary liquid chromatographic separation coupled with tandem mass spectrometry unveils the Escherichia coli proteome on a microarray scale. Anal Chem 2010; 82:2616-20. [PMID: 20222674 DOI: 10.1021/ac100343q] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We successfully identified the proteome expressed in Escherichia coli (E. coli) cells on a microarray scale using one-dimensional capillary liquid chromatography-tandem mass spectrometry (LC-MS/MS) with a 350 cm long, 100 microm i. d., monolithic silica-C(18) capillary column. E. coli tryptic digest (4 microg) was injected onto the column, and a 41 h gradient was applied with a flow rate of 500 nL/min at less than 20 MPa. In total, 22,196 nonredundant tryptic peptides from 2602 proteins, including 830 membrane proteins, were identified from the E. coli cells (triplicate analysis), in which an equivalent number of genes was detected by transcriptome analysis. Approximately a 5-fold larger peak response on average was obtained in this system, compared with that obtained by conventional capillary LC-MS/MS analysis with a 15 cm long, 3 microm diameter C(18) silica particle-packed column. The higher response suggests that the influence of ionization suppression was drastically reduced by the high-efficiency separation on the long monolithic silica column coupled with the shallow gradient. Because this high-resolution system does not require any additional separation prior to LC-MS/MS, this "one-shot" proteomics approach can simplify the workflow of shotgun proteomics and minimize the sample amount, as well as reduce the total analysis time, despite the use of prolonged shallow gradient elution.
Collapse
|
39
|
Raineri E, Ribeca P, Serrano L, Maier T. A more precise characterization of chaperonin substrates. ACTA ACUST UNITED AC 2010; 26:1685-9. [PMID: 20519287 DOI: 10.1093/bioinformatics/btq287] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Molecular chaperones prevent the aggregation of their substrate proteins and thereby ensure that they reach their functional native state. The bacterial GroEL/ES chaperonin system is understood in great detail on a structural, mechanistic and functional level; its interactors in Escherichia coli have been identified and characterized. However, a long-standing question in the field is: What makes a protein a chaperone substrate? RESULTS Here we identify, using a bioinformatics-based approach a simple set of quantities, which characterize the GroEL-substrate proteome. We define three novel parameters differentiating GroEL interactors from other cellular proteins: lower rate of evolution, hydrophobicity and aggregation propensity. Combining them with other known features to a simple Bayesian predictor allows us to identify known homologous and heterologous GroEL substrateproteins. We discuss our findings in relation to established mechanisms of protein folding and evolutionary buffering by chaperones.
Collapse
Affiliation(s)
- Emanuele Raineri
- CNAG Centro Nacional de Análisis Genómico, Parc Cientific de Barcelona, Baldiri Reixac 4, E-08028 Barcelona, Spain
| | | | | | | |
Collapse
|
40
|
Beaume M, Hernandez D, Farinelli L, Deluen C, Linder P, Gaspin C, Romby P, Schrenzel J, Francois P. Cartography of methicillin-resistant S. aureus transcripts: detection, orientation and temporal expression during growth phase and stress conditions. PLoS One 2010; 5:e10725. [PMID: 20505759 PMCID: PMC2873960 DOI: 10.1371/journal.pone.0010725] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 04/29/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Staphylococcus aureus is a versatile bacterial opportunist responsible for a wide spectrum of infections. The severity of these infections is highly variable and depends on multiple parameters including the genome content of the bacterium as well as the condition of the infected host. Clinically and epidemiologically, S. aureus shows a particular capacity to survive and adapt to drastic environmental changes including the presence of numerous antimicrobial agents. Mechanisms triggering this adaptation remain largely unknown despite important research efforts. Most studies evaluating gene content have so far neglected to analyze the so-called intergenic regions as well as potential antisense RNA molecules. PRINCIPAL FINDINGS Using high-throughput sequencing technology, we performed an inventory of the whole transcriptome of S. aureus strain N315. In addition to the annotated transcription units, we identified more than 195 small transcribed regions, in the chromosome and the plasmid of S. aureus strain N315. The coding strand of each transcript was identified and structural analysis enabled classification of all discovered transcripts. RNA purified at four time-points during the growth phase of the bacterium allowed us to define the temporal expression of such transcripts. A selection of 26 transcripts of interest dispersed along the intergenic regions was assessed for expression changes in the presence of various stress conditions including pH, temperature, oxidative shocks and growth in a stringent medium. Most of these transcripts showed expression patterns specific for the defined stress conditions that we tested. CONCLUSIONS These RNA molecules potentially represent important effectors of S. aureus adaptation and more generally could support some of the epidemiological characteristics of the bacterium.
Collapse
MESH Headings
- Base Sequence
- Conserved Sequence
- DNA, Complementary/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Bacterial
- Genome, Bacterial/genetics
- High-Throughput Screening Assays
- Methicillin-Resistant Staphylococcus aureus/genetics
- Methicillin-Resistant Staphylococcus aureus/growth & development
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/classification
- RNA, Bacterial/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Reproducibility of Results
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, RNA
- Stress, Physiological/genetics
- Time Factors
Collapse
Affiliation(s)
- Marie Beaume
- Genomic Research Laboratory, Infectious Diseases Service, Geneva University Hospitals, Geneva, Switzerland.
| | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Wigginton NS, de Titta A, Piccapietra F, Dobias J, Nesatyy VJ, Suter MJF, Bernier-Latmani R. Binding of silver nanoparticles to bacterial proteins depends on surface modifications and inhibits enzymatic activity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2010; 44:2163-8. [PMID: 20158230 DOI: 10.1021/es903187s] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Here we describe results from a proteomic study of protein-nanoparticle interactions to further the understanding of the ecotoxicological impact of silver nanoparticles (AgNPs) in the environment. We identified a number of proteins from Escherichia coli that bind specifically to bare or carbonate-coated AgNPs. Of these proteins, tryptophanase (TNase) was observed to have an especially high affinity for both surface modifications despite its low abundance in E. coli. Purified TNase loses enzymatic activity upon associating with AgNPs, suggesting that the active site may be in the vicinity of the binding site(s). TNase fragments with high affinities for both types of AgNPs were identified using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Differences in peptide abundance/presence in mass spectra for the two types of AgNPs suggest preferential binding of some protein fragments based on surface coating. One high-binding protein fragment contained a residue (Arg103) that is part of the active site. Ag adducts were identified for some fragments and found to be characteristic of strong binding to AgNPs rather than association of the fragments with ionic silver. These results suggest a probable mechanism for adhesion of proteins to the most commonly used commercial nanoparticles and highlight the potential effect of nanoparticle surface coating on bioavailability.
Collapse
Affiliation(s)
- Nicholas S Wigginton
- Environmental Microbiology Laboratory, Ecole Polytechnique Federale de Lausanne, CH-1015 Lausanne, Switzerland
| | | | | | | | | | | | | |
Collapse
|
42
|
Hori M, Asanuma T, Inanami O, Kuwabara M, Harashima H, Kamiya H. Effects of overexpression and antisense RNA expression of Orf17, a MutT-type enzyme. Biol Pharm Bull 2010; 29:1087-91. [PMID: 16754998 DOI: 10.1248/bpb.29.1087] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Escherichia coli Orf17 (NtpA, NudB) protein, a MutT-type enzyme, hydrolyzes oxidized deoxyribonucleotides, including 8-hydroxy-2'-deoxyadenosine 5'-triphosphate and 8-hydroxy-2'-deoxyguanosine 5'-triphosphate, in vitro. To examine its in vivo role(s) in bacteria, plasmid DNAs containing the orf17 gene in the sense and antisense orientations were introduced. When the Orf17 protein was overexpressed in mutT cells, the rpoB mutant frequency was decreased. On the other hand, similar effects were not observed when Orf17 was overexpressed in wild type and orf135 cells. Expression of the antisense RNA of the orf17 gene did not produce an obvious phenotype, such as increased mutant frequency and resistance to ionizing radiation. These results suggest that the role of the Orf17 protein is to back up the MutT function, and to assist in the elimination of 8-hydroxy-2'-deoxyguanosine nucleotides.
Collapse
Affiliation(s)
- Mika Hori
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | | | | | | | | | | |
Collapse
|
43
|
François P, Scherl A, Hochstrasser D, Schrenzel J. Proteomic approaches to study Staphylococcus aureus pathogenesis. J Proteomics 2010; 73:701-8. [DOI: 10.1016/j.jprot.2009.10.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 10/07/2009] [Accepted: 10/22/2009] [Indexed: 12/25/2022]
|
44
|
Zhao NW, Yao JT. Characterization and sequence identification of angiotensin II by a novel method involving ultra-fast liquid chromatography assay coupled with matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight five tandem mass spectrometry analysis. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2010; 16:663-671. [PMID: 21173463 DOI: 10.1255/ejms.1099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
High-throughput proteomics aims to investigate dynamically changing proteins expressed by a full organism, specific tissue or cellular compartment under certain conditions. High-sensitivity mass spectrometry has gradually become a significant tool for characterizing peptides. Here, we analyzed angiotensin II using ultra-fast liquid chromatography (UFLC) coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS). First, we applied UFLC in isolating and collecting the angiotensin II, and then Axima-Resonance (MALDI-QIT-ToF MS(5)) was adopted, which enables collision-induced dissociation-MS(5) analysis for fine structural characterization of angiotensin II. Resultant MS, MS(2), MS(3) and MS(4) spectra of interested [M+H](+) ions selected as precursor ions yielded detailed information about the sites of fragmentation as well as the amino acid sequence for angiotensin II; meanwhile, the average deviation between theoretical mass and actually measured mass from MS to MS(5) spectra was only 0.32 Da. It indicated that Axima-Resonance was capable of analyzing the peptide sequence accurately and provide the corresponding fragmentation information thoroughly, thus suggesting a potential strategy involving UFLC assay coupled with MALDI-QIT-ToF MS(5) analysis on high-throughput proteomics study in future.
Collapse
Affiliation(s)
- Ning-wei Zhao
- Shimadzu Global COE for Application & Technical Development, Shanghai 200052, China.
| | | |
Collapse
|
45
|
Arike L, Nahku R, Borrisova M, Adamberg K, Vilu R. Identification and relative quantification of proteins in Escherichia coli proteome by "up-front" collision-induced dissociation. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2010; 16:227-235. [PMID: 20212332 DOI: 10.1255/ejms.1068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A method for identifying and quantifying proteins with relatively low-cost orthogonal acceleration time-of- flight mass spectrometry (oa-ToF-MS) was tested. Escherichia coli (E. coli) K12 MG1655 cell lysate was separated by 1D gel-electrophoresis; fractions were digested and separated fast and reproducibly by ultra-performance liquid chromatography (UPLC). Peptides were identified using oa-ToF-MS to measure exact masses of parent ions and the fragment ions generated by up-front collision-induced dissociation. Fragmentation of all compounds was achieved by rapidly cycling between high- and low values of energy applied to ions. More than 100 proteins from E. coli K12 proteome were identified and relatively quantified. Results were found to correlate with transcriptome data determined by DNA microarrays.
Collapse
Affiliation(s)
- Liisa Arike
- Competence Centre of Food and Fermentation Technologies, 12618 Tallinn, Estonia.
| | | | | | | | | |
Collapse
|
46
|
Shinoda K, Tomita M, Ishihama Y. emPAI Calc--for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry. ACTA ACUST UNITED AC 2009; 26:576-7. [PMID: 20031975 DOI: 10.1093/bioinformatics/btp700] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
SUMMARY emPAI Calc is an open-source web application for the estimation of protein abundance. It uses the correlation between the number of identified peptides and protein abundance in mass spectrometry-based proteomic experiments. The program is the first implementation of our previously reported emPAI algorithm; it calculates the emPAI from the protein identification results obtained by database search engines such as Mascot.
Collapse
Affiliation(s)
- Kosaku Shinoda
- Human Metabolome Technologies, Inc., Tsuruoka, Yamagata, Japan
| | | | | |
Collapse
|
47
|
Pin C, Rolfe MD, Muñoz-Cuevas M, Hinton JCD, Peck MW, Walton NJ, Baranyi J. Network analysis of the transcriptional pattern of young and old cells of Escherichia coli during lag phase. BMC SYSTEMS BIOLOGY 2009; 3:108. [PMID: 19917103 PMCID: PMC2780417 DOI: 10.1186/1752-0509-3-108] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 11/16/2009] [Indexed: 11/18/2022]
Abstract
Background The aging process of bacteria in stationary phase is halted if cells are subcultured and enter lag phase and it is then followed by cellular division. Network science has been applied to analyse the transcriptional response, during lag phase, of bacterial cells starved previously in stationary phase for 1 day (young cells) and 16 days (old cells). Results A genome scale network was constructed for E. coli K-12 by connecting genes with operons, transcription and sigma factors, metabolic pathways and cell functional categories. Most of the transcriptional changes were detected immediately upon entering lag phase and were maintained throughout this period. The lag period was longer for older cells and the analysis of the transcriptome revealed different intracellular activity in young and old cells. The number of genes differentially expressed was smaller in old cells (186) than in young cells (467). Relatively, few genes (62) were up- or down-regulated in both cultures. Transcription of genes related to osmotolerance, acid resistance, oxidative stress and adaptation to other stresses was down-regulated in both young and old cells. Regarding carbohydrate metabolism, genes related to the citrate cycle were up-regulated in young cells while old cells up-regulated the Entner Doudoroff and gluconate pathways and down-regulated the pentose phosphate pathway. In both old and young cells, anaerobic respiration and fermentation pathways were down-regulated, but only young cells up-regulated aerobic respiration while there was no evidence of aerobic respiration in old cells. Numerous genes related to DNA maintenance and replication, translation, ribosomal biosynthesis and RNA processing as well as biosynthesis of the cell envelope and flagellum and several components of the chemotaxis signal transduction complex were up-regulated only in young cells. The genes for several transport proteins for iron compounds were up-regulated in both young and old cells. Numerous genes encoding transporters for carbohydrates and organic alcohols and acids were down-regulated in old cells only. Conclusion Network analysis revealed very different transcriptional activities during the lag period in old and young cells. Rejuvenation seems to take place during exponential growth by replicative dilution of old cellular components.
Collapse
Affiliation(s)
- Carmen Pin
- Institute of Food Research, Norwich NR4 7UA, UK.
| | | | | | | | | | | | | |
Collapse
|
48
|
Zhang W, Li F, Nie L. Integrating multiple 'omics' analysis for microbial biology: application and methodologies. MICROBIOLOGY-SGM 2009; 156:287-301. [PMID: 19910409 DOI: 10.1099/mic.0.034793-0] [Citation(s) in RCA: 281] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Recent advances in various 'omics' technologies enable quantitative monitoring of the abundance of various biological molecules in a high-throughput manner, and thus allow determination of their variation between different biological states on a genomic scale. Several popular 'omics' platforms that have been used in microbial systems biology include transcriptomics, which measures mRNA transcript levels; proteomics, which quantifies protein abundance; metabolomics, which determines abundance of small cellular metabolites; interactomics, which resolves the whole set of molecular interactions in cells; and fluxomics, which establishes dynamic changes of molecules within a cell over time. However, no single 'omics' analysis can fully unravel the complexities of fundamental microbial biology. Therefore, integration of multiple layers of information, the multi-'omics' approach, is required to acquire a precise picture of living micro-organisms. In spite of this being a challenging task, some attempts have been made recently to integrate heterogeneous 'omics' datasets in various microbial systems and the results have demonstrated that the multi-'omics' approach is a powerful tool for understanding the functional principles and dynamics of total cellular systems. This article reviews some basic concepts of various experimental 'omics' approaches, recent application of the integrated 'omics' for exploring metabolic and regulatory mechanisms in microbes, and advances in computational and statistical methodologies associated with integrated 'omics' analyses. Online databases and bioinformatic infrastructure available for integrated 'omics' analyses are also briefly discussed.
Collapse
Affiliation(s)
- Weiwen Zhang
- Center for Ecogenomics, Biodesign Institute, Arizona State University, Tempe, AZ 85287-6501, USA
| | - Feng Li
- Division of Biometrics II, Office of Biometrics/OTS/CDER/FDA, Silver Spring, MD 20993-0002, USA
| | - Lei Nie
- Division of Biometrics IV, Office of Biometrics/OTS/CDER/FDA, Silver Spring, MD 20993-0002, USA
| |
Collapse
|
49
|
Goodsell DS. Escherichia coli. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2009; 37:325-332. [PMID: 21567766 DOI: 10.1002/bmb.20345] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Diverse biological data may be used to create illustrations of molecules in their cellular context. I describe the scientific results that support a recent textbook illustration of an Escherichia coli cell. The image magnifies a portion of the bacterium at one million times, showing the location and form of individual macromolecules. Results from biochemistry, electron microscopy, and X-ray crystallography were used to create the image.
Collapse
Affiliation(s)
- David S Goodsell
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California.
| |
Collapse
|
50
|
Thompson MR, Chourey K, Froelich JM, Erickson BK, VerBerkmoes NC, Hettich RL. Experimental approach for deep proteome measurements from small-scale microbial biomass samples. Anal Chem 2009; 80:9517-25. [PMID: 19072265 DOI: 10.1021/ac801707s] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many methods of microbial proteome characterizations require large quantities of cellular biomass (>1-2 g) for sample preparation and protein identification. Our experimental approach differs from traditional techniques by providing the ability to identify the proteomic state of a microbe from a few milligrams of starting cellular material. The small-scale, guanidine lysis method minimizes sample loss by achieving cellular lysis and protein digestion in a single-tube experiment. For this experimental approach, the freshwater microbe Shewanella oneidensis MR-1 and the purple non-sulfur bacterium Rhodopseudomonas palustris CGA0010 were used as model organisms for technology development and evaluation. A 2-D LC-MS/MS comparison between a standard sonication lysis method and the small-scale guanidine lysis techniques demonstrates that the guanidine lysis method is more efficient with smaller sample amounts of cell pellet (i.e., down to 1 mg). The described methodology enables deeper proteome measurements from a few milliliters of confluent bacterial cultures. We also report a new protocol for efficient lysis from small amounts of natural biofilm samples for deep proteome measurements, which should greatly enhance the emerging field of environmental microbial community proteomics. This straightforward sample boiling protocol is complementary to the small-scale guanidine lysis technique, is amenable for small sample quantities, and requires no special reagents that might complicate the MS measurements.
Collapse
Affiliation(s)
- Melissa R Thompson
- Graduate School of Genome Science and Technology, Oak Ridge National Laboratory-University of Tennessee, Knoxville, Tennessee 37830, USA
| | | | | | | | | | | |
Collapse
|