Improved SILAC method for double labeling of bacterial proteome

Han, Junlong; Yi, Shuhong; Zhao, Xinlu; Zheng, Yun-Dan; Yang, Donghong; Du, Gaofei; Yang, Xiao-Yan; He, Qing‐Yu; Sun, Xia

doi:10.1016/j.jprot.2018.12.011

Cited by 5 publications

(3 citation statements)

References 51 publications

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“…37 Metabolic in vivo labeling techniques like SILAC (stable isotope labeling with amino acids in cell culture) and 15 N labeling makes it possible to measure smaller measurement bias. 38 A chemical in vitro labeling methods like the ICAT (isotope-coded affinity tag), 18 O labeling, TMT (tandem mass tags) and iTRAQ (isobaric tags for relative and absolute quantification) can be used for static samples such as clinical samples. 39,40 Another identical strategy called isotope-coded protein label (ICPL) labels both N-termini and lysine side chains and is used at the protein level.…”

Section: Quantitative Proteomicsmentioning

confidence: 99%

<p>Proteomic Applications in Antimicrobial Resistance and Clinical Microbiology Studies</p>

Khodadadi

Zeinalzadeh

Taghizadeh

et al. 2020

IDR

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Sequences of the genomes of all-important bacterial pathogens of man, plants, and animals have been completed. Still, it is not enough to achieve complete information of all the mechanisms controlling the biological processes of an organism. Along with all advances in different proteomics technologies, proteomics has completed our knowledge of biological processes all around the world. Proteomics is a valuable technique to explain the complement of proteins in any organism. One of the fields that has been notably benefited from other systems approaches is bacterial pathogenesis. An emerging field is to use proteomics to examine the infectious agents in terms of, among many, the response the host and pathogen to the infection process, which leads to a deeper knowledge of the mechanisms of bacterial virulence. This trend also enables us to identify quantitative measurements for proteins extracted from microorganisms. The present review study is an attempt to summarize a variety of different proteomic techniques and advances. The significant applications in bacterial pathogenesis studies are also covered. Moreover, the areas where proteomics may lead the future studies are introduced.

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Section: Quantitative Proteomicsmentioning

confidence: 99%

<p>Proteomic Applications in Antimicrobial Resistance and Clinical Microbiology Studies</p>

Khodadadi

Zeinalzadeh

Taghizadeh

et al. 2020

IDR

View full text Add to dashboard Cite

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“…Moreover, proteins produced by microbes can be used to produce bioplastics [10][11][12], biofuels [13,14] and other essential microbial-derived products. There are several conventional and effective techniques to study microbial proteomes such as mass spectrometry [15,16], protein microarrays [17,18], shotgun proteomics [16,19] and isotope labelling [7,20]. These methods are highly sensitive but are invasive and destructive in nature, limiting their applicability to study the proteome in its physiological intracellular environment.…”

Section: Introductionmentioning

confidence: 99%

Reverse stable isotope labelling with Raman spectroscopy for microbial proteomics

Karlo,

Dhillon,

Siddhanta

et al. 2023

Journal of Biophotonics

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Global proteome changes in microbes affect the survival and overall production of commercially relevant metabolites through different bioprocesses. The existing methods to monitor proteome level changes are destructive in nature. Stable isotope probing (SIP) coupled with Raman spectroscopy is a relatively new approach for proteome analysis. However, applying this approach for monitoring changes in a large culture volume is not cost‐effective. In this study, for the first time we are presenting a novel method of combining reverse SIP using 13C‐glucose and Deuterium to monitor the proteome changes through Raman spectroscopy. The findings of the study revealed visible changes (blue shifts) in proteome related peaks that can be used for monitoring proteome dynamics, that is, synthesis of nascent amino acids and its turnover with time in a non‐destructive, cost‐effective, and label‐free manner.

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“…Within the labeling methods, there are several different techniques. These include metabolic labeling, such as stable isotope labeling using amino acids in cell culture (SILAC) [ 26 ] or bacterial growth media [ 27 ], and chemical labeling on peptide level, such as isobaric tags for relative and absolute quantitation (iTRAQ) [ 28 ] or tandem mass tags (TMT) [ 29 ]. Other more targeted labeling techniques, such as pulsed labeling, can be used to study protein turnover, since it will only label proteins synthesized after, for example, antibiotic treatment.…”

Section: Introductionmentioning

confidence: 99%

The Role of Proteomics in Bacterial Response to Antibiotics

et al. 2020

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For many years, we have tried to use antibiotics to eliminate the persistence of pathogenic bacteria. However, these infectious agents can recover from antibiotic challenges through various mechanisms, including drug resistance and antibiotic tolerance, and continue to pose a global threat to human health. To design more efficient treatments against bacterial infections, detailed knowledge about the bacterial response to the commonly used antibiotics is required. Proteomics is a well-suited and powerful tool to study molecular response to antimicrobial compounds. Bacterial response profiling from system-level investigations could increase our understanding of bacterial adaptation, the mechanisms behind antibiotic resistance and tolerance development. In this review, we aim to provide an overview of bacterial response to the most common antibiotics with a focus on the identification of dynamic proteome responses, and through published studies, to elucidate the formation mechanism of resistant and tolerant bacterial phenotypes.

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Improved SILAC method for double labeling of bacterial proteome

Cited by 5 publications

References 51 publications

<p>Proteomic Applications in Antimicrobial Resistance and Clinical Microbiology Studies</p>

<p>Proteomic Applications in Antimicrobial Resistance and Clinical Microbiology Studies</p>

Reverse stable isotope labelling with Raman spectroscopy for microbial proteomics

The Role of Proteomics in Bacterial Response to Antibiotics

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