Comparison of protein solubilization methods suitable for proteomic analysis of soybean seed proteins

Natarajan, Savithiry; Xu, Chenping; Caperna, Thomas J.; Garrett, Wesley M.

doi:10.1016/j.ab.2005.04.046

Cited by 186 publications

(184 citation statements)

References 30 publications

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“…The addition of 1M ThU to 4M urea caused extreme agent destruction (>4 logs), and ThU is known to have a co-operative enhanced unfolding effect on many proteins and structures when combined with urea. 51,52 The above data further showed that 6M urea itself can be part of a decontamination strategy for CJD agents. Moreover, the new combination of urea with ThU may be even more effective for processing delicate instruments.…”

Section: Urea and Thiourea Reduce Fu-cjd Infectivitymentioning

confidence: 93%

Rapid chemical decontamination of infectious CJD and scrapie particles parallels treatments known to disrupt microbes and biofilms

Botsios

Tittman²,

Manuelidis

2015

Virulence

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Neurodegenerative human CJD and sheep scrapie are diseases caused by several different transmissible encephalopathy (TSE) agents. These infectious agents provoke innate immune responses in the brain, including lateonset abnormal prion protein (PrP-res) amyloid. Agent particles that lack detectable PrP sequences by deep proteomic analysis are highly infectious. Yet these agents, and their unusual resistance to denaturation, are often evaluated by PrP amyloid disruption. To reexamine the intrinsic resistance of TSE agents to denaturation, a paradigm for less resistant viruses and microbes, we developed a rapid and reproducible high yield agent isolation procedure from cultured cells that minimized PrP amyloid and other cellular proteins. Monotypic neuronal GT1 cells infected with the FU-CJD or 22L scrapie agents do not have complex brain changes that can camouflage infectious particles and prevent their disruption, and there are only 2 reports on infectious titers of any human CJD strain treated with chemical denaturants. Infectious titers of both CJD and scrapie were reduced by >4 logs with Thiourea-urea, a treatment not previously tested. A mere 5 min exposure to 4M GdnHCl at 22 C reduced infectivity by >5 logs. Infectious 22L particles were significantly more sensitive to denaturation than FU-CJD particles. A protocol using sonication with these chemical treatments may effectively decontaminate complicated instruments, such as duodenoscopes that harbor additional virulent microbes and biofilms associated with recent iatrogenic infections.

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Section: Urea and Thiourea Reduce Fu-cjd Infectivitymentioning

confidence: 93%

Rapid chemical decontamination of infectious CJD and scrapie particles parallels treatments known to disrupt microbes and biofilms

Botsios

Tittman²,

Manuelidis

2015

Virulence

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“…Optimal conditions for sample preparation from plant tissues prior to 2-De have also been reported (Jacobs et al, 2001;wang et al, 2003a;Giavalisco et al, 2003;islam et al, 2004;Saravanan and rose, 2004;natarajan et al, 2005;vasconcelos et al, 2005;Carpentier et al, 2005;da Silva et al, 2010). Direct protein precipitation in acetone containing 10% trichloroacetic acid (mechin et al, 2007) and phenol partitioning (Hurkman and Tanaka, 1986) are the two main protein extraction procedures that have been adopted for 2-De analysis in plant tissues.…”

mentioning

confidence: 97%

“…methods using chaotropic buffers that are used to extract total protein from plant cells and tissues are usually based on urea and thiourea, also containing nonionic and/or zwitterionic detergents, reducing agents, carrier ampholytes and inhibitors of proteases, phosphatases and oxidoreductases natarajan et al, 2005); however, this step of protein extraction from plant tissues usually results in poorly resolved protein maps.…”

mentioning

confidence: 99%

“…Proteomic research on poorly characterized experimental systems, like tropical plants, is often hampered by the lack of routine sample preparation procedures. in this way, special attention should be devoted to preparing a preliminary, baseline sample of tropical plants, which could be used to test different extraction methods and isolate and fractionate proteins from plant material (Carpentier et al, 2005;natarajan et al, 2005). excellent reviews have indicated the most successful guidelines to be followed in order to perform the adequate protein extraction prior to 2-De (Shaw et al, 2003;rose et al, 2004;Gorg et al, 2004;Carpentier et al, 2005;natarajan et al, 2005;weiss and Gorg, 2008).…”

mentioning

confidence: 99%

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Challenges in proteome analyses of tropical plants

Balbuena¹,

Dias²,

Martins³

et al. 2011

Braz. J. Plant Physiol.

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Genome sequencing of various organisms allow global analysis of gene expression, providing numerous clues on the biological function and involvement in the biological processes studied. Proteomics is a branch of molecular biology and biotechnology that has undergone considerable development in the post-genomic era. Despite the recent significant advancements in proteomics techniques, still there is much to be improved. Due to peculiarities to the plant kingdom, proteomics approaches require adaptations, so as to improve efficiency and accuracy of results in plants. Data generated by proteomics can substantially contribute to the understanding and monitoring of plant physiological events and development of biotechnological strategies. especially for tropical species, challenges are even greater, in the light of the abundance of secondary metabolites, as well as of the lack of complete genome sequences. This review discusses current topics in proteomics concerning challenges and perspectives, with emphasis on the proteomics of tropical plant species.Key words: 2-De, mass spectrometry, recalcitrant species, proteomics, unknown genome resuMo O sequenciamento dos genomas de diversos organismos tornou praticável a análise global da expressão gênica, fornecendo numerosas pistas quanto à função biológica e envolvimento de inúmeros genes nos processos biológicos estudados. A proteômica é um dos ramos da biologia molecular e da biotecnologia que passou por expressivo desenvolvimento na era pós-genômica. Apesar dos recentes avanços nas técnicas em proteômica, muito resta a ser aprimorado. Devido às particularidades do reino vegetal, várias abordagens devem ser adaptadas no sentido de aumentar a eficiência e a acurácia de resultados das análises proteômicas em plantas. nesse sentido, os dados gerados pela proteômica podem contribuir substancialmente para a compreensão e acompanhamento de eventos fisiológicos e para o desenvolvimento de estratégias biotecnológicas. no que tange às espécies tropicais, as dificuldades são ainda maiores, devido ao fato de serem ricas em metabólitos secundários e ainda não terem seus genomas totalmente sequenciados. esta revisão trata de tópicos atuais em estudos de proteômica de plantas, desafios e perspectivas, com ênfase em espécies tropicais. palavras-chave: 2-De, espectrometria de massas, espécies recalcitrantes, genomas desconhecidos, proteômica.

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“…Protein digestion was performed as described previously (Natarajan et al, 2005). Gel spots were washed with CH 3 CN:H 2 O (1:1, v/v) containing 25 mM ammonium bicarbonate to remove the dye, dehydrated with 100% ACN, dried under vacuum, and incubated overnight at 37°C with 20 lL of 10 lg/mL trypsin (modified porcine trypsin, sequencing grade, Promega, Madison, WI) in 20 mM ammonium bicarbonate.…”

Section: Spots Digestion and Msmentioning

confidence: 99%

Impact of solar Ultraviolet-B on the proteome in soybean lines differing in flavonoid contents

Sullivan

Garrett

et al. 2008

Phytochemistry

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Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) was used to systematically investigate the impact of solar ultraviolet-B (UV-B) radiation on the soybean leaf proteome. In order to investigate the protective role of flavonoids against UV-B, two isolines of the Clark cultivar (the standard line with moderate levels of flavonoids and the magenta line with reduced flavonoids) were grown in the field with or without natural levels of UV-B. The 12-day-old first trifoliates were harvested for proteomic analysis. More than 300 protein spots were reproducibly resolved and detected on each gel. Statistical analysis showed that 67 protein spots were significantly (P < 0.05) affected by solar UV-B. Many more spots were altered by UV-B in the magenta line than in the standard line. Another 12 protein spots were not altered by UV-B but showed significantly (P < 0.05) different accumulations between the two lines, and for most spots the line-specific differences were also observed under UV-B exclusion. Most of the differentially accumulated spots were identified by mass spectrometry. The proteins were quite diverse, and were involved in metabolism, energy, protein destination/storage, protein synthesis, disease/defense, transcription, and secondary metabolism. The results suggest that high levels of flavonoids lead to a reduction in UV-B sensitivity at the proteomic level. Published by Elsevier Ltd.

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Comparison of protein solubilization methods suitable for proteomic analysis of soybean seed proteins

Cited by 186 publications

References 30 publications

Rapid chemical decontamination of infectious CJD and scrapie particles parallels treatments known to disrupt microbes and biofilms

Rapid chemical decontamination of infectious CJD and scrapie particles parallels treatments known to disrupt microbes and biofilms

Challenges in proteome analyses of tropical plants

Impact of solar Ultraviolet-B on the proteome in soybean lines differing in flavonoid contents

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