1-DE MS and 2-D LC-MS analysis of the mouse bronchoalveolar lavage proteome

Guo, Yurong; Fan, Shwu; Grigoryev, Dmitry N.; Eyk, Jennifer E. Van; Garcia, Joe G.N.

doi:10.1002/pmic.200500052

Cited by 42 publications

(38 citation statements)

References 32 publications

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“…Proteins copurifying with TAP-tagged Rpf2 or Rrs1 or protein A-tagged Rpf2 were identified by mass spectrometry as described in Eng et al (1994), Horsey et al (2004), Guo et al (2005), and Krutchinsky et al (2001).…”

Section: Methodsmentioning

confidence: 99%

Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes

Zhang

Harnpicharnchai²,

Jakovljevic³

et al. 2007

Genes Dev.

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180

271

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More than 170 proteins are necessary for assembly of ribosomes in eukaryotes. However, cofactors that function with each of these proteins, substrates on which they act, and the precise functions of assembly factors-e.g., recruiting other molecules into preribosomes or triggering structural rearrangements of pre-rRNPs-remain mostly unknown. Here we investigated the recruitment of two ribosomal proteins and 5S ribosomal RNA (rRNA) into nascent ribosomes. We identified a ribonucleoprotein neighborhood in preribosomes that contains two yeast ribosome assembly factors, Rpf2 and Rrs1, two ribosomal proteins, rpL5 and rpL11, and 5S rRNA. Interactions between each of these four proteins have been confirmed by binding assays in vitro. These molecules assemble into 90S preribosomal particles containing 35S rRNA precursor (pre-rRNA). Rpf2 and Rrs1 are required for recruiting rpL5, rpL11, and 5S rRNA into preribosomes. In the absence of association of these molecules with pre-rRNPs, processing of 27SB pre-rRNA is blocked. Consequently, the abortive 66S pre-rRNPs are prematurely released from the nucleolus to the nucleoplasm, and cannot be exported to the cytoplasm. In eukaryotes, 79 ribosomal proteins associate with ribosomal RNA (rRNA) to produce 40S and 60S ribosomal subunits (Woolford and Warner 1991). Three of the four rRNAs in mature ribosomes are derived from the 35S-45S rRNA precursor (pre-rRNA) transcribed by RNA polymerase I, while the fourth rRNA, 5S rRNA, is transcribed from separate genes by RNA polymerase III. The 35S-45S primary transcript is packaged into a 90S ribonucleoprotein particle (RNP), together with a subset of assembly factors and ribosomal proteins. Subsequent steps trigger folding, modification, and processing of prerRNAs and association of additional assembly factors and ribosomal proteins in 43S and 66S assembly intermediates. These pre-rRNPs undergo further maturation in the nucleolus, nucleoplasm, and then cytoplasm to form functional 40S and 60S ribosomal subunits, respectively ( Fig. 1A; FromontRacine et al. 2003;Raué 2003;Granneman and Baserga 2004). Preribosomal particles in the assembly pathway are distinguished by the presence of successive prerRNA processing intermediates (Fig. 1A). However, it is not clear into which of the consecutive preribosomes 5S rRNA and each ribosomal protein are incorporated, which assembly factors are required to recruit these molecules, or how they do so. Furthermore, the mechanisms by which constituents of nascent ribosomes facilitate folding, processing, and modification of pre-rRNAs remain elusive.5S rRNA is essential for maturation of preribosomes and for the function of mature ribosomes (Van Ryk et al. 1992;Dechampesme et al. 1999;Kiparisov et al. 2005). Steitz and coworkers defined a pathway of assembly of 5S rRNA into ribosomes in HeLa cells. Newly synthesized 5S pre-rRNA binds transiently to the La protein (Rinke and Steitz 1982;Yoo and Wolin 1994). Following 3Ј-end maturation, 5S rRNA binds to ribosomal protein rpL5, then assembles into ribosomes (...

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Section: Methodsmentioning

confidence: 99%

Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes

Zhang

Harnpicharnchai²,

Jakovljevic³

et al. 2007

Genes Dev.

Self Cite

180

271

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“…For the purification of AMPA-R complex from rat brain, matured membrane proteins were then enriched as described in a previous study (29). AMPA-R complexes were then purified through large-scale IP followed by Mass Spectrometry analysis as described in the SI Methods and a previous study (30) in detail. Purification of synaptosome and postsynaptic density were performed based on a method described previously (31).…”

Section: Methodsmentioning

confidence: 99%

AMPA receptor and GEF-H1/Lfc complex regulates dendritic spine development through RhoA signaling cascade

Kang

Guo

Huganir

2009

Proc. Natl. Acad. Sci. U.S.A.

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AMPA receptors (AMPA-R) are major mediators of synaptic transmission and plasticity in the developing and adult central nervous system. Activity-dependent structural plasticity mediated by dynamic changes in the morphology of spines and dendrites is also essential for the formation and tuning of neuronal circuits. RhoA and Rac1 are known to play important roles in the regulation of spine and dendrite development in response to neuronal activity. These Rho GTPases are activated by guanine nucleotide exchange factors (GEFs). In this study, we identified GEF-H1/Lfc as a component of the AMPA-R complex in the brain. GEF-H1 is enriched in the postsynaptic density and is colocalized with GluR1 at spines. GEF-H1 activity negatively regulates spine density and length through a RhoA signaling cascade. In addition, AMPA-R-dependent changes in spine development are eliminated by down-regulation of GEF-H1. Altogether, these results strongly suggest that GEF-H1 is an important mediator of AMPA-R activity-dependent structural plasticity in neurons.glutamate receptor ͉ GTPase ͉ learning and memory ͉ structural plasticity ͉ synaptic plasticity

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“…However, none of the other 3 proteins were detected by either the IP method or the 2D GE method. This phenomenon, that different separation techniques lead to the detection of different proteins, is frequently observed in proteomic studies (Guo et al 2005).…”

Section: Solution Isoelectric Focusing Followed By 1d Sds-pagementioning

confidence: 99%

Proteomic analysis of protein nitration in rat cerebellum: effect of biological aging

Gokulrangan

Zaidi

Michaelis

et al. 2006

Journal of Neurochemistry

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3-Nitrotyrosine (3-NT) is a useful biomarker of increasing oxidative stress and protein nitration during biological aging. The proteomic analysis of cerebellar homogenate from Fisher 344/Brown Norway (BN/F1) rats shows an age-dependent increase in protein nitration, monitored by western-blot analysis after two-dimensional gel electrophoresis (2DE), mainly in the acidic region. Analysis of in-gel digests by nanoelectrospray (NSI)-MS/MS resulted in the identification of 16 putatively nitrated proteins. The selective isolation of nitrated proteins using immunoprecipitation, followed by SDS-PAGE and in-gel digest/NSI-MS/MS analysis led to the identification of 22 putatively nitrated proteins, of which 7 were identical to those detected after 2DE. When proteins were separated by solution isoelectrofocusing and analyzed by NSI MS/MS, we obtained MS/MS spectra of 3-NT containing peptides of four proteins -similar to ryanodine receptor 3, low density lipoprotein related receptor 2, similar to nebulin-related anchoring protein isoform C and 2,3 cyclic nucleotide 3-phosphodiesterase. Although the functional consequences of protein nitration for these targets are not yet known, our proteomic experiments serve as a first screen for the more targeted analysis of nitrated proteins from aging cerebellum for functional characterization. Oxidative stress and biological aging contribute to elevated levels of reactive oxygen species (ROS) and reactive nitrogen species (RNS), causing reversible as well as irreversible covalent protein modifications (Oliver et al.

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1-DE MS and 2-D LC-MS analysis of the mouse bronchoalveolar lavage proteome

Cited by 42 publications

References 32 publications

Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes

Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes

AMPA receptor and GEF-H1/Lfc complex regulates dendritic spine development through RhoA signaling cascade

Proteomic analysis of protein nitration in rat cerebellum: effect of biological aging

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