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  • 1.
    Amelina, Hanna
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Apraiz, Itxaso
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Sun, Wei
    Cristobal, Susana
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Proteomics-based method for the assessment of marine pollution using liquid chromatography coupled with two-dimensional electrophoresis2007In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 6, no 6, p. 2094-2104Article in journal (Refereed)
    Abstract [en]

    Using a proteomic approach, we have developed a new method for the assessment of marine pollution that generates highly reproducible protein expression patterns and it is simple and scalable. The protocol is based on applying liquid chromatography (LC) coupled with two-dimensional electrophoresis (2-DE) to analyze changes in the protein expression pattern after exposure to marine pollution. The digestive gland of the sentinel “blue mussel” (Mytilus edulis) was batch-processed through a simple cell fractionation followed by ion-exchange chromatography and 2-DE. The selection of ligands, elution method, and small volume design was carefully considered to define a protocol that could be mainly robotized. A pilot study with samples collected from different Gothenburg harbor areas indicated that the clean area could be distinguished from the polluted ones based on a protein expression pattern (PES) composed of 13 proteins. Principal component analysis (PCA) and hierarchical clustering confirmed that the PES was sufficient to discriminate polluted and unpolluted areas and to provide a spatial gradient from the polluted source. Several proteins from the PES were identified by electrospray ionization tandem mass spectrometry (ESI−MS/MS), and they are involved in β-oxidation, amino acid metabolism, detoxification, protein degradation, organelle biogenesis, and protein folding. In the near future, this methodology could show potential advantages to assess marine pollution and could become a stable platform to elucidate ecotoxicological questions.

  • 2.
    Amelina, Hanna
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Cristobal, Susana
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Proteomic study on gender differences in aging kidney of mice2009In: Proteome Science, ISSN 1477-5956, E-ISSN 1477-5956, Vol. 7, no 16Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: This study aims to analyze sex differences in mice aging kidney. We applied a proteomic technique based on subfractionation, and liquid chromatography coupled with 2-DE. Samples from male and female CD1-Swiss outbred mice from 28 weeks, 52 weeks, and 76 weeks were analysed by 2-DE, and selected proteins were identified by matrix assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS).

    RESULTS: This proteomic analysis detected age-related changes in protein expression in 55 protein-spots, corresponding to 22 spots in males and 33 spots in females. We found a protein expression signature (PES) of aging composed by 8 spots, common for both genders. The identified proteins indicated increases in oxidative and proteolytic proteins and decreases in glycolytic proteins, and antioxidant enzymes.

    CONCLUSION: Our results provide insights into the gender differences associated to the decline of kidney function in aging. Thus, we show that proteomics can provide valuable information on age-related changes in expression levels of proteins and related modifications. This pilot study is still far from providing candidates for aging-biomarkers. However, we suggest that the analysis of these proteins could suggest mechanisms of cellular aging in kidney, and improve the kidney selection for transplantation.

  • 3.
    Amelina, Hanna
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Holm, Tina
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Langel, Ülo
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    Cristobal, Susana
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Delivering catalase to yeast peroxisomes using cell-penetrating peptidesIn: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658Article in journal (Refereed)
  • 4.
    Amelina, Hanna
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Sjodin, Marcus O. D.
    Bergquist, Jonas
    Cristobal, Susana
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Quantitative subproteomic analysis of age-related changes in mouse liver peroxisomes by iTRAQ LC-MS/MS2011In: Journal of chromatography. B, ISSN 1570-0232, E-ISSN 1873-376X, Vol. 879, no 30, p. 3393-3400Article in journal (Refereed)
    Abstract [en]

    Aging is a complex multifactorial phenomenon, which is believed to result from the accumulation of cellular damage to biological macromolecules. Peroxisomes recently emerged as another important source of reactive oxygen species (ROS) production in addition to mitochondria. However, the role of these organelles in the process of aging is still not clear. The aim of this study was to characterize the changes in protein expression profiles of young (10 weeks old) versus old (18 months old) mouse liver peroxisome-enriched fractions. We have applied shotgun proteomic approach based on liquid chromatography and tandem mass spectrometry (LC-MS/MS) combined with iTRAQ (isobaric tags for relative and absolute quantitation) labeling that allows comparative quantitative multiplex analysis. Our analysis led to identification and quantification of 150 proteins, 8 out of which were differentially expressed between two age groups at a statistically significant level (p < 0.05), with folds ranging from 1.2 to 4.1. These proteins involved in peroxisornal beta-oxidation, detoxification of xenobiotics and production of ROS. Noteworthy, differences in liver proteome have been observed between as well as within different age groups. In conclusion, our subproteomic quantitative study suggests that mouse liver proteome is sufficiently maintained until certain age.

  • 5.
    Amelina, Hanna
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Sjödin, Marcus O. D.
    Bergquist, Jonas
    Cristobal, Susana
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Quantitative subproteomic analysis of age-related changes in mouse liver peroxisomes by iTRAQ LC-MS/MSIn: Journal of chromatography. B, ISSN 1570-0232, E-ISSN 1873-376XArticle in journal (Refereed)
  • 6.
    Apraiz, Itxaso
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Cajaraville, Miren P.
    Department of Zoology and Cell Biology, University of the Basque Country.
    Cristobal, Susana
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Peroxisomal proteomics, biomonitoring in mussles after the Prestige's oil spill2009In: Marine Pollution Bulletin, ISSN 0025-326X, E-ISSN 1879-3363, Vol. 58, no 12, p. 1815-1826Article in journal (Refereed)
    Abstract [en]

    Peroxisomal proteomics was applied to assess possible biological effects after the Prestige's oil spill. Mussels were sampled in July 2004 and 2005 in four stations in the NW (closest to the spill) and NE coasts of the Iberian Peninsula. Principal components analysis (PCA) suggested differences in protein expression among stations and sampling years. Several proteins were putatively identified by mass spectrometry and immunolocalization. PC1 separated the NW stations in 2004 from the rest of the stations and sampling years mainly due to up-regulation of peroxisomal β-oxidation proteins and PMP70. PC3 separated the NE-stations, based on up-regulation of the antioxidant enzyme catalase in 2004 compared to 2005. PC4 separated the stations in the NE and the NW. This work shows that environmental proteomics, together with multivariate data analysis, could provide information to interpret the effects of oil spills at cellular level in mussels also in the absence of historical data.

  • 7.
    Apraiz, Itxaso
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Leoni, Giulia
    Lindenstrand, David
    Stockholm University, Faculty of Science, Department of Mathematics.
    Persson, Jan-Olov
    Stockholm University, Faculty of Science, Department of Mathematics.
    Cristobal, Susana
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Proteomic analysis of mussels exposed to fresh and weathered Prestige's oilManuscript (Other academic)
    Abstract [en]

    Biomonitoring
programs
that
use
mussels to assess the
water
quality
around
the
world, could
benefit
from
the
use
 of
proteomics
techniques. These
could
be
applied to obtain
protein expression
signatures
of
exposure to
pollution
that
could
be further
used
for
prediction purposes. This
would
require
that
a
combination
of
univariate
and
multivariate
 statistical
analyses
of
proteomics data
were
utilized
to
obtain
robust
models.
We
show an
application
of
this approach
on
mussels
exposed
to
fresh
fuel, and weathered
fuel
in
a
laboratory experiment
that
tried
to
mimic
the
effects of the
Prestige's
oil
spill.
A
set
of
protein
spots
were
selected
that
could
be used
to
classify
mussels exposed
to
the two
types
of
fuel
oil.
As
an
example
of the possibilities
this
approach
could offer to biomonitoring
programs, mussels were collected from ten sampling stations
along
the
NW
and
NE of the Iberian Peninsula, and their protein expression patterns monitored.

     

     

  • 8.
    Apraiz, Itxaso
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Mi, Jia
    Cristobal, Susana
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Identification of proteomic signatures of exposure to marine pollutants in mussels (Mytilus edulis)2006In: Molecular & Cellular Proteomics, ISSN 1535-9476, E-ISSN 1535-9484, Vol. 5, no 7, p. 1274-1285Article in journal (Refereed)
  • 9.
    Hedin, Linnea E.
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Öjemalm, Karin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Bernsel, Andreas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Hennerdal, Aron
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Illergård, Kristoffer
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Enquist, Karl
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Kauko, Anni
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Cristobal, Susana
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    von Heijne, Gunnar
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Lerch-Bader, Mirjam
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Nilsson, IngMarie
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Elofsson, Arne
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Membrane Insertion of Marginally Hydrophobic Transmembrane Helices Depends on Sequence Context2010In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 396, no 1, p. 221-229Article in journal (Refereed)
    Abstract [en]

    In mammalian cells, most integral membrane proteins are initially inserted into the endoplasmic reticulum membrane by the so-called Sec61 translocon. However, recent predictions suggest that many transmembrane helices (TMHs) in multispanning membrane proteins are not sufficiently hydrophobic to be recognized as such by the translocon. In this study, we have screened 16 marginally hydrophobic TMHs from membrane proteins of known three-dimensional structure. Indeed, most of these TMHs do not insert efficiently into the endoplasmic reticulum membrane by themselves. To test if loops or TMHs immediately upstream or downstream of a marginally hydrophobic helix might influence the insertion efficiency, insertion of marginally hydrophobic helices was also studied in the presence of their neighboring loops and helices. The results show that flanking loops and nearest-neighbor TMHs are sufficient to ensure the insertion of many marginally hydrophobic helices. However, for at least two of the marginally hydrophobic helices, the local interactions are not enough, indicating that post-insertional rearrangements are involved in the folding of these proteins.

  • 10.
    Kauko, Anni
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Hedin, Linnea E
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Thebaud, Estelle
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Cristobal, Susana
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Elofsson, Arne
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    von Heijne, Gunnar
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Repositioning of transmembrane alpha-helices during membrane protein folding2010In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 397, no 1, p. 190-201Article in journal (Refereed)
    Abstract [en]

    We have determined the optimal placement of individual transmembrane helices in the Pyrococcus horikoshii Glt(Ph) glutamate transporter homolog in the membrane. The results are in close agreement with theoretical predictions based on hydrophobicity, but do not, in general, match the known three-dimensional structure, suggesting that transmembrane helices can be repositioned relative to the membrane during folding and oligomerization. Theoretical analysis of a database of membrane protein structures provides additional support for this idea. These observations raise new challenges for the structure prediction of membrane proteins and suggest that the classical two-stage model often used to describe membrane protein folding needs to be modified.

  • 11. Mi, J.
    et al.
    Apraiz, I.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Cristobal, S.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Peroxisomal proteomic approach for protein profiling in blue mussels (Mytilus edulis) exposed to crude oil2007In: Biomarkers, ISSN 1354-750X, E-ISSN 1366-5804, Vol. 12, no 1, p. 47-60Article in journal (Refereed)
  • 12. Mi, Jia
    et al.
    Garcia-Arcos, Itsaso
    Alvarez, Ruben
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Cristobal, Susana
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Age-related subproteomic analysis of mouse liver and kidney peroxisomes.2007In: Proteome Sci, ISSN 1477-5956, Vol. 5, no 1, p. 19-Article in journal (Other academic)
  • 13. Mi, Jia
    et al.
    Kirchner, Eva
    Cristobal, Susana
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Quantitative proteomic comparison of mouse peroxisomes from liver and kidney.2007In: Proteomics, ISSN 1615-9853, Vol. 7, no 11, p. 1916-28Article in journal (Other academic)
  • 14.
    Vereshchaga, Yana
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Hedin, Linnea E
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Cristobal, Susana
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Elofsson, Arne
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Lindahl, Erik
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Insertion Properties of Marginally Hydrophobic Helices in the LacY Lactose Permease TransporterManuscript (preprint) (Other academic)
    Abstract [en]

    Transmembrane helices are generally believed to be recognized individually by the translocon based on theirhydrophobicity, but it has been proposed that they could also be recognized as pairs of helices. The fact thatmost transmembrane helices are individually clearly hydrophobic seems to support separate helix insertion,but there are important exceptions where the helices are only borderline hydrophilic, at least according tosequence-based prediction. Conrming these patterns and characterizing their role for insertion of helices isan important part in deciphering membrane protein insertion and folding. Here, we use a combination ofsequence bioinformatics, simplied physical modeling, and experiments to investigate whether helices in theLacY lactose permease transporter are recognized by the translocon, and if not whether helix-helix interactionsmight stabilize their insertion. From the experimentally determined biological hydrophobicity scale, ve out of thetwelve transmembrane segments of LacY are predicted to have low spontaneous insertion, which is qualitativelyconrmed in a simplied simulation model using an implicit membrane environment as well as experimentallyin vitro. For some pairs a small, but signicant, increase in insertion eciency was seen both in the simulationsand in the in vitro system. However, the overall insertion eciency is only marginally increased when pairsof borderline hydrophobic helices are co-inserted, which suggests that translocon-mediated membrane insertionpredominantly recognizes individual helices. It also seems to imply that stabilization of marginally hydrophobichelices - at least for LacY - is a collective eect in the nal folded membrane protein, rather than caused by favorable interactions and hairpin formation during insertion.

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