Thursday, July 29, 2010

Peroxisome Posters in Yeast Meet 2010

Yeast Genetics and Molecular Biology Meeting 2010
Date - July 27 – August 1, 2010
Place - University of British Columbia, Vancouver, Canada.

Program and Abstract Book
http://www.yeast-meet.org/2010/pdf/book.pdf#pagemode=bookmarks

NOTE - The abstract hyperlinks are not properly landing on the abstract page, though I update them everyday with working links. Inconvenience Regretted

Poster Sessions
Cell Biology: Mitochrondria/Vacuoles/Peroxisomes
(I am mentioning only Presenting author under the abstract title, for full author list and abstract visit the Conference website)

28 July 2010 (Wednesday)
101A
Genome-wide analyses of the function of Pex11, a protein involved in processes beyond peroxisome proliferation.
Uros Petrovic

466A
Integrated Phosphoproteomic Analysis of a Signaling Network Governing Nutrient Response and Peroxisome Induction.
Ramsey Saleem

481A
A new fluorescent probe to assess intra-cellular and intra-organellar redox states.
Masahide Oku

97B
Interrogation of Integral Membrane Protein Complexes in Peroxisome Biogenesis.
Arvind Jamakhandi

217B
Novel anti-aging compounds extend yeast life span by targeting a programmed necrotic cell death pathway.
Vladimir Titorenko

29 July 2010 (Thursday)
103C
The role of Pex11 family members in peroxisome proliferation in Hansenula polymorpha.
Ruchi Saraya

30 July 2010 (Friday)
574D
Metabolic Engineering of Yarrowia lipolytica: Production of Eicosapentaenoic Acid-Rich Oil for Commercialization.
Zhixiong Xue

105E
Oxidative stress resistance and peroxisomal proliferation in lager fermentation.
Natalia Solodovnikova

Wednesday, July 28, 2010

New Peroxisome Articles (Update 21-28 July 2010 )

Pex11pβ-mediated growth and division of mammalian peroxisomes follows a maturation pathway
JCS Online accepted article
Delille HK et al
Prof. Michael Schrader Group

(From the Note in above paper, Paper not yet online on JCS)
PEX11-family members are membrane elongation factors that coordinate peroxisome proliferation and maintenance
JCS in press article
Koch et al.
Prof. Cecile Brocard and coworkers

Identification of an unusual variant peroxisome biogenesis disorder caused by mutations in the PEX16 gene
Journal of Medical Genetics (Impact Factor 5.75)
Ebberink MS et al
Dr. Sacha Ferdinandusse, University of Amsterdam

Targeting of Pex8p to the peroxisomal importomer
European Journal of Cell Biology (Impact Factor 3.3)
Deckers M et al
Prof. Ralf Erdmann Group

De novo synthesis of peroxisomes upon mitochondrial targeting of Pex3p
European Journal of Cell Biology (Impact Factor 3.3)
Rucktäschel R et al
Prof. Ralf Erdmann Group

Review
Protein Import Machineries of Peroxisomes
Biochimica et Biophysica Acta (BBA) - Biomembranes (Impact Factor 3.9)
Rucktäschel R et al.
Prof. Ralf Erdmann Group

Clinical, Biochemical and Molecular Characterization of Peroxisomal Diseases in Arabs
Clinical Genetics (Impact Factor 3.3)
Shaheen R et al
Dr. Fowzan Alkuraya Group
King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia

Catabolite repression of Aox in Pichia pastoris is Dependent on Hexose Transporter PpHxt1 and Pexophagy
Applied and Environmental Microbiology (Impact Factor 3.8)
Zhang P et al
Prof. Xiangshan Zhou, East China University of Science and Technology

The Arabidopsis peroxisomal ABC transporter, comatose, complements the Saccharomyces cerevisiae pxa1 pxa2Δ mutant for metabolism of long chain fatty acids and exhibits fatty acyl-coa stimulated atpase activity
JBC
Nyathi Y et al
Prof. Alison Baker Group

A proteomic approach towards the identification of the matrix protein content of the two types of microbodies in Neurospora crassa
Managadze D et al
Proteomics (Impact Factor 4.58)
Dr. Hanspeter Rottensteiner, Ruhr-University Bochum

Saturday, July 17, 2010

Obsoletely Correct..My Toilet Philosophy applied to Peroxisomes

Hello Peroxisome Blog Readers,

I have a blog on Nature Blogs titled "GeeK of Science"
In a series of posts, I am trying to generate philosophy about science from day to day activities.

This time it is Toilet Philosophy.
In new post "Obsoletely Correct" I tried to apply this new term on small scale to peroxisomes..
I hope you will find the blog article Very Funny yet Insightful...

Wednesday, July 14, 2010

Updates of the week 12-18 July 2010

New Peroxisome Papers

Niche - High-Throughput screening
Journal - International Journal of High Throughput Screening
North Carolina Central University
Fig.1 from the paper..



Niche - Three Minireviews in the FEBS Journal.
MINIREVIEW SERIES - Peroxisomes as dynamic organelles
Introduction to review series by Prof. Ida J. van der Klei

Peroxisomes as dynamic organelles: autophagic degradation
Masahide Oku et al.
From the group of Prof. Yasuyoshi Sakai,
Kyoto University, Japan

Peroxisomes as dynamic organelles: peroxisome abundance in yeast
Ruchi Saraya et al.
From the group of Prof. Ida J. van der Klei
University of Groningen, Netherlands

Peroxisomes as dynamic organelles: peroxisomal matrix protein import
Janina Wolf et al.
From the group of Prof. Ralf Erdmann
Ruhr-Universität Bochum, Germany

Niche - Review
Peroxin 5: a cycling receptor for protein translocation into peroxisomes
Chris P. Williams, Will Stanley
Journal - The International Journal of Biochemistry & Cell Biology

Niche - Case report
Refsum’s Disease – Use of the Intestinal Lipase Inhibitor, Orlistat as a Novel Therapeutic Approach to a Complex Disorder
Journal - Journal of Obesity
Provisional PDF from the publisher - Link 
Nimalie Perera et al.
From the group of Prof. David R. Sullivan
Authors report the results of novel therapy on Refsum disease patients with intestinal lipase inhibitor orlistat. Authors observed significant reduction in phytanic acid levels and retardation of dermatological and neurological symptoms.

Niche - Cell signalling
Spermidine Oxidase-derived H2O2 Regulates Pollen Plasma Membrane Hyperpolarization-activated Ca2+-permeable Channels and Pollen Tube Growth
Journal - The Plant Journal
Juyou Wu et al.
From the group of Prof. Shaoling Zhang
Nanjing Agricultural University, China
Authors identified that Arabidopsis peroxisomal polyamine oxidases (PAO) oxidize spermidine to release H2O2 which acts as messenger for inducing the opening of Ca2+-permeable channels. This event is critical for pollen tube growth.
(on larger note, this paper hints towards peroxisome as source for critical cellular signal transduction events like mitochondria.)

(This simplified diagrammatic representation of the results from above paper is made by me using www.proteinlounge.com.)



Mitochondrial dysfunction and reduced prostaglandin synthesis in skeletal muscle of group VIB Ca2+-indpendent phospholipase A2 (iPLA2γ) deficient mice
Journal - Journal of Lipid Research
Emiko Yoda et al.
From the group of Prof. Shuntaro Hara
iPLA2γ (Group VIB Ca2+-independent phospholipase A2) has dual mitochondrial (N-terminal) as well as peroxisomal localization signals (C-terminal SKL). (Ref.)

Niche - From EBEC Abstract book
Biochimica et Biophysica Acta (BBA) - Bioenergetics
Peroxisomal transporters associated with β-oxidation
Theodoulou et al.

Tuesday, July 13, 2010

Peroxisome Puzzles..

Gene. 2010 Jan 15;450(1-2):18-24.
Duhita N et al (Japan)

Gene. 2010 Jun 25. [Epub ahead of print]
Gabaldón T et al (Spain)

Phylogenetic analysis of Pex1/6 proteins was used as basis for determining the relatedness of these peroxins to actinobacterial or ER proteins and to determine the evolutionary ancestor of peroxisomes.
At least one of the paper has to be wrong. or there is third possibility that phylogenetic analysis of Pex1/6 itself is insufficient criteria to determine the origin of peroxisomes.!

Friday, July 9, 2010

Before Pubmed..!





New High Impact Peroxisome Paper in Current Biology (Cell Press) (2009 Impact Factor - 10.992)

Vps35 Mediates Vesicle Transport between the Mitochondria and Peroxisomes
Emélie Braschi et al.
Prof.Dr.Heidi M. McBride.
University of Ottawa Heart Institute, Canada.
Lab webpage

McBride group had previously shown that Mitochondria derived vesicles(MDV) can carry specific cargos to peroxisomes.
Cargo-Selected Transport from the Mitochondria to Peroxisomes Is Mediated by Vesicular Carriers
Neuspiel et al, Current Biology, 2008

In the recent stunning findings, McBride group reports that MDV transport between mitochondria and peroxisomes requires Vps35 and Vps26a, the components of Retromer complex which is required for endosome to golgi complex transport.

"Does Peroxisome turn Midwife??"

Fis1, Dnm1, MAVS, maybe prohibitins... the list of mitochondrial proteins having roles in peroxisome function is increasing.

There is another new paper accepted in MCB (Impact factor 5.9) 

This paper establishes Hep27 as authentic mitochondrial protein but also somehow localized to nucleus. Interestingly, Hep27 has a putative PTS1 (TRL) and hence also predicted to be peroxisomal (Ref.). This type of targeting signal architecture does indeed regulate spatio-temporal distribution of proteins, since a protein with both N-terminal MTS and C-terminal PTS1 will get sorted to mitochondria first and since mature form lacks MTS the PTS1 can function for further peroxisomal sorting

Authors of the above MCB paper speculate whether mature mitochondrial Hep27 is transported to nucleus via peroxisomes by Mitochondria Derived Vesicles (see MDV-peroxisome paper in Current Biology).
If confirmed, this novel route of "Mitochondria --> Peroxisomes--> ER? --> Nucleus" might uncover unanticipated complexities than ever expected!!
since Hep27 is interacting with C-Myb (Proto-oncogene), Mdm2 and stabilizing p53, it will be under intense investigation in future.

Identification of Mitochondrial-derived Vesicles


P Rippstein,M Neuspiel,A Schauss,V Soubannier,E Braschi and HM McBride (2010).

Thursday, July 8, 2010

All yeasts are not equal.. The chromatin regulation differs for peroxisome genes.

Recent paper from PLoS Biology
The Role of Nucleosome Positioning in the Evolution of Gene Regulation
Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ (2010)
PLoS Biol 8(7): e1000414. doi:10.1371/journal.pbio.1000414

Following is the reproduction of peroxisome specific data and figures from the above paper.
The data is reproduced here for academic purposes of researchers interested in peroxisome research. 
The blog readers are thankful to PLoS publishers for providing the free access to the articles.

Peroxisome genes are highly expressed in D. hansenii, C. albicans, and Y. lipolytica, where they are packaged with long (but not deep) NFRs, despite no enrichment for Poly(dA:dT) tracts.


Changes in GRFs Contribute to Chromatin Divergence Between Species in Peroxisomal Genes
In some cases, the gain or loss of binding sites for GRFs can contribute to divergence in chromatin organization, coupled to phenotypic changes. Most notably, peroxisomal genes are associated with wider NFRs in Y. lipolytica, C. albicans, and D. hansenii, and shorter NFRs in subsequently divergent species (Figures 3E and S15F), but are not associated with intrinsic anti-nucleosomal poly(dA:dT) tracts in any of the 12 species. Instead, we find that these genes' promoters are enriched for PolyG and Rsc3/30-like sites in Y. lipolytica, C. albicans, and D. hansenii, but not in other species. This suggests an evolutionary scenario where either a Rsc-like motif or PolyG-based nucleosome depletion was the ancestral mechanism controlling peroxisomal genes, and was subsequently lost in the LCA of the clade spanning S. kluyverii and S. cerevisiae. This scenario is consistent with the higher expression of peroxisomal genes in Y. lipolytica (where peroxisomes are particularly central for carbon metabolism) and C. albicans (where peroxisomes play a key role in virulence).



(Note - I tried to understand the chromatin biology of peroxisome genes, but i need to read more about basic concepts. So I will come up with detailed article about this paper later..)

Tuesday, July 6, 2010

Future Event - 2010 SSIEM Annual Symposium

Society for the Study of Inborn Errors of Metabolism (SSIEM)
31st August - 3rd September 2010
Istanbul

Peroxisome related talks on 1st September 2010 (Wednesday)

11:00 – 11:15
New insights into quarternary structure of PEX26 point to potential alternative functions of this peroxin
A.S. Lotz, Germany

Plenary Session IV
16:30–17:00 -
Peroxisomal Disorders of Bile Acid Metabolism
Sacha Ferdinandusse, Amsterdam, The Netherlands

Monday, July 5, 2010

Peroxisome Abstracts from Future..

SEB Annual Main Meeting 2010
Clarion Congress Hotel, Prague, Czech Republic
30th June - 3rd July 2010

Peroxisome related abstracts in poster session

From the session - Plant Cell Biology: Cell Biology of Plant Defense http://www.sebiology.org/meetings/Prague/Abstracts/C5.pdf

Poster Session 1st July 2010 (Thursday) 17:00 – 19:00

C5.38 
Cross-kingdom characterization of peroxisomal ABC transporters
Xuebin Zhang (Rothamsted Research) et al. 
The authors have performed heterologous expression of mammalian ABC transporter proteins adrenoleukodystrophy protein (ALDP), ALD related protein, PMP70 and P70R which are properly sorted to peroxisomes(ALDP,ALDRP,PMP70) and ER(P70R) in plants(tobacco epidermis cells). They observed that Arabidopsis Pex19_1 can interact with both plant as well as human ABC proteins. The major observation by the authors is that disease causing mutant human ALDP proteins which are either degraded or mislocalized in human cells, are still properly targeted to peroxisomes in plants upon heterologous expression and are stable. 

C5.43
Novel chemical inhibitors provide fresh insights into peroxisome form and function 
Laura-Anne Brown (University of Leeds) et al. 
Different yet elegant approach is being used by Dr. Alison Baker group to gain better understanding of peroxisome biogenesis in plants. To overcome the limitations of lethality or redundancy in classical genetics approach, the authors are using chemical genetics approach to screen small molecule compounds which perturb peroxisome biogenesis by mislocalizing peroxisome directed GFP reporter. The authors have come up with two compounds, one being potent inhibitor of peroxisomal protein import while other inhibits peroxisomal β-oxidation. 

C5.44 
Dissecting the peroxisomal protein import pathway using novel small molecule probes 
Catherine O’Leary-Steele (University of Leeds) et al. 
Authors present the data about the chemical genetic screen for the compounds disturbing peroxisomal protein import in plants. Authors identified three small molecule inhibitors of peroxisomal import affecting both PTS1 as well as PTS2 proteins. Authors are optimizing these lead compounds to reduce the cytotoxicity, and finding the binding partners using surface Plasmon Resonance analysis. The efforts are also going to identify the interactors (peroxisome membrane fraction proteins) by pull down experiments and proteomics.