Tuesday, July 26, 2011

Forthcoming Peroxisome meetings 2011

July 31 – August 2, 2011
Omaha, Nebraska

In Sex, Life, Development and Disease
August 7-12, 2011
University of New England
Biddeford, ME

8 August 2011, Monday  
9:10 am - 9:40 am                                                                   
Randy Schekman (UC Berkeley, USA)
"Mechanism of Sorting and Traffic of Peroxisomal Proteins from the ER"


satellite meeting to Plant Biology 2011
August 11, 2011
Hilton Minneapolis, Minneapolis, Minnesota, USA
17 talks, 21 posters and 42 registered researchers..
online registration is available till 11 August 2011 

FEBS workshop 2011
from algae to higher plants

Primošten, Croatia
31 August - 3 September 2011

Peroxisome related talks -
31 August  - Wednesday

12:00 –12:15
OEF18 is a novel calcium binding protein at peroxisomes and chloroplasts

14:00 –14:15
The PEX11 family: Deciphering a key player of peroxisomal proliferation

Saturday 10 September, 10:00 to 17:15
Part of the Special Interest symposia during EMBO meeting 2011 Vienna, Austria.
Organisation: Ida van der Klei, Marten Veenhuis
12 talks by European peroxisome researchers.

6-10 November 2011
Kumamoto, Japan

09 November 2011
09:00 - 09:30
Ralf Erdmann (Ruhr-Univ. Bochum, Germany)
Functional role of the yeast AAA-peroxins Pex1p and Pex6p in peroxisome biogenesis      
09:30 - 10:00
Yukio Fujiki (Kyushu Univ, Japan)
To be announced

Sunday, July 24, 2011

New player in ER-Peroxisome field

Peroxisomes proliferate by growth and division as well as they can arise de novo from Endoplasmic reticulum. In yeast, it was recently shown that most PMPs transit to peroxisomes via ER. In mammalian cells, Pex16 and Pex3 are known to target peroxisomes via ER. But the key players involved in this ER-peroxisome transport are still poorly known.

The new study published in PNAS identifies Sec16B as factor essential for Pex16 export from ER to peroxisomes. 
Yonekawa et al, Online published before print on 18 july 2011, PNAS

Sec16B(Sec16S) is a vertebrate specific isoform which is less extensively studied than the Sec61A(Sec16L). Comparing the sizes, Sec16B is almost half the size that of Sec16A and these proteins are able to form heteromeric complexes too.

This study found that, overexpression of Sec16B results in reduced number of peroxisomes and ER localization of Pex16 and Pex3. On the other hand, siRNA mediated knockdown of Sec16B results in tubulated peroxisomes, ER localization of pex16 and degradation of Pex3 by Ubiquitin proteasomal system. Authors also characterized different regions of Sec16B and found that C-terminal of Sec16B which differs from Sec16A, is required for its function in peroxisome biogenesis. Peroxisome vesicle formation from ER is known to be independent of COPII vesicle budding. Sec16A as well as Sec16B are involved formation of COPII vesicles and are targeted to ERES(ER Exit Sites). Authors meticulously shown that, stretch of Sec16B  responsible for its recruitment to ERES is not required for its peroxisome related function.

Further reading

PNAS, May 2011

PNAS, December 2011

BBA Mol Cell Research, in press

Sunday, April 17, 2011

New high impact articles - Novel family of stress-protective proteins and pexophagy

A novel family of dehydrin-like proteins is involved in stress response in the human fungal pathogen Aspergillus fumigates
Sak Hoi et al
MBoC in Press, published April 13, 2011
Authors identified two novel proteins DprA and DprB which are important for peroxisome functioning. Both of these proteins when fused to eGFP localize to peroxisomes and cytosol. Dpr mutants exhibit  altered catalase levels and impaired peroxisomal beta-oxidation.

Zutphen et al
Autophagy (Impact Factor - 6.829)
Volume 7, Issue 8   August 2011
Authors identified the massive peroxisome degradation process resembling both micro and macro-pexophagy using Pex3 fused with temperature sensitive degron sequence at N-terminus.

Wednesday, April 13, 2011

Latest peroxisome articles from high impact journal "The Plant Cell"

Two latest articles about plant peroxisomes from journal "The Plant Cell"
Impact Factor - 10.679

Identification of Novel Plant Peroxisomal Targeting Signals by a Combination of Machine Learning Methods and in Vivo Subcellular Targeting Analyses
Lingner T et al.
First Published on April 12, 2011

Arabidopsis ABERRANT PEROXISOME MORPHOLOGY9 Is a Peroxin That Recruits the PEX1-PEX6 Complex to Peroxisomes
Shino Goto et al.
First Published on April 12, 2011

Treat for the eyes

I thought of introducing an additional feature to this research blog by making it semi-informal.
I would extend the blogposts about peroxisomes with suitable interesting and sometimes non-scientific material like pictures suiting the mood of article or useful links, pictures, video etc.

Stunning photography by my friend Rakesh Chandode
"Beauty of plants"
Link to other galleries of eye-catching pics by Rakesh Chandode on National Geogrpahic

Saturday, April 2, 2011

Postdoctoral position at The University of Stavanger, Norway

Title of project - “Molecular analyses of peroxisome-mediated pathogen defense mechanisms in Arabidopsis
University of Stavanger
Faculty of Science and Technology,
Department of Mathematics and Natural Science,
The Centre for Organelle Research (CORE.)

Funding Agency - Norwegian Research Council (project 204822/F20)

Salary - NOK 448.400 per annum

Date of beginning fellowship - July 1, 2011

Closing date for applications - April 26th, 2011

Link -

Tuesday, March 29, 2011

A Novel micropexophagy specific protein 'Atg35' identified in Pichia pastoris

Atg35, a micropexophagy-specific protein that regulates micropexophagic apparatus formation in Pichia pastoris
Nazarko VY et al,
Autophagy, Volume 7, Issue 4,   April 2011, Pages 375 - 385

Pexophagy can occur by two distinct pathways termed as macropexophagy and micropexophagy. In Pichia pastoris, methanol to ethanol shift causes macropexophagy while methanol to glucose shift results in peroxisome degradation by micropexophagy.

During micropexophagy, peroxisome cluster is first step-wisely surrounded by engulfing vacuole and requires a specific component called micropexophagy apparatus (MIPA) for the complete engulfment and subsequent degradation.

Using Atg28 as a bait in Yeast two hybrid screen, Authors identified a novel protein Atg35 which is micropexophagy-specific and important for efficient MIPA formation. Overexpression or deletion of this protein abolished MIPA formation without affecting other autophagic pathways. It is also observed that Atg28 bridges the interaction between Atg17 and Atg35. Authors also characterized the novel site PNS (Perinuclear Structure) where Atg35 is recruited by Atg17.

More pexophagy related recent literature -

CCZ1, MON1 and YPT7 genes are involved in pexophagy, the Cvt pathway and non-specific macroautophagy in the methylotrophic yeast Pichia pastoris
Cell Biol Int. 2011 Feb

The phosphoinositide 3-kinase Vps34p is required for pexophagy in Saccharomyces cerevisiae
Biochem J. 2011 Jan

A yeast MAPK cascade regulates pexophagy but not other autophagy pathways
J Cell Biol. 2010 Apr

Saturday, March 26, 2011

Novel yeast Peroxin identified - Pex34

The Peroxin Pex34p Functions with the Pex11 Family of Peroxisomal Divisional Proteins to Regulate the Peroxisome Population in Yeast
Robert J. Tower, Andrei Fagarasanu, John D. Aitchison, and Richard A. Rachubinski
Molecular Biology of the Cell 2011, doi:10.1091/mbc.E11-01-0084

Authors have characterized the protein encoded by YCL056c gene. Currently the protein is annotated as "Protein of unknown function" in Saccharomyces Genome Database and described as green fluorescent protein (GFP)-fusion protein localizing to the cytoplasm in a punctate pattern. (schematic image from SGD)

Authors have renamed the protein as Pex34 which is an integral peroxisomal membrane protein. Pex34 is found to be positive regulator of peroxisome population under constitutive as well as inducing conditions. Pex34 deletion led to reduced number and enlarged peroxisomes whereas overexpression led to increased peroxisome number. Authors also found interaction of pex34 with itself and other Pex11 family peroxins using yest two hybrid analysis. Notably Pex34 interacts with Fis1 but not with Vps1.

Note - Recently Pex33 was identified from Neurospora crassa
Identification of PEX33, a novel component of the peroxisomal docking complex in the filamentous fungus Neurospora crassa
Managadze D et al.

Thursday, March 10, 2011

PhD position: Control of peroxisome abundance in metabolic diseases & cancer

Employer : Institute of Cell Biology, ETH Zurich, Switzerland
Website : http://www.cell.biol.ethz.ch
Last date of application : April 15, 2011

Interested applicants should email their CV, short statement of research interests(half page), and names of 2 referees by email to: Werner.kovacs@cell.biol.ethz.ch
Or by using Online application link

Our research interests are on the genetic and biochemical mechanisms underlying the control of peroxisome abundance in metabolic diseases and cancer. Peroxisomes are highly versatile and dynamic organelles whose number, size and function are vastly dependent on the cell type and growth conditions. The abundance of peroxisomes within a cell is dynamically controlled by environmental cues and (patho)physiological conditions. We apply a wide range of experimental cues technologies (e.g. live-cell imaging, RNAi-screening, functional genomics, proteomics, metabolomics) and model disease states in the mouse.

The successful candidate will be enrolled in the Ph.D. Program of the Life Science Zurich Graduate School. The position is located in Science City, the Life Science Campus of ETH Zurich. The research campus offers state-of-the-art facilities for advanced light and electron microscopy, high-throughput, image-based RNAi screening, quantitative proteomics, functional genomics, and computational analysis of large data-sets.

For further scientific information please contact: werner.kovacs@cell.biol.ethz.ch (http://www.cell.biol.ethz.ch/research/krek/group_members/kovacsw/index).

Dr. Werner Kovacs
ETH Zürich
Institute of Cell Biology
Schafmattstrasse 18, HPM F39
CH-8093 Zürich, Switzerland

Tuesday, March 8, 2011

New Paper - Study on Pex5 ancillary binding site for SCP2

The Peroxisomal Targeting Signal 1 in sterol carrier protein 2 is autonomous and essential for receptor recognition
Williams CP et al.
BMC Biochemistry 2011, 12:12
Published: 4 March 2011
Brief Summary - Authors studied the second, ancillary receptor-cargo binding site in Pex5 for the PTS1 protein SCP2 distinct from the PTS1 itself. Point mutation in Pex5 were done to check the effects on Pex5-SCP2 binding which was found to be moderately reduced in binding assays but the effect was not visible using in vivo localisation assays. Authors conclude that the second binding site in Pex5 is not essential for at least SCP2 indicating PTS1 is alone sufficient for its peroxisomal targeting.

Mutations within the ancillary SCP2 binding site of Pex5p do not impair peroxisomal import

PTS1 of SCP2 is essential and sufficient for peroxisomal targeting

(Thanks to Biomedcentral BMC, Open Access Publisher for the open access policy)

Monday, January 24, 2011

2012 Peroxisome talks

Keystone Symposia 
Cell Biology of Virus Entry, Replication and Pathogenesis
March 26 - 31, 2012

March 30, Friday
Talk - 
Peroxisomes, MAVS and Innate Immunity
Jonathan C. Kagan, Boston Children's Hospital, USA 

Link - http://www.keystonesymposia.org/Meetings/ViewMeetings.cfm?MeetingID=1167

Monday, January 10, 2011

Peroxisome related events in 2011

EMBO Conference
Protein Transport Systems
Structures, mechanisms and medical aspects
16 - 20.04.2011, Santa Margherita di Pula, Italy

20:30 - 21:00
Ralf Erdmann
The peroxisomal protein import machinery

17:00 - 17:30
Adabella van der Zan
lluminating the peroxisomal biogenesis pathway

9th international conference on AAA proteins
6-10 November 2011, Kumamoto Japan

9 November 2011
09:00 - 09:30
Ralf Erdmann (Ruhr-Univ. Bochum, Germany)
Functional role of the yeast AAA-peroxins Pex1p and Pex6p in peroxisome biogenesis

09:30 - 10:00
Yukio Fujiki (Kyushu Univ, Japan)
To be announced

Sunday, January 9, 2011

Peroxisomes - Alzheimer's Disease and Hepatitis

Hepatitis B Virus Regulatory HBx Protein Binds to Adaptor Protein IPS-1 and Inhibits the Activation of Beta Interferon
Journal of Virology, January 2011
Kumar M et al.
From the group of Prof. B. L. Slagle
Baylor College of Medicine, Texas
Brief Description -
IPS1 is also known as MAVS (mitochondrial antiviral signaling) protein. Last year it was discovered that MAVS subpopulation also resides on peroxisomes and is responsible for rapid but transient type I-interferon independent antiviral gene expression(Dixit et al, Cell, 2009). It was known that Hepatitis A and Hepatitis C viral proteins target IPS1 to inactivate host innate immune response. This paper establishes that Hepatitis B viral protein HBx also modulates host signalling by targeting IPS1. Since IPS1 also resides on peroxisomes, there arises the possibility of HBV acting at this organelle.

Plasmalogen synthesis is regulated via alkyl-dihydroxyacetonephosphate-synthase (AGPS) by amyloid precursor protein (APP) processing and is affected in Alzheimer’s disease
Grimm et al.
Journal of Neurochemistry, January 2011 (Accepted Article)
Brief Description -
Alkyl-dihydroxyacetonephosphate-Synthase (AGPS) is a PTS2 containing peroxisomal protein involved in ether lipid biosynthesis. Plasmalogen synthesis is also defective in PBDs (Peroxisome Biogenesis Disorders). This paper shows that APP protein in Alzheimer disease regulates AGPS.