Saturday, June 26, 2010

Notable Peroxisome articles of the week

This is the list of most recent peroxisome related articles accepted in different journals last week.
  1. Axonal integrity in the absence of functional peroxisomes from projection neurons and astrocytes
    Journal - Glia (Impact Factor - 5.6)
    Authors - Astrid Bottelbergs et al. (Myriam Baes Group)
    Brief Description - Studies on neuronal cells from Pex5 knockout mice

  2. Peroxisomes in zebrafish: distribution pattern and knockdown studies
    Journal - Histochemistry and Cell Biology (Impact Factor - 2.32)
    Authors - Krysko O et al. (Myriam Baes Group)

  3. Identification of a substrate-binding site in a peroxisomal β-oxidation enzyme by photoaffinity labeling with a novel palmitoyl derivative
    Journal - JBC (Impact Factor - 5.3)
    Authors - Kashiwayama Y et el. (Tsuneo Imanaka Group)

  4. A Mutation in the Mitochondrial Fission Gene Dnm1l Leads to Cardiomyopathy
    Journal - PLoS Genetics (Impact Factor - 9.5)
    Authors - Ashrafia H. et al (T. Neil Dear group, Leeds, UK)
    Brief Description - Python (Dnm1l, Dynamin 1 like protein) mutation directly involved in morphological impairment of mitochondria and peroxisomes, leading to heart disease (dilated cardiomyopathy)

Friday, June 25, 2010

Role of Peroxisomes in Dengue response

The recent paper in PLoS NTD caught my attention since Pex14 and Pex13 are reported to be among 273 “Common Dengue Response genes” which are up-regulated in Dengue virus infections. So I thought of having a closer look into the microarray data and I fished out peroxisomal genes that are up or down-regulated in Dengue infection.

Citation -
Loke P, Hammond SN, Leung JM, Kim CC, Batra S, et al. (2010)
PLoS Negl Trop Dis 4(6): e710. doi:10.1371/journal.pntd.0000710

(Kindly note that authors report vast microarray data, but I am discussing only about peroxisome specific genes in this post. Please consult the original paper for other details and proper context)


Dengue Virus (DENV) is single stranded RNA virus transmitted to human by mosquito Aedes aegypti. Dengue viral infection elicits wide spectrum of clinical manifestations. The authors performed transcriptional profiling of patient samples and found that there is distinct transcriptional profile associated with each clinical outcome.

*  DF    - Dengue Fever
*  DHF - Dengue Hemorrhagic Fever
*  DSS  - Dengue Shock Syndrome

Peroxins/Peroxisomal proteins significantly up/down regulated in Dengue infections

It should be noted that Pxmp2, the peroxisomal integral membrane protein is up-regulated in all Dengue clinical outcomes. So I will discuss about Pxmp2 in detail.

Confusion between PMP22 and Pxmp2

Pxmp2 is a peroxisomal multipass integral membrane protein which is highly expressed in tissues like liver, heart and kidney. Another peroxisomal membrane protein PMP70 is now known as Pxmp1. Since size of Pxmp2 is 22kD, it was also known as PMP22. But currently, PMP22 is official name of Peripheral Myelin Protein which is totally unrelated to Pxmp2.

Pxmp2 carries two distinct peroxisomal targeting signals, one in each N-terminal and C-terminal domain, both of which interact with Pex19 and get sorted to peroxisome membrane. Pxmp2 is the first peroxisomal protein experimentally shown to be a channel forming protein by Hiltunen group (Rokka et al). It is speculated by the authors that since Pxmp2 channel is open for longer times, it might allow non-specific small molecule transport.

Figure 1 from the paper of Rokka et al. (Compare the electron density between two)

Friday, June 18, 2010

Crispy Hot Peroxisome Papers.. Fresh from the oven of science.

Peroxisomes in zebrafish: distribution pattern and knockdown studies

Histochem Cell Biol. 2010 Jun 17. [Epub ahead of print]
by the group of M. Baes at Katholieke Universiteit Leuven, Belgium

Abstract - (from Pubmed)
          Peroxisomes are organelles that are essential for normal development in men and mice. In order to explore whether zebrafish could be used as a model system to study the role of peroxisomes, we examined their distribution pattern in developing and adult zebrafish and we tested different approaches to eliminate them during the first days after fertilization. In 4-day-old embryos, catalase-containing peroxisomes were obvious in the liver, the pronephric duct and the wall of the yolk sac, but transcripts for peroxisomal matrix and membrane proteins were also detected in the head region from 24 h post-fertilization. In adult zebrafish, catalase-containing peroxisomes remained prominent in the hepatocytes, the renal proximal tubules and the intestinal epithelium. Several peroxins, essential proteins for the biogenesis of peroxisomes, were targeted using knockdown approaches. Two morpholinos, blocking, respectively, splice sites in pex3 and pex13, only induced a short in frame deletion or insertion in the transcripts and did not result in the elimination of peroxisomes after injection into one-cell embryos. A morpholino blocking translation of pex13 was able to reduce the number of peroxisomes to variable extents. Finally, overexpression of a potential dominant negative fragment of Pex3p did not result in deletion of peroxisomes from developing zebrafish. 
We conclude that in zebrafish 
(1) peroxisomes, as visualized by DAB cytochemistry for catalase activity, are most conspicuous in the liver and renal tubular epithelium; this pattern is reminiscent of peroxisome occurrence in mammalian organs
(2) our approaches to eliminate these organelles during development by targeting peroxins were not successful.



New Review accepted in Journal of Lipid Research (JLR)
Biochemistry and genetics of inherited disorders of peroxisomal fatty acid metabolism
Paul P. Van Veldhoven
K.U.Leuven, Belgium

Monday, June 14, 2010

AOP (Advance Online Post)

Dear Researchers,

Its getting exciting each time.
My exercise of reading every bits and pieces of current peroxisome literature, has led me to know very interesting features of peroxisomes. I can bet that you wont get to know them anywhere else in one place but here..!

I would be researching more information on these topics and post on the blog in coming weeks
  1. Peroxisome fields in Deepest sea basin.! 
  2. How an organism uses extensive peroxisome network to survive in toxic sulfide rich but oxygen depleted environment of the deep sea basin. (surprisingly, the same peroxisome network is absent when they are grown in oxygen rich conditions... time to rethink our notion that peroxisomes evolved for aerobic life!)

  3. Crystal structure of peroxisome?
  4. Alcohol oxidase and urate oxidase are widely known for forming crystalloid cores in yeast and humans respectively. Catalase was never thought to do so. But recent discovery of catalase cores in plants surviving in extreme cold environment and protozoans living in anoxic deep sea basins... Does peroxisome play structural role and not just metabolic one?

  5. Going to the roots of symbiosis
  6. Legume plants fix nitrogen using symbiotic association with rhizobia. The establishment of this symbiosis is regulated by complex host-symbiont signalling. The missing links in this cascade and involvement of peroxisomes is emerging..!

Saturday, June 12, 2010

Ubiquitination Unplugged

Of various post-translational modifications, multi-faceted roles of Ubiquitination are being uncovered in recent years. Ubiquitination had once became synonymous with proteasomal degradation in eukaryotes. But two discoveries marked departure from this notion. One was the identification of Prokaryotic Ubiquitin-like protein (Pup) and the equivalent process termed Pupylation. Second discovery was that Ubiquitin conjugation can indeed modulate cellular signalling apart from proteasomal degradation.

In case of peroxisomes, Ubiquitination process is exploited by the cell to exert quality control as well as recycling of some peroxins for import cycles. Pex5 was the first peroxin shown to be mono or polyubiquitinated for different purposes. Pex4 mediated monoubiquitination marks Pex5 for recycling the receptor for next round of import. Whereas if the Pex5 is no longer functional or has stuck in the membrane, Ubc4 dependant polyubiquitination primes Pex5 for proteasomal degradation. (Ref.)
Pex7 is the cognate receptor for PTS2 containing proteins but requires auxiliary proteins(co-receptors) Pex18, Pex21 or Pex20 in yeasts. These co-receptors are functionally equivalent to N-terminal part of Pex5 involved in peroxisomal docking and recycling. Pex18 is constitutively degraded via polyubiquitination and seems not to be recycled unlike Pex5. Pex20 is also polyubitinated and signals the degradation.

What are common misconceptions

Monoubiquitination means one Ubiquitin?
Yes, but Pex5 can be ubiquitinated at more than one amino acid residue using single Ubiquitin moiety. While polyubiquitination indicates attachment of Ubiquitin chain of at least 4 Ub molecules.

Lysine residues in a protein are the only site for Ubiquitination?
Not in all cases. At least for mammalian Pex5, unconventionally Cysteine residue is also utilized for ubiquitination.

Polyubiquitination is the signal only for proteasomal degradation?
NO.! 
K48-linked polyUb chains do signal for proteasomal degradation. But Ubiquitin has seven lysine residues and in a stunning observation made by Peng J. et al that all Lysine residues can be utilized for this “Atypical” chain formation and K63-linked Poly-Ub chains are emerging as regulator of diverse processes unlike proteasomal degradation via K48-chains



Recent CELL paper by Zeng et al. titled “Reconstitution of the RIG-I Pathway Reveals a Signaling Role of Unanchored Polyubiquitin Chains in Innate Immunity”, makes staggering discoveries.
First is that, K63-linked polyubiquitin chains have important functional role. And most interestingly, that these chains need not be conjugated to a protein, but can associate through protein interaction domains. The authors show for the first time that free poly-Ubiquitin chains in the cytosol can directly associate with a cytosolic protein without being conjugated by isopeptide bond and modulate cell signalling. The Unanchored K63-ubiquitin chains in the cytosol were found to activate RIG-I which detects RNA viruses and signals antiviral response through MAVS.

CAspase Recruitment Domain (CARD) is the hallmark feature of RIG-I family members and MAVS. CARD domains of RIG-I interact with unanchored K63-Ub chains leading to RIG-I activation. The activated RIG-I in turn interacts with Mitochondrial MAVS leading to activation of downstream targets. It was also demonstrated by the authors that CARD domain of MAVS is not ubiquitinated unlike RIG-I.

Though this discovery is of general scientific interest,
Why it would be interesting for peroxisome researchers?

In another recent paper in CELL by Dixit et al. titled “Peroxisomes Are Signaling Platforms for Antiviral Innate Immunity”, it was unequivocally established that MAVS resides not only on mitochondria but also on peroxisomes. Surprisingly peroxisome localized MAVS elicits rapid but transient antiviral response in the form of activation of ISG (Interferon Stimulated Genes), albeit independent of type I-interferon. This downstream cascade differs from that of MAVS localized on mitochondria!!! How same protein (MAVS) residing on two different organelles induce entirely different downstream signalling cascade remains unknown.


I propose some possible hypothetical explanations


- It will be interesting to know whether peroxisome localized MAVS also requires activation of RIG-I by K63-branched PolyUb or not. It might be possible that viral RNA-RIG complex could somehow directly activate MAVS on peroxisomes. Whereas sustained Mitochondrial MAVS might require stable association of RIG-I and K63-Ub chains.

- Possibly other peroxisomal components are involved. maybe peroxisomal membrane proteins?
Trans-membrane domain of MAVS is essential for its self-association as well as functionality. But It could be replaced by TM from other membrane proteins such as Bcl-xl. This indicates that TM domain of MAVS can interact not only with itself but with TM of other membrane proteins. And this fact can give rise to differences in downstream cascade.

- Does Peroxisome motility an important factor determining rapid response by peroxisomal MAVS?
Peroxisomes exhibit dynamic cytoskeleton dependant movement within the cytoplasm. Mitochondria also show such motility but peroxisomes are faster..!

The information from above two CELL papers can be summarized in this representative figure. 
Some things remain unknown (Question mark) 



Coming back to fascinating ubiquitins, there is an excellent review in SCIENCE titled “Anchors Away for Ubiquitin Chains” which discusses the Zeng et al paper and speculates whether the Unanchored polyUb chains are involved in more pathways other than RIG-I-MAVS in innate immunity… (And in case of our interest, in peroxisome biogenesis!).

To close the topic on a high note, It must be noted that K11-linked Ub chains are as abundant as K63 ones in S.cereviseae, yet their function is not even remotely known. And interestingly even branched PolyUb chains containing multiple K-linkages in a single chain have also been discovered….

Thus the complexity heightens so does the Curiosity!!

Friday, June 11, 2010

Listen to what plants say...

American Society for Plant Biologists.
31 July - 4 August
Montrèal, Canada

Following is the collection of Peroxisome related talks and posters from this future event


- Talks -

Minisymposium - Organelle Biology
3 Aug 2010, 9:20AM
Kyaw Aung (Student of Jianping Hu lab, Michigan state uni.)
An Arabidopsis C-terminal tail-anchored protein in peroxisomal and mitochondrial division and positioning.
Authors have identified a novel Plant specific protein, Peroxisomal and Mitochondrial Division Factor1 (PMD1) which is C-terminally tail anchored on outer membrane of peroxisomes and mitochondria whereas N-terminus contains four coiled-coil domains. PMD1 Null mutant contains enlarged peroxisomes and elongated mitochondria whereas over-expression leads to aggregated peroxisomes and mitochondria.  Since PMD1 did not interact with Pex11, Fis1 and Drp3, it is speculated that PMD1 follows completely novel pathway in organelle maintenance.


Minisymposium 19. Enzyme Structure & Function
3 Aug 2010 10:40 M
Acyl CoA oxidase catalyse first step in peroxisomal fatty acid beta-oxidation. The authors have studied different acx mutants and characterized the biochemical activities and respective phenotypes.

- Posters -

Indole-3- Butyric Acid response mutant 3: Dehydrogenase in the Peroxisome?
Robert Barlow (Bethany K. Zolman Lab)
Indole-3-Acetic Acid (IAA) is a plant hormone. Authors observed that conversion of Indole-3-butyric Acid (IBA) to IAA occurs in peroxisomes in a process resembling fatty acid beta oxidation. Authors identified in screen, IBR3, a protein having Acyl CoA dehydrogenase activity as well as aminoglycoside phosphotransferase domain and peroxisomal targeting signal.

Rapid organelle responses to reactive oxygen species
Jaideep Mathur
The authors have characterized morphological changes in peroxisomes and mitochondria in response to ROS stress. Peroxules and matrixules are tubular extentions of peroxisome and mitochondria. Photo-convertible EosFP PTS1 was used to study peroxisome morphology and dynamics. Prolonged ROS stress causes peroxule and matrixule inhibition and leads to asynchronous, asymmetric fission mediated organelle division.

Systemic phenotypic analysis of mutants of novel peroxisomal genes in Arabidopsis
Gaëlle Cassin (Post-doc in Jianping Hu Lab)
Authors have identified over 50 Arabidopsis peroxisomal proteins by proteomics and bioinformatics approach. Authors will present the characterization of T-DNA insertion mutants of these genes and their biochemical and phenotypic outcomes.

Suppression of peroxisome biogenesis factor 10 reduces cuticular wax accumulation by disrupting the ER network in Arabidopsis thaliana.
Kamigaki Akane
Pex10 RNAi in Arabidopsis leads to defects in ER morphology, cytosolic mislocalization of ER resident proteins involved in wax biosynthesis CER1, CER4, WAX2. (The paper is already published in Plant and Cell Physiol., interestingly this seems first and sole report of Pex10 affecting ER.)

Transcriptome Analysis Reveals the Involvement of Genes from Different Metabolic Pathways during Adventitious Root Formation (ARF) in Petunia
Amirhossein Ahkami
I found the abstract very interesting. Adventitious roots are essential for establishing new plantlet from parts cut from mother plant. Transcritome analysis identified more than 3500 genes significantly induced in various phases of ARF. Activation of peroxisomal beta oxidation was observed by authors and speculated to be involved in lipid catabolism and plant hormones like Jasmonic acid and IAA.

Isotopic Signature of Photorespiration
Dianne Pater
Authors are characterizing stoichiometric changes in CO2 release and O2 uptake in Peroxisomal malate dehydrogenase (PMDH) mutants as well as from Wild type.

Saturday, June 5, 2010

Challenges for peroxisome research in coming decades

  • Taking translation to the Peroxisomal membrane.
  • Conclusive proof (or lack thereof) for peroxisome evolution from endosymbiont.
  • Visualization of peroxisome protein translocation event.
  • Pathogen strategies to subvert immune response originating from host peroxisome. 
  • PTS3 - Type 3 Consensus sequence for Peroxisomal proteins??
(Detailed article in preparation)

Thursday, June 3, 2010

The life of peroxisome.. (My Birthday Post)

Exactly one year before, I was at home celebrating my most memorable Birthday ever. ALL cousins, uncles, aunts were present at my home on my last birthday which was a rarest event in my life. One year has passed since, now I am in Germany, with not even a single relative or friend around today. But still I am not feeling alone. I have someone special to accompany me in the loneliness and Its a great company. There seems to be an eternal bond formed between me and my friend, Peroxisome!!!

I was wondering what to do today, since the university as well as city was closed due to a public holiday. I thought why not write a special post about peroxisome..

Brief timeline

1954 - First description of cytoplasmic organelle Microbody by J.rhodin
1964 - “Principles of Tissue fractionation” authored by de Duve.
1974 - The Nobel Prize in Physiology or Medicine.
            Albert Claude, Christian de Duve, George E. Palade
            "for their discoveries concerning the structural and functional organization of the cell"
1984 (3rd June) - My Birthday (highly insignificant event!)

What’s special about peroxisomes?
I initially started working with glycosomes from trypanosomes. Glycosomes are related to peroxisomes but derive their name after glycolysis which is compartmentalized in glycosomes as opposed to glycolysis occurring in cytoplasm of all other eukaryotes.

I got a chance to work in peroxisome research group at Ruhr-University Bochum with my DAAD short term fellowship. I started reading more about peroxisomes which attracted me further and further towards peroxisomes. I felt so passionate about this organelle, that I decided to quit my PhD in India and stay in peroxisome research. I started writing weekly review of new peroxisome related papers for our group. And now I made it into a Scientific Blog "Peroxisome-Research"  (http://peroxisome-research.blogspot.com)

What makes peroxisome my beloved entity is its unique features and our limited understanding of them. It is still a debate whether peroxisome is endosymbiont in origin or just an extension of endomembrane system. Many people consider peroxisome is not just an organelle for free radical detoxification or fatty acid metabolism. It’s the same place where fireflies produce wonderful light. Peroxisomes are shown to be involved in immunity in human as well as in plants very recently (1,2). More intriguing is the protein transport across the peroxisome membrane in folded active form. Now it has been proved that receptor protein can form transient channels to allow such folded protein transport(3). But still peroxisome membrane is synonymous with a giant wall which can allow elephant(Oligomeric protein) to pass through it, yet restrict ants(for e.g. small metabolites)!.

Peroxisome talk with other organelles. Ranging from ER, mitochondria, chloroplast to lipid droplets..(4,5,6,7) Peroxisomes can swim in the cytosol (8), signal the cell through peroxide, NO or calcium (9,10,11) and so on. Peroxisomes can arise from ER, rely on fission for proliferation and they die by pexophagy (12,13,14).

The peroxisome is still like a bunch of mysteries for me. Every time I read a new paper about peroxisome, I feel that those mysteries are unfolding. Something that doesn’t let you sleep and keeps dreaming about it, that is the passion which I feel about peroxisomes. And I would love to live with this passion about peroxisomes for coming years, unfold some mysteries on my own and celebrate my Birthdays with them!!