Newsletter - Faculty of Medicine, Nursing and Health Sciences ...

Newsletter
Department of Biochemistry and Molecular Biology
NEWS AND EVENTS
Discovery of an Archetypal Protein Transport System
in Bacterial Outer Membranes
Dr Joel Selkrig (Lithgow Lab) and colleagues
have discovered a novel protein transport
system, the translocation and assembly
module (TAM).
Joel summarised the discovery;
“Autotransporters are bacterial virulence
factors critical for the pathogenesis of many
organisms. Exactly how they are assembled
onto the bacterial cell surface remains
contentious. We discovered a novel protein
transport system, the TAM, found in most
sequenced gram-negative bacteria that’s
required for autotransporter biogenesis.
This discovery sheds new light on how autotransporters are assembled and
may provide a useful target at which to aim antibacterial therapies.”
Joel’s paper was discussed during the first 40 minutes of Microbe World’s
broadcast TWiM #31: Screen door on a submarine, link:
http://www.microbeworld.org/index.php?option=com_content&view=articl
e&id=1180:twim-31-screen-door-on-a-submarine&catid=107:this-week-inmicrobiology&Itemid=275
Joel Selkrig, Khedidja Mosbahi, Chaille T. Webb, Matthew J. Belousoff, Andrew J. Perry,
Timothy J. Wells , Faye Morris, Denisse L. Leyton, Makrina Totsika, Minh-Duy Phan, Nermin
Celik, Michelle Kelly, Clare Oates, Elizabeth L. Hartland, Roy M. Robins-Browne, Sri Harsha
Ramarathinam, Anthony W. Purcell, Mark A. Schembri, Richard A. Strugnell, Ian R. Henderson,
Daniel Walker and Trevor Lithgow. Discovery of an archetypal protein transport system in
bacterial outer membranes. Nat Struct Mol Biol. 2012
ABSTRACT: Bacteria have mechanisms to export proteins for diverse purposes,
including colonization of hosts and pathogenesis. A small number of archetypal
bacterial secretion machines have been found in several groups of bacteria
and mediate a fundamentally distinct secretion process. Perhaps erroneously,
proteins called ‘autotransporters’ have long been thought to be one of these
protein secretion systems. Mounting evidence suggests that autotransporters
might be substrates to be secreted, not an autonomous transporter system. We
have discovered a new translocation and assembly module (TAM) that promotes
efficient secretion of autotransporters in proteobacteria. Functional analysis of the
TAM in Citrobacter rodentium, Salmonella enterica and Escherichia coli showed
that it consists of an Omp85-family protein, TamA, in the outer membrane and
TamB in the inner membrane of diverse bacterial species. The discovery of the
TAM provides a new target for the development of therapies to inhibit colonization
by bacterial pathogens.
Seminars in May
Issue 22: April 2012
4 pm on Wednesdays in Building 13A,
Lecture Theatre M2
May 2nd
A/Prof Katharina Gaus (University of NSW)Insights
into the molecular mechanisms of early T cell
signalling
May 9th
Dr Kieran Harvey (PMCI)
The Hippo pathway: organ growth and cell-fate
choices
May 16th
Dr. Aleksandra Filipovska (WAIMR)
Regulation of the mitochondrial transcriptome
****************
Please send suggestions for future speakers to
committee members:
Travis Beddoe, Melanie Pritchard,
Martin Stone, Ana Traven, Catherine Itman,
Peter Boag
LATEST MEMBERS OF STAFF
Lab Head New Staff Member Position
Dr Lee Wong Lyn Chan RF
Dr Lee Wong James McGhie RA
New Biochem
webpage banner
photo.
See page 6
www.med.monash.edu.au/biochem

Prof Trevor Lithgow, an ARC Federation Fellow and Fellow of the Australian Academy of Science,
was asked what it takes to become independent and what research means for him.
Newsletter: April 2011, Issue 22
I completed my Honours (BSc) Degree and PhD in the Biochemistry Department at La Trobe University,
one of the two best Biochemistry Departments in the country. Before signing on for my PhD, I worked for
two years as a research assistant with Dick Wettenhall on ribosomal protein S6 and then took six months
off, back-packing around Europe and trying to decide whether science was the right career choice for
me. I learned many things as a postgraduate student, one of the most important was to never stay in
one place for too long. My PhD supervisors, Nick Hoogenraad and Peter Høj, often talked with us about
hothouse flowers, and insisted that the best move for a postdoctoral position was to go to the best place
you could find overseas. The second best move for a postdoctoral position was to move to the best place
you could find in Australia. There was no “third best” option that didn’t involve moving. So I read papers
all around a growing interest in protein targeting, to try and work out “the best place overseas” and in the
end settled on three options: Tom Silhavy’s lab at Princeton, Hugh Pelham’s lab at the LMB in Cambridge
or Gottfried Schatz’s lab at the Biozentrum in Basel.
In large part swayed by a beautiful study by Dietmar Vestweber who was a postdoc in the Schatz lab
[1]. I started a fax correspondence with Gottfried (Jeff) Schatz. Jeff was an Austrian who had spent his
postdoctoral time at several places in the United States (hence “Jeff”) and was the foundation professor of
Biochemistry at the University of Basel’s Biozentrum. With amazing foresight, the University had purpose
built the Biozentrum in 1971 to house its Departments of Biochemistry, Biophysics, Pharmacology and Cell
Biology and working there was a fabulous interdisciplinary experience, well ahead of “interdisciplinary”
becoming a buzz word. When I arrived in 1993, the Schatz lab had just experienced its first “golden
age” sketching out the basic principles of protein targeting into mitochondria (as told by Jeff) [2]. His new
generation of postdocs (there were ~12 of us in the lab at any given time over the years 1993-1995) had
big shoes to fill, and we were charged with determining the mechanisms that drove this protein import
pathway in mitochondria. I spent an intense and hugely rewarding time in Jeff’s lab, made some great
friends and still sometimes feel home-sick for Basel. I also learned a couple of things that I continue to pass
on to students and post-docs who work with me.
Firstly, Peter and Nick were right. Staying at La Trobe for my postdoctoral work would not have been a
good move. The Department is fabulous, but moving overseas to a different (fabulous) Department gave
me experience of things that I continue to draw on today. It forced me to “grow up” as a scientist and it
made me feel like a scientist – not a recently graduated student, not an apprentice in training, but part of
the international enterprise that is science. This will sound elitist, but science is an elite sport.
Living the dream in Europe also allowed me to drop any insecurities that I’d had about whether or not I
was as good as the postdocs that student-me had imagined working at places like Princeton, Cambridge
etc. We don’t talk about this much, but I suspect that many Australian students have a similar cultural
cringe, however unwarranted it is. You can tell yourself you’re as good as the best, other people can tell
you this, but if you want to be certain that your PhD really did bring you up to scratch - to an internationallycompetitive
standard of excellence - there is nothing like working for a few years shoulder to shoulder with
the best of your peers from around the world.
Department of Biochemistry and Molecular Biology
University of Basel’s Biozentrum
Gottfried Schatz, who elucidating the
biogenesis of mitochondria and was a
co-discoverer of mitochondrial DNA.
The experience in Basel also showed me the value of starting in a new area. I moved away from rats and the physiology/enzymology of my PhD to a
project bedded in yeast genetics. At that time, I had never seen a plate of yeast colonies and yeast genetics was as voodoo to me. But this was true
for all of the postdocs that Jeff recruited. Likewise, very few of the postdocs leaving his lab after their training continued to research the same biological
questions as in their postdoctoral project. Ben Glick, Sabine Rospert, Andreas Matouschek, Volker Haucke … all took what they learned in Basel and
started work on big, new questions when they moved back home.
Important too was a lesson on success (or otherwise) with grant and fellowship applications. It is all too easy, these days included, to be dismayed
by unfavourable outcomes. But chasing funding success should not be the driver for the work you will pursue or the approach you will take. I applied
for three Fellowships to work in Basel: an NHMRC C.J. Martin Fellowship, a HFSP Long-term Fellowship and an EMBO Postdoctoral award. I was
awarded the HFSP and EMBO Fellowships, published some pretty nice “research outcomes” and was ultimately awarded as one of the top ten
postdocs in the first ten years of the HFSP. I failed to get the CJ Martin Fellowship, on the grounds that the NHMRC panel saw a lack of feasibility for
success. The letter from the NHMRC was the first one I received and it was a hard knock to take. Many of us have had (and still have) many of these
letters; don’t let them sway you from your course.
Continued page 3
Page 2

Prof Trevor Lithgow continued
TJL lab, University of Melbourne, 2004
Front: Trevor, Dejan Bursac (WEHI),
Lena Burri (Aker BioMarine Antarctic),
Michael Dagley (McEwen Centre for
Regenerative Medicine, Toronto),
Katherine Vascotto (Nursing)
Rear: Nickie Chan (CalTech), Joanne
Hulett/Hildebrand (WEHI), Ian Gentle
(University of Freiburg).
TJL Lab 2012
Back: Victoria Hewitt, Miguel Shingu-
Vasquez, Chaille Webb, Hsin-Hui Shen
Front: Trevor Lithgow, Matthew Belousoff,
Denisse Leyton, Rhys Dunstan, Eva
Heinz
Trevor and his son, Maro.
CONTACT US:
Department of Biochemistry and Molecular Biology
Newsletter: April 2011, Issue 22
Jeff Schatz is one of the greatest advocates for teaching being part-and-parcel of research. He is famous for
his lecturing workload (and the undergraduates in Basel love him) and famous too for having occasionally
taken only a stick of chalk to scientific meetings for his plenary presentations. The years under his influence
left me inspired and in no doubt that a teaching and research position was the career choice for me. I returned
to Melbourne and, after a couple of years as a Level B Lecturer at La Trobe getting my first ARC grants to
start up my own laboratory, I took a Level C position at The University of Melbourne. When I arrived, the
University was planning the first inception of its Biomedical Sciences degree, and I was given the “opportunity”
of designing the curriculum for three new subjects and serving as coordinator (convenor) for all three. That sort
of workload should have been terrible for an ECR, but we rolled up our sleeves and ensured that three very
special subjects were created. The student feedback was always very positive, and my research ran in a way
that I was both happy with and proud of. I enjoyed the ten years that I spent at The University of Melbourne,
and I miss teaching.
Over that time the focus of research in my lab evolved from following the pathway by which relatively simple
“tail-anchored proteins”, like Bcl-2 and its cousins, are inserted into the mitochondrial outer membrane, to
looking at the assembly of more complex proteins of beta-barrel architecture. We identified and characterized
molecular machines that drive these processes and this, in turn, led to a growing awareness that the
molecular machines doing the job in mitochondria were inherited from the bacterial ancestors of these
organelles.
My move to our Department at Monash was made possible by an ARC Federation Fellowship awarded to
investigate the bacterial and mitochondrial machines in parallel: comparing the mitochondrial system and the
bacterial system for insight into evolution, for a better understanding of how they both function, and for any
sniff of practical applications that might flow from inhibiting this process in bacterial pathogens. Our research
effort is running really well, the team is smiling (pictured) and the facilities at Monash for this sort of work
are better than anywhere; I honestly don’t think our current research could be done so well anywhere else.
For me though, the best thing about the move to Monash was being part of the new Unit for Host-Pathogen
Molecular Biology; for the collegiality between the research groups and the “buzz” of so much exciting new
research. The Unit has recruited many new staff and students and has resulted in Monash securing new
grants and fellowships from the ARC, NHMRC and international sources. The other five group leaders are
ECRs and moved to Monash to start-up new laboratories. They have or are looking towards teaching and
research positions. They’ve come from training in the best labs around the world, with new ideas, new
research directions and new approaches to big, exciting questions ... stop me if you think that you’ve heard
this one before [3].
[1] Vestweber, D., Brunner, J., Baker, A. & Schatz, G. (1989) A 42K outer-membrane protein is a component
of the yeast mitochondrial protein
import site. Nature 341: 205-209
[2] Schatz, G. (2012) The fires of life. Annu. Rev. Biochem. 81 (in press)
[3] Morrisey & Marr, J. (1987) Strangeways here we come. Sire records
Prof Lithgow’s Webpage: http://www.med.monash.edu.au/biochem/staff/lithgow.html
Monash University, Ground Floor, Building 77, Wellington Road, Clayton VIC 3800 Australia
Website: www.med.monash.edu.au/biochem
Tel: +61 3 990 29400 Fax: +61 3 990 29500
Content and Layout: Yvonne.Dooley@monash.edu Photography: MNHS Multimedia Services
Department of Biochemistry and Molecular Biology
Page 3

POSTGRADUATE MATTERS
Faculty of Medicine Research Supervisor Accreditation Level 1
Workshops - Semester 1, 2012
Online Registration now open.
Accreditation is compulsory for:
• staff intending to supervise
• postgraduate research students (with more than 25% supervision load)
• all Honours student supervisors
Intending research supervisors need to complete a series of nine modules.
Approximately 80 per cent of the requirements of these nine modules can be covered by attendance to both of the Faculty’s Research
Supervisor Accreditation Training workshops.
You will need to have a mentor allocated to you by your department or centre before you may attend the workshop.
These workshops are run free of charge.
To apply for a place at the workshops, please register online
(please note, your Monash login details will be required):
http://www.mrgs.monash.edu.au/seminars/medicine/
*Registrations close Monday 4th June 2012
Please contact Phyllis Di Palma, (Research Degrees Office, Faculty of Medicine, Nursing & Health Sciences)
on ext 20047 or email Phyllis.DiPalma@monash.edu with any queries.
Dates and time of workshops
The accreditation program is split into 2 workshops (attendance to both workshops is required) for prospective supervisors (Monash
staff members only- your staff ID number will be required from all departments within the Faculty of Medicine, Nursing & Health
Sciences.
Workshop 1 - Friday 8th June 2012
Workshop 2 - Friday 15th June 2012
Registrations from 9.20am, with each workshop concluding around 12.45pm
Venue: S2 Lecture Theatre, Building 25
Environmental Sustainability At Monash
Anyone concerned with any environmental issues should
either contact:
Leigh Yang (li.yang@monash.edu)
or visit The Office of Environmental Sustainability (TOES)
http://www.fsd.monash.edu.au/environmental-sustainability.
STUDENT SOCIETY
Newsletter: April 2011, Issue 22 Department of Biochemistry and Molecular Biology
Necessary Outlets for Tertiary Doctoral Research Students
2012 Committee
The Student Society is still in the process of establishing a new
committee for this year. When this is finalised, their positions
and contact details will be published.
Page 4

INTRODUCING: Dr Ruby Law
Newsletter: April 2011, Issue 22
Background
I started my research career upon accepting a postgraduate scholarship in the Yeast Molecular Biology Group at
the Department of Biochemistry, Monash University, working under the supervision of Professors Rodney Devenish
and Phillip Nagley. This was hard-core molecular biology! My project was focused on the functional relocation of
mitochondrial genes into the nucleus to explore the feasibility of correcting hereditary mitochondrial gene mutations
causing diseases such as diabetes, muscle pain, deafness and blindness.
After leaving this exciting work, I went along to acquire more skills working in a number of biotechnology projects, one
of which was to produce the human glutamic acid decarboxylase GAD65 in the Autoimmunity Group lead by Professors
Merrill Rowley and Ian Mackay also in the Department of Biochemistry at Monash University. GAD65 is one of the
auto-antigens found in Type 1 Diabetes and Stiff Person Syndrome, and one of the key enzymes that produce gamma amino-butyric acid (GABA), a
neurotransmitter inhibitor in the CNS. Our aim was to generate large quantities of GAD65 protein for potential diagnostic development and therapeutic
applications. I had a fantastic time building the GAD protein production “factory” whilst juggling to raise our young family. I am still not sure which one was
more tricky.
After the GAD project, I decided to do something a little different – working on worms looked good. I was attracted to a parasite called liver fluke because
this parasite costs millions of dollars each year through loss of livestock production, stock deaths, human infections and costs of treatment and prevention.
More importantly its main effect is in poor rural communities where animals are their main source of income (e.g. Buffalo for meat, milk and to plough
their rice fields). For many years, detection of liver fluke infected livestock was not possible, especially in developing countries. I joined the Molecular
Parasitology Group led by Professor Terry Spithill, focused on expression and purification of fluke-proteins for the development of vaccines and diagnostic
kits for fluke infections. The project was very stimulating and I learnt lots about the areas of vaccine development and parasite immunology. Although we
didn’t develop a commercial vaccine and work is still ongoing, I was involved in the development of a diagnostic kit now used in Indonesia. This was very
satisfying and I continue to help out with this research in my spare time (which isn’t a lot!).
When my old boss picked up a new post in Canada as the director for the Centre for Host-Parasite Interactions at McGill University in 2003, Professor
James Whisstock had just started his new Structural Biology Group in the Department. He kindly invited me to join his laboratory and I moved back to the
“hard-core” research projects, firstly working part-time and then gradually full-time, and have been part of his laboratory ever since (some might say I have
become part of the Monash woodwork). It has been a fascinating experience from my point of view to see how he started with 2-3 people inside Professor
Rob Pike’s laboratory (with one power pack) to a large and fully equipped laboratory of more than 20 people. During this time I have again reinvented
myself, switching from a protein chemist to a structural biologist, thanks to James’s patience and understanding. During the past many years, James has
been a fantastic leader and mentor and I have learnt a lot and excitingly have been involved in several high impact publications. I have also been very
fortunate to work closely many extraordinary colleagues who were always ready to help and share ideas. I owe my special thanks to our very supportive
team of research assistants Adam Quek, Dharsh Jeevarajah and Gordon Lloyd, as well as those who have left the laboratory to develop their careers
further. Below are some of the exciting projects I am currently involved with in the Whisstock laboratory.
Projects
Fibrinolytic system: This work is funded by NHMRC in collaboration with A/Professor Paul Coughlin and Dr Anita Horvath from the Australian Blood
Disease Centre; and Drs Tom Caradoc-Davis and Nathan Cowieson from the Australian Synchrotron. Plasminogen is the zymogen form of plasmin and
is the most formidable protease in the plasma. It is responsible for the removal of blood clots (fibrinolysis) in the circulating system in order to maintain
the blood flow. As well as that, plasminogen can also bind to the surface of cells and become activated to plasmin, which breaks down the basement
membrane and extra-cellular matrix hence promotes cell migration and, in the case of cancer, cell invasion. We crystallized and determined the crystal
structure of plasminogen, and the results were recently published in Cell Reports (2012). The structure reveals how circulating plasminogen resists
activation until it binds to a fibrin clot or target cell surface. It also explains how pathogens (such as Streptococcus) hijack this potent plasma protease
during invasion. Our current focus is to understand the molecular interactions during plasminogen activation and plasmin inhibitions, especially in disease
conditions such as thrombosis and uncontrolled bleeding. We employ various techniques including mutagenesis, characterization of enzyme activities,
protein complex formation, X-ray crystallography and small angle X-ray scattering.
Structure and regulation of function of human glutamic decarboxylase (GAD): Gamma aminobutyric acid (GABA) produced by GAD is the most abundant
neurotransmitter inhibitor in the CNS and is critical for the control of movements, and neuroplasticity during development, learning and recovery from brain
damage. Neurological conditions, such as anxiety, autism and post-traumatic stress disorder, are closely related to the imbalance of GABA homeostasis.
This project is a continuation and expansion of my previous work on the GAD project with Professors Merrill Rowley and Ian Mackay. We published the
crystal structures of both GAD65 and GAD67 isoforms in Nature Structure and Molecular Biology (2007). We observed that the mechanism through which
GABA produced in mammals is regulated by a dynamic catalytic loop. The two isoforms of GAD cooperate to meet different physiological circumstances;
GAD67 is a housekeeping enzyme which maintains the basal level of GABA in the CNS and stably binds to the cofactor pyridoxal 5’ phosphate (as a holoenzyme),
whilst GAD65 switches between the apo and holo-form through a process called autoinactivation. The current project studies firstly, the structural
motifs involved in the autoinactivation and secondly, small molecules which can modulate the rate of GAD activity. These studies involve measuring
enzyme activity and using X-ray crystallography; with our outstanding research assistant turned PhD student Chris Langendorf being the key contributor
to this project. Our aim is to comprehensively understand the process of auto-inactivation and allosteric regulation of GAD, with the long term aim of
developing therapeutic treatments for GAD neurological diseases through the modulation of GAD activities.
Continued page 6
Department of Biochemistry and Molecular Biology
Page 5

Dr Ruby Law continued
Transmembrane pore formation in perforin: Perforin plays a critical role in the immune homeostasis and surveillance against viral infection and cancer cells
and deficiency is associated with impaired cytotoxic T-lymphocyte function. Perforin is a pore-forming MACPF protein (Membrane Attack Complex and
Perforin-like) stored as a soluble conformer in the cytoplasmic granules of natural killer cells and cytotoxic T-lymphocytes. Upon conjugation with targets
cells, perforin oligomerises and adopts a new conformation during pore formation. The perforin trans-membrane pores mediate the delivery of pro-apototic
granzymes which induce cytolysis. In collaboration with Professor Joe Trapani and Dr Ilia Voskoboinik from Peter MacCullum Cancer Research Institute,
we characterized the X-ray crystal structure of the monomeric perforin. At the same time Professor Helen Saibil’s group from Birkbeck College in London
determined the perforin monomer and pore structure by cryo-electron microscopy. Together we were able to model how perforin assembles on the surface
of the target cell upon formation of transmembrane pores; these results were published in Nature (2010). This publication is a very fulfilling outcome
following our previous paper (in collaboration with Dr Michelle Dunstone) published in Science (2007) describing for the first time that the MACPF proteins
including those found in the mammalian immunity defense system adopt the same fold as the bacterial cholesterol dependent cytolysins. Our current
objective is to understand at the molecular level how perforin binds to the cell membrane and forms pores on the surface of the target cells.
New Biochem Webpage Banner Photo
A montage depicting a model of the poxvirus immature particles combining EM and X-ray data
(Hyun et al, PLoS Pathogens, 2011).
The Achilles’ heel of poxviruses
Newsletter: April 2011, Issue 22
Department of Biochemistry and Molecular Biology
In April, the new landing page for the Biochem
website was released. All linked webpages are in
the process of being updated to the new format.
http://www.med.monash.edu.au/biochem/
Thanks are extended to Dr Fasseli Coulibaly, who
provided the current webpage banner photo
We would like to change the banner photo on a
regular basis. If you have photos that maintains
high res at 700 x 230pixels, please forward these
to yvonne.dooley@monahs.edu.
Poxviruses are among the largest viruses infecting humans and have a complex architecture that sets them apart in the virus world. They
produce infectious particles that, in contrast to most enveloped viruses, do not acquire their internal lipid membrane by budding through
cellular compartments. Instead, poxvirus immature virions are generated from atypical crescent-shaped precursors that appear to form
de novo in the cellular cytoplasm. Using a combination of X-ray crystallography and electron microscopy, we provided the first model of
the honeycomb scaffold at the surface of crescents and immature virions. This model establishes evolutionary links between poxviruses
and viruses infecting all kingdoms of life. Importantly, it also opens new avenues to develop assembly inhibitors as antivirals against
poxviruses that may emerge from an animal reservoir or be deliberately released.
Courtesy: Dr Fasseli Coulibaly
Research in the Coulibaly Laboratory
Spheroids: crystalline armours of poxviruses
Another aspect of our research focuses on in vivo crystals that represent the infectious form of
potential bioinsecticides including insect poxviruses. Virus particles are protected inside these
crystalline armours that are remarkably stable and persist in the environment like bacterial
spores. We use innovative X-ray microcrystallography to analyse crystals directly purified from
infected cells and elucidate the structure of the most complex of these crystalline armours.
Our research will contribute to engineering improved bioinsecticides and novel crystalline
microparticles for vaccination.
http://www.med.monash.edu.au/biochem/staff/coulibaly.html
Page 6

FIRST AIDERS & BREATHING APPARATUS
Reminder for all first aiders to update their training, and check their immunization status.
The Level 2 First Aid course is to be completed every 3 years,also a CPR Refresher/Anaphylaxis every other year.
Anyone interested in becoming a First Aider or a Breathing Apparatus volunteer for the department can send their request to the Safety
Officer Irene Hatzinisiriou or the Deputy Safety Officer Gavin Higgins.
OHS training sessions are subsidized by Monash OHS but you need to get the relevant approval and fund/cost centre numbers for the
Safety Officer before applying online.
Links to apply for the relevant training:
CPR Refresher:
http://www.adm.monash.edu.au/staff-development/ws/ohs/cpr-refresher.html
Level 2 First Aider (mixed mode):
http://www.adm.monash.edu.au/staff-development/ws/ohs/first-aid-mixedmode.html
Breathing Apparatus:
http://www.adm.monash.edu.au/staff-development/ws/ohs/breathing-apparatus.html
OHS MATTERS
1. Chemical Segregation
Compliance is required by Victorian State Government Legislation. This has been discussed for some months now and should be
completed by Easter 2012. However, there are some lab areas still working on their segregation, and hopefully we will endeavor to help
them complete this process by the end of May 2012 and no later!
Our Safety Officer Irene Hatzinisiriou and Deputy Safety Officer Gavin Higgins are available for consultation, guidance and assistance.
The SO and deputy SO will do a quick inspection in May 2012, to ensure that all labs have implemented and are maintaining the
segregation, as well to help out with any other related issues that may arise. If the SOs find that NO action has been taken. I will be
asking the relevant Lab Heads for a please explain and offering the complete removal of the relevant chemicals at the lab’s expense.
2. Leave and After Hours Policy
http://www.monash.edu.au/ohs/topics/procedures/after-hours.pdf
A. If on “leave” (conference, sick, annual etc) you should not be engaged in laboratory research at Monash as you are not covered for
insurance purposes and it is in breach of Workplace legislation.
B. Normal working hours are regarded as 8am-6pm Mon-Fri. If a protocol / procedure is deemed as high risk (such as liquid Nitrogen
handling, use of radioisotopes or primary sources of radiation, dangerous chemicals),it should only be carried out if approved by the
Supervisor and the Safety Officer with the requirement that a second suitably trained person is available to assist in the case of
emergency. Documentation must be kept to support the granting of such approvals.
Thank you for your assistance in meeting our obligations for these important matters.
QUICK OVERVIEW OF WHAT TO DO WHEN AN EMERGENCY ARISES:
1. Remain CALM…
2. Yell out for a First Aider (don’t go looking for one yourself, get someone else to go looking)
3. First Aiders: Read MSDS before treating any chemical injury
4. First Aiders: Call Med Centre if necessary ext. 53175
5. First Aiders: Call the Safety Officer and/or Safety Representative as soon as possible
Newsletter: April 2011, Issue 22 Department of Biochemistry and Molecular Biology
Page 7

SPOTLIGHT ON: Andrey Shubin
Background
After completing both a Bachelors and
Masters Degree in Chemical Technology
and Biotechnology at Moscow
State University of Fine Chemical
Technology, I was enrolled in a PhD
course in Biotechnology at the Institute
of Molecular Genetics of Russian
Academy of Sciences (IMG RAS). From
the beginning of my research activity I
have been working at the Laboratory of
Protein Engineering (IMG RAS) under
the supervision of Dr. Ilya Demidyuk.
The main objectives of investigation in
our laboratory are proteolytic enzymes;
with a core focus on their maturation
and activation pathways, mechanisms of
substrate recognition and functioning, as
well as possible applications of proteases
in medicine and industry.
My current PhD project considers
proteases as potential therapeutic agents
with the capability to induce death of
cancer cells. In the course of the project
we have found that one of the tested
enzymes - 3C protease of human hepatitis
A virus - has a prominent cytotoxic effect,
accompanied by massive cytoplasmic
vacuolation. Since the vacuolation might
result from the impairment of autophagy
pathway and could reflect a natural
role of the protease during infection, I
was interested in uncovering a deeper
characterisation of this effect. Luckily,
due to the Australia Awards Fellowship
Program, I have an excellent opportunity
to carry this out at the Yeast Laboratory
here at Monash University under the
supervision of Professor Rod Devenish.
Projects
All the research projects I participate
in are related to different aspects of
proteolytic enzyme functioning. One
of the investigations considers the
information value of expression profiling
of proprotein convertases (PC) and
matrix metalloprotease (MMP) genes in
malignant tissues of human lungs. The
key function of PC is processing and/
Newsletter: April 2011, Issue 22
or activation of numerous proteins and
peptides, many of which are associated
with malignant diseases. MMPs are
substrates of PCs and key factors in
tumor invasion and metastasis. Systems
of PCs and MMPs respond to malignant
transformation, which suggests their
expression status can be utilised as a
possible marker for cancer typing and
prognosis. The most interesting result of
the project obtained so far is evidence
that expression of PCs and MMPs genes
in human lung tumors changes in a limited
number of scenarios. These scenarios
are characterised by a sharp increase
in the expression level of a single PC
without significant changes in expression
of other proteases. We believe this result
reflects the different pathways of tumor
development and hope to confirm this
finding in other types of cancer.
Our laboratory is also focused on the
investigation of the roles of propeptides
in protease functioning. Most proteases
are synthesised as propeptide-containing
Department of Biochemistry and Molecular Biology
precursors. These structural elements
can determine folding of the cognate
protein, function as an inhibitor/activator
peptides, mediate enzyme sorting,
and the interaction of a protease with
other molecules and supramolecular
structures. Even minor changes in
propeptide structure can crucially alter
protein function in the living organism.
Modulatory activity coupled with
high variation allows one to consider
propeptides as specific evolutionary
modules that can transform biological
properties of proteases without significant
changes in the highly conserved catalytic
domains. As the considered properties of
propeptides are not unique to proteases,
propeptide-mediated evolution seems to
be a universal biological mechanism.
For our investigations, we use the
thermolysin-like M4 protease family
as an experimental model. We have
revealed that according to structure of
their propeptides, M4 proteases are
divided into two distinct groups, even
though the mature enzymes have largely
similar sequences. Proteases of the first
group have relatively long propeptides,
are known to act as intramolecular
chaperones and inhibitors of cognate
mature proteins. Proteins of the second
group have short propeptides and
resemble protealysin from Serratia
proteamaculans. We have obtained a
crystal structure of protealysin (which
was the first example of thermolysin-like
peptidase precursor crystal structure)
and revealed an inhibitor function of its
short propeptide. However, the existence
of two different groups of propeptides
makes one think that short propeptides
have other specific functions which are
still to be clarified.
In spite of our focus in the fields mentioned
above, we are always interested in
collaborations and new projects related to
different aspects of protease functioning
and keen to broaden our research
horizons.
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Newsletter: April 2011, Issue 22
RECENT PUBLICATIONS
Buckle, A.M., M.A. Bate, S. Androulakis, M. Cinquanta, J. Basquin, F. Bonneau, D.K. Chatterjee, D. Cittaro, S. Graslund, A. Gruszka,
R. Page, S. Suppmann, J.X. Wheeler, D. Agostini, M. Taussig, C.F. Taylor, S.P. Bottomley, A. Villaverde, and A. de Marco, Recombinant
protein quality evaluation: proposal for a minimal information standard. Stand Genomic Sci, 2011. 5(2): p. 195-197
Denton, A.E., R. Wesselingh, S. Gras, C. Guillonneau, M.R. Olson, J.D. Mintern, W. Zeng, D.C. Jackson, J. Rossjohn, 3P.D. Hodgkin,
P.C. Doherty, and S.J. Turner, Affinity thresholds for naive CD8+ CTL activation by peptides and engineered influenza A viruses. J
Immunol, 2011. 187(11): p. 5733-5744
Heinz, E. and T. Lithgow, Back to basics: A revealing secondary reduction of the mitochondrial protein import pathway in diverse
intracellular parasites. Biochim Biophys Acta, 2012 E-pub.
Knaupp, A.S. and S.P. Bottomley, Structural change in beta-sheet A of Z alpha(1)-antitrypsin is responsible for accelerated
polymerization and disease. J Mol Biol, 2011. 413(4): p. 888-98
Ou, L., D. Duan, J. Wu, E.C. Nice, and C. Huang, The Application of High-throughput siRNA Screening Technology to Study Host-
Pathogen Interactions. Comb Chem High Throughput Screen, 2012. 15(4): p. 299-205
Kinross, K.M., K.G. Montgomery, M. Kleinschmidt, P. Waring, I. Ivetac, A. Tikoo, M. Saad, L. Hare, V. Roh, T. Mantamadiotis, K.E.
Sheppard, G.L. Ryland, I.G. Campbell, K.L. Gorringe, J.G. Christensen, C. Cullinane, R.J. Hicks, R.B. Pearson, R.W. Johnstone, G.A.
McArthur, and W.A. Phillips, An activating Pik3ca mutation coupled with Pten loss is sufficient to initiate ovarian tumorigenesis in mice.
J Clin Invest, 2012. 122(2): p. 553-7
Pelosi, A., D. Smith, R. Brammananth, A. Topolska, H. Billman-Jacobe, P. Nagley, P.K. Crellin, and R.L. Coppel, Identification
of a Novel Gene Product That Promotes Survival of Mycobacterium smegmatis in Macrophages. PLoS One, 2012. 7(2): p. e31788
[MICRO,BCH]
Poreba, M., S. McGowan, T.S. Skinner-Adams, K.R. Trenholme, D.L. Gardiner, J.C. Whisstock, J. To, G.S. Salvesen, J.P. Dalton, and
M. Drag, Fingerprinting the Substrate Specificity of M1 and M17 Aminopeptidases of Human Malaria, Plasmodium falciparum. PLoS
One, 2012. 7(2): p. e31938
Rada, P., P. Dolezal, P.L. Jedelsky, D. Bursac, A.J. Perry, M. Sedinova, K. Smiskova, M. Novotny, N.C. Beltran, I. Hrdy, T. Lithgow, and
J. Tachezy, The core components of organelle biogenesis and membrane transport in the hydrogenosomes of Trichomonas vaginalis.
PLoS One, 2011. 6(9): p. e24428
Reantragoon, R., L. Kjer-Nielsen, O. Patel, Z. Chen, P.T. Illing, M. Bhati, L. Kostenko, M. Bharadwaj, B. Meehan, T.H. Hansen, D.I.
Godfrey, J. Rossjohn, and J. McCluskey, Structural insight into MR1-mediated recognition of the mucosal associated invariant T cell
receptor. J Exp Med, 2012. 209(4): p. 761-74
Tilkorn, D.J., E.M. Davies, E. Keramidaris, A.M. Dingle, Y.W. Gerrand, C.J. Taylor, X.L. Han, J.A. Palmer, A.J. Penington, C.A. Mitchell,
W.A. Morrison, G.J. Dusting, and G.M. Mitchell, The in vitro preconditioning of myoblasts to enhance subsequent survival in an in vivo
tissue engineering chamber model. Biomaterials, 2012. E-pub: p. 1-12
Wagstaff, K.M., H. Sivakumaran, S.M. Heaton, D. Harrich, and D.A. Jans, Ivermectin is a specific inhibitor of importin alpha/betamediated
nuclear import able to inhibit replication of HIV-1 and dengue virus. Biochem J, 2012. 443(3): p. 851-856
Wu, J., N. Xie, X. Zhao, E.C. Nice, and C. Huang, Dissection of aberrant GPCR signaling in tumorigenesis--a systems biology approach.
Cancer Genomics Proteomics, 2012. 9(1): p. 37-50
Yoga, Y.M., D.A. Traore, M. Sidiqi, C. Szeto, N.R. Pendini, A. Barker, P.J. Leedman, J.A. Wilce, and M.C. Wilce, Contribution of the
first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides. Nucleic Acids Res, 2012.
E-pub: p. 1-14
Zhou, Y., Y.S. Zhou, F. He, J. Song, and Z. Zhang, Can simple codon pair usage predict protein-protein interaction? Mol Biosyst, 2012.
E-pub
Department of Biochemistry and Molecular Biology
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