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INSIGHTS INTO BIOPLASTICS SYNTHESIS IN BACTERIA
27 July 2018 — Finally we have an idea how bioplastics are made in bacteria.
Many bacteria can produce a certain type of bioplastics, polyhydroxyalkanoates (PHAs), which the bacteria actually use to store carbon and energy. The key enzyme is the PHA synthase PhaC, which combines hydroxyalkanoate (HA) monomers into long PHA chains. PhaC had been studied since the 1980s, but its mechanism had been eluding scientists until now.
One way to understand how a protein functions is to determine its three-dimensional structure. Recently two PhaC structures had been determined for the first time, but unfortunately the structures were in a closed form — no tunnel was observed for the PHA chains to exit the enzyme — and hence the mechanism was still not fully revealed.
CCB's Structural Biology team then constructed a model of the PhaC enzyme from the bacterium Aquitalea sp. USM4, and successfully identified a three-branched channel that could serve as the entry for the HA monomers (blue) and exit for the PHA polymers (cyan in the figure above). Docking of a growing PHA chain into the catalytic site further suggested a unique elongation mechanism, which requires a ∼180° rotation of the monomer being added to the chain.
The properties of the PHA bioplastics — flexible, brittle, hard, etc — depend on the types and length of the HA monomers. For example, the PHA made up of the shortest monomer is brittle and stiff, but adding longer polymers increases its flexibility. Our model has also been able to explain how the PhaC enzyme recognizes monomers of different length.
With these fresh insights to further facilitate PhaC engineering, we hope we are now closer to designer bioplastics that can cater for our daily needs and, more importantly, also help reduce the pollution created by humans.
(Link valid until 17 September)
CENTRE FOR CHEMICAL BIOLOGY-MICROBIAL BIODIVERSITY LIBRARY (CCB-MBL) SERVICE
We are delighted to introduce Centre for Chemical Biology's microbial collection. The Centre for Chemical Biology Microbial Biodiversity Library (CCB-MBL) house a variety of microorganisms isolated from various natural habitats. These isolates are taxonomically supported by conventional identification methods. Visit the library's catalog (online) to view the collection. Contact us if you are keen to obtain isolates for your research/development or teaching.
ENVIRONMENTAL MICROBIOLOGY TEAM WON A GOLD MEDAL IN ITEX'18
Environmental microbiology team (Dr. Go Furusawa and Ms. Nur Hasyimah) participated in ITEX18 (International Invention, Innovation & Technology Exhibition) recently. Their invention, Bioflocculant AuDC, competed under the “Chemical” category. This innovation is an organic flocculant consisted of dead cells of a locally isolated marine bacteria. These cells can quickly remove organic particles, and selected heavy metals from water, making it a potential solution for wastewater treatment.
After evaluation by judges, the entry won a gold medal. A patent application based on this innovation is currently pending.
HEVEA’S FIRST GENOME DATABASE PAPER PUBLISHED
Dr. Lau Nyok Sean and Prof. Ahmad Sofiman Othman from CCB, together with Dr. Yuko Makita, Mika Kawashima and Prof. Minami Matsui from Riken have published a research article entitled “Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches” in BMC Genomics. A rubber tree genome and transcriptome database was constructed in the study. The database provides information including gene functional annotation, multi-transcriptome data of RNA-seq, full-length cDNA, PacBio isoform sequencing (Iso-Seq), expressed sequenced tags (ESTs) and cap analysis of gene expression (CAGE). The database will assist both researchers and breeders in using the Hevea brasiliensis genomic and transcriptomic information. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4333-y
VISIT OF DELEGATION FROM UNIVERSITAS PEMBANGUNAN PANCA BUDI (UNPAB)
23rd January 2018 – Centre for Chemical Biology (CCB) received a visit from 20 lecturers of Universitas Pembangunan Panca Budi (UNPAB), Indonesia. The objective of the visit was to build a relationship in research and higher education opportunities in Malaysia. Dr. Teh Aik Hong, CCB's lecturer, gave his welcoming remarks to the delegation members. He also presented an overview of CCB's research projects and promoted CCB's postgraduate intake programmes for 2018 to the visitors. The visit continued with a lab tour of CCB before they proceeded with a visit to the main campus of USM.
MICROBULBIFER AGGREGANS SP. NOV., ISOLATED FROM ESTUARINE SEDIMENT FROM A MANGROVE FOREST
Moh Tsu Horng, a MSc. student, Dr. Go Furusawa from CCB and Prof. Dr. Amirul Al-Ashraf Abdullah have published a research article entitled “Microbulbifer aggregans sp. nov., isolated from estuarine sediment from a mangrove forest” in International journal of Systematic and Evolutionary Microbiology. In this study, strain CCB-MM1 was isolated from estuarine mangrove sediment of Matang Mangrove Forest, Malaysia. 16S rRNA sequences of the strain exhibited 98.1~97.3% similarity to closely related species of the genus Microbulbifer. The Biolog profiles showed that the biochemical characteristics of the strain were different from that of the reference strains. Interestingly, strain CCB-MM1 showed robust cell aggregation and adhesion to the wall of the polypropylene tube in which the cell aggregation and adhesion were not observed in reference strains. These data indicate that strain ST2L12T represents a novel species of the genus Microbulbifer, for which the name Microbulbifer aggregans sp. nov. is proposed.
THIS IS HOW CCB TRAINS FUTURE SCIENTISTS!!
On the 16th of September 2017, Centre for Chemical Biology (CCB) launched the first roadshow for the Future Scientist Programme, at MyDin Bukit Mertajam, Pulau Pinang. This programme specifically trains kids to explore science through a variety of interesting hands-on experiments, like a scientist. We will have demonstrations of fun science experiments by our scientists, and also exciting hands-on sessions for the kids.
Our Future Scientists Programme is open to everyone aged 5 to 17 years old. We are eager to inspire more scientists! Contact amrinarosyada@usm (04-6535505) now to book your session or to inquire for more details.
GENOME OF MICROBULBIFER sp. CCB-MM1
Moh Tsu Horng , a MSc student alongside Dr. Lau Nyok Sean, Dr. Go Furusawa and Prof. Dr. Amirul Al-Ashraf Abdullah have published a research article titled “Complete genome sequence of Microbulbifer sp. CCB-MM1, a halophile isolated from Matang Mangrove Forest, Malaysia” in Standards in Genomic Sciences. The strain CCB-MM1 was isolated from an estuarine sediment sample taken from Matang Mangrove Forest, Malaysia. 16s rRNA shows the strain only shares 98.1% similarity to Microbulbifer rhizosphaerae Cs16bT. The one of unique features found of Microbulbifer sp. CCB-MM1 is that the bacteria has the ability to alter its shape depending on its growth cycle, cocci-shaped in growth phase upon reaching exponential phase the shape of the bacterium changes to a rod-shaped. This strain is also known to produce a secondary metabolite, ectoine, which has cell protectant and protein stabilizing properties. https://doi.org/10.1186/s40793-017-0248-0