Natural Product Biology

NG Siew Bee
Senior Principal Investigator

GOH Qi Yun Falicia, MUNUSAMY Madhaiyan Senior Post-Doctoral Research Fellows

THAPPETA Kishore Reddy V, Yudistira SARWONO Albertus Eka Post-Doctoral Research Fellow

CRASTA Sharon Research Manager

LEONG Chung Yan, NG Wee Pin Veronica, TAN Yi Qi Zann, TAN Qiu Ning Serene, CHANG Mun Leng Amanda, CHAN Kar Yarn Grace, LEE Shi Min Michele, Shahul Hameed Nazihah Beevi Research Associates

GAKUUBI Martin Muthee PhD Student

NG Siew Bee
Senior Principal Investigator

GROUP MEMBERS:

GOH Qi Yun Falicia, MUNUSAMY Madhaiyan
Senior Post-Doctoral Research Fellows

THAPPETA Kishore Reddy V, Yudistira SARWONO Albertus Eka
Post-Doctoral Research Fellow

CRASTA Sharon
Research Manager

LEONG Chung Yan, NG Wee Pin Veronica, TAN Yi Qi Zann, TAN Qiu Ning Serene, CHANG Mun Leng Amanda, CHAN Kar Yarn Grace, LEE Shi Min Michele, Shahul Hameed Nazihah Beevi
Research Associates

GAKUUBI Martin Muthee
PhD Student

Our group study the biology of natural products, in particular how they are made and what are their effects on biological systems. To this end we develop and implement biochemical and cellular assays to screen organic extracts derived from plants, fungal fruiting bodies and fermentates of microorganisms, for the discovery of naturally occurring bioactive secondary metabolites. Once an interesting and novel bioactive compound has been isolated and its structure elucidated we will identify and study its biosynthetic pathway. We also investigate methods to turn on the expression of secondary metabolite biosynthetic gene clusters that are cryptic under standard laboratory growth conditions.

Discovery Resources

We manage the A*STAR Natural Product Library (NPL), which comprises of approximately 37,000 plant samples and 122,000 microbial strains, and their organic extracts (Figure 1). The genetic diversity within NPL is exceptional. With 57% of all known cultured fungal genera, over 67% of the world's plant families and 70% of filamentous bacterial genera represented, the collection has been described as "the most diverse and comprehensive collection of plant and microbial samples in the world" (Prof Geoffrey A. Cordell, University of Illinois). This huge collection of plants and microbes serves as our resources for the discovery of bioactive compounds and industrial enzymes.

To complement our traditional bioassay-guided compound discovery through extract screening, we are in the process of creating a genomic DNA library for our microbial strains. Work is also in progress to create a digital database for these microbial genomes to enable genome mining.

Figure 1
Figure 1 - A*STAR Natural Product Library

Bioactive Compounds

We collaborate closely with external partners in industry and academia to discover natural bioactive compounds for a wide variety of applications, ranging from pharmaceuticals, food ingredients, flavours and preservatives, to personal care and cosmetics. We have developed and validated several cellular and biochemical assays with suitable technologies and formats for automated high-throughput screening in 384-well format. These include a cell-based transient transfection assay using a dual luciferase reporter system and an enzyme assay that is based on fluorescence resonance energy transfer. Most recently we have established a panel of high-throughput antimicrobial susceptibility assays against human pathogens and food spoilage microorganisms for antibiotics and natural preservatives discovery. Assay development is in progress for several enzymes relevant for the screening of active ingredients for cosmetics and functional food applications. All developed assays will be used to screen our extracts for the identification of bioactive compounds using bioassay-guided compound isolation approach.

To date more than 2,000 bioactive compounds have been isolated from NPL. As purification of these compounds from the crude mixture is a tedious and labour intensive process, to conserve the use of the purified materials we collaborate with Dr Hao Fan (Structure-based Ligand Discovery and Design) to in silico screen these compounds against molecular targets with structural information and perform experimental validation only on the in silico hits.

For new bioactive compounds with interesting activity profile we will embark on mode-of-action study in collaboration with Dr Prakash Arumugam (Chemical Gonomics), chemical screening (Dr Yoganathan Kanagasundaram, Natural Product Chemistry) to identify alternative producers and genome sequencing of their producers to understand their biosynthetic pathway (Frank & Birgit Eisenhaber, Gene Function Prediction Group).

Biocatalysts

Microbial enzymes are widely used as biocatalysts in industries owing to their stability, catalytic activity, ease of production and optimization compared to plant and animal enzymes. Our collection of > 100,000 microbe is a rich resource for enzyme discovery for industrial applications, such as waste treatment, food processing, drug manufacturing, food flavour generation or diagnostics. An industrial collaboration to search for six different enzymes found numerous fungal strains showing at least one enzymatic activity of interest with sufficient production levels for follow-up studies. One of the enzymes has been successfully identified, cloned and expressed, and is being evaluated for product development. We are collaborating with Biotransformation Innovation Platform (https://www.a-star.edu.sg/biotrans) to screen for enzymes for food industry application. And we are collaborating with the Metabolic Engineering Research Laboratory to discover and characterise tailoring enzymes from producers of bioactive compounds for possible application in advanced biomanufacturing.

Biosynthetic Gene Clusters

We have accumulated the genome sequence data for more than 150 microbial strains from NPL, and the sequencing of at least another 2,000 strains is in progress. From the sequenced genomes putative biosynthetic gene clusters (BGCs) for secondary metabolites were identified using antiSMASH. Putative biosynthetic gene clusters of bioactive compounds with interesting activity profile or structure will be identified, validated and engineered through our collaboration with Molecular Engineering Laboratory and Metabolic Engineering Research Laboratory.

A biodiversity study of 32 ascomycete strains (Figure 2) isolated from St. John’s Island was undertaken to characterize the biosynthetic and antimicrobial potential of fungi from Singapore. Selected strains showing bioactivity were sequenced and analysed for putative biosynthetic gene clusters. The extracts derived from the fermentates of these bioactive strains were also analysed for secondary metabolite production. Comparison of their biosynthetic potential and the secondary metabolite profiles indicated the presence of silent or cryptic BGCs. We are applying the use of co-cultivation and chemical elicitors to activate the expression of these BGCs. Similar study was performed on approximately 50 strains each of marine actinomycetes and endophytic fungi. Most recently we were awarded NRF-funded grant with co-workers from Natural Product Chemistry group, Metabolic Engineering Laboratory and Metabolic Engineering Research Laboratory to leverage on our respective expertise to discover, characterise and engineer bioactive alkaloids from NPL actinomycetes collection.

Figure 2
Figure 2 - 32 fungal strains (Ascomycetes) isolated from and around St. John's Island, Singapore.

Natural Product Biology Members

Dr. Ng Siew Bee
Principal Investigator
 
  Biography Details
NameTitle
Dr. NG Siew BeePrincipal Investigator
Dr. MUNUSAMY MadhaiyanPostdoctoral Fellow
Dr. Albertus Eka Yudistira SARWONOPostdoctoral Fellow
Dr. GOH Qi Yun FaliciaPostdoctoral Fellow
Dr. THAPPETA VENKATA Kishore ReddyPostdoctoral Fellow
Ms. CRASTA SharonResearch Manager
Ms. LEE Michele Shi MinResearch Officer
Mr. LEONG Chung YanResearch Officer
Mr. CHEE Zhao yanResearch Officer
Ms. TAN Yi Qi ZannResearch Officer
Ms. CHAN Kar Yarn, GraceResearch Officer
Ms. CHANG Mun Leng, Amanda Research Officer
Ms. NG Wee Pin VeronicaResearch Officer
Ms. LIM Tian RuResearch Officer
Ms. TAN Qiu Ning, SereneResearch Officer
Ms. SHAHUL HAMEED Nazihah BeeviLaboratory Technician
Mr. GAKUUBI Martin Muthee PhD student
No Publications

Our group study the biology of natural products, in particular how they are made and what are their effects on biological systems. To this end we develop and implement biochemical and cellular assays to screen organic extracts derived from plants, fungal fruiting bodies and fermentates of microorganisms, for the discovery of naturally occurring bioactive secondary metabolites. Once an interesting and novel bioactive compound has been isolated and its structure elucidated we will identify and study its biosynthetic pathway. We also investigate methods to turn on the expression of secondary metabolite biosynthetic gene clusters that are cryptic under standard laboratory growth conditions.

Discovery Resources

We manage the A*STAR Natural Product Library (NPL), which comprises of approximately 37,000 plant samples and 122,000 microbial strains, and their organic extracts (Figure 1). The genetic diversity within NPL is exceptional. With 57% of all known cultured fungal genera, over 67% of the world's plant families and 70% of filamentous bacterial genera represented, the collection has been described as "the most diverse and comprehensive collection of plant and microbial samples in the world" (Prof Geoffrey A. Cordell, University of Illinois). This huge collection of plants and microbes serves as our resources for the discovery of bioactive compounds and industrial enzymes.

To complement our traditional bioassay-guided compound discovery through extract screening, we are in the process of creating a genomic DNA library for our microbial strains. Work is also in progress to create a digital database for these microbial genomes to enable genome mining.

Figure 1
Figure 1 - A*STAR Natural Product Library

Bioactive Compounds

We collaborate closely with external partners in industry and academia to discover natural bioactive compounds for a wide variety of applications, ranging from pharmaceuticals, food ingredients, flavours and preservatives, to personal care and cosmetics. We have developed and validated several cellular and biochemical assays with suitable technologies and formats for automated high-throughput screening in 384-well format. These include a cell-based transient transfection assay using a dual luciferase reporter system and an enzyme assay that is based on fluorescence resonance energy transfer. Most recently we have established a panel of high-throughput antimicrobial susceptibility assays against human pathogens and food spoilage microorganisms for antibiotics and natural preservatives discovery. Assay development is in progress for several enzymes relevant for the screening of active ingredients for cosmetics and functional food applications. All developed assays will be used to screen our extracts for the identification of bioactive compounds using bioassay-guided compound isolation approach.

To date more than 2,000 bioactive compounds have been isolated from NPL. As purification of these compounds from the crude mixture is a tedious and labour intensive process, to conserve the use of the purified materials we collaborate with Dr Hao Fan (Structure-based Ligand Discovery and Design) to in silico screen these compounds against molecular targets with structural information and perform experimental validation only on the in silico hits.

For new bioactive compounds with interesting activity profile we will embark on mode-of-action study in collaboration with Dr Prakash Arumugam (Chemical Gonomics), chemical screening (Dr Yoganathan Kanagasundaram, Natural Product Chemistry) to identify alternative producers and genome sequencing of their producers to understand their biosynthetic pathway (Frank & Birgit Eisenhaber, Gene Function Prediction Group).

Biocatalysts

Microbial enzymes are widely used as biocatalysts in industries owing to their stability, catalytic activity, ease of production and optimization compared to plant and animal enzymes. Our collection of > 100,000 microbe is a rich resource for enzyme discovery for industrial applications, such as waste treatment, food processing, drug manufacturing, food flavour generation or diagnostics. An industrial collaboration to search for six different enzymes found numerous fungal strains showing at least one enzymatic activity of interest with sufficient production levels for follow-up studies. One of the enzymes has been successfully identified, cloned and expressed, and is being evaluated for product development. We are collaborating with Biotransformation Innovation Platform (https://www.a-star.edu.sg/biotrans) to screen for enzymes for food industry application. And we are collaborating with the Metabolic Engineering Research Laboratory to discover and characterise tailoring enzymes from producers of bioactive compounds for possible application in advanced biomanufacturing.

Biosynthetic Gene Clusters

We have accumulated the genome sequence data for more than 150 microbial strains from NPL, and the sequencing of at least another 2,000 strains is in progress. From the sequenced genomes putative biosynthetic gene clusters (BGCs) for secondary metabolites were identified using antiSMASH. Putative biosynthetic gene clusters of bioactive compounds with interesting activity profile or structure will be identified, validated and engineered through our collaboration with Molecular Engineering Laboratory and Metabolic Engineering Research Laboratory.

A biodiversity study of 32 ascomycete strains (Figure 2) isolated from St. John’s Island was undertaken to characterize the biosynthetic and antimicrobial potential of fungi from Singapore. Selected strains showing bioactivity were sequenced and analysed for putative biosynthetic gene clusters. The extracts derived from the fermentates of these bioactive strains were also analysed for secondary metabolite production. Comparison of their biosynthetic potential and the secondary metabolite profiles indicated the presence of silent or cryptic BGCs. We are applying the use of co-cultivation and chemical elicitors to activate the expression of these BGCs. Similar study was performed on approximately 50 strains each of marine actinomycetes and endophytic fungi. Most recently we were awarded NRF-funded grant with co-workers from Natural Product Chemistry group, Metabolic Engineering Laboratory and Metabolic Engineering Research Laboratory to leverage on our respective expertise to discover, characterise and engineer bioactive alkaloids from NPL actinomycetes collection.

Figure 2
Figure 2 - 32 fungal strains (Ascomycetes) isolated from and around St. John's Island, Singapore.

Natural Product Biology Members

Dr. Ng Siew Bee
Senior Principal Investigator
 
  Biography Details
NameTitle
Dr. NG Siew BeePrincipal Investigator
Dr. MUNUSAMY MadhaiyanPostdoctoral Fellow
Dr. Albertus Eka Yudistira SARWONOPostdoctoral Fellow
Dr. GOH Qi Yun FaliciaPostdoctoral Fellow
Dr. THAPPETA VENKATA Kishore ReddyPostdoctoral Fellow
Ms. CRASTA SharonResearch Manager
Ms. LEE Michele Shi MinResearch Officer
Mr. LEONG Chung YanResearch Officer
Mr. CHEE Zhao yanResearch Officer
Ms. TAN Yi Qi ZannResearch Officer
Ms. CHAN Kar Yarn, GraceResearch Officer
Ms. CHANG Mun Leng, Amanda Research Officer
Ms. NG Wee Pin VeronicaResearch Officer
Ms. LIM Tian RuResearch Officer
Ms. TAN Qiu Ning, SereneResearch Officer
Ms. SHAHUL HAMEED Nazihah BeeviLaboratory Technician
Mr. GAKUUBI Martin Muthee PhD student
No Publications