Metabolic peculiarities of Aspergillus niger disclosed by comparative metabolic genomics

1. Metabolic peculiarities of Aspergillusnigerdisclosed by comparative metabolic genomics Authors : Jibin Sun1 , Xin Lu1 , Ursula Rinas1 and An Ping Zeng1,2 1Helmholtz Centre for Infection Research, Inhoffenstr., 38124 Braunschweig, Germany2Hamburg University of Technology, Institute of Bioprocess and Biosystems Engineering, Denickestr., 21071 Hamburg, Germany Presented By -> Gaurav Jain { gauravj@udel.edu } Instructor : Dr. Li Liao {lliao@cis.udel.edu }

2. In Short • A.niger: an important industrial microorganism. • Used for the production of : • metabolites : such as citric acid. • Proteins: such as fungal enzymes or heterologous proteins. Despite its extensive industrial applications, the genetic inventory of this fungus is only partially understood. The recently released genome sequence opens a new horizon for both scientific studies and biotechnological applications. 2

3. Overview • Introduction • Terminologies • Background • Results and Discussion • Genomic annotation of ATCC 9029 • Comparative genomics  • Reconstruction and comparative analysis of the metabolic network • Metabolic network reconstruction • Comparative assessment of the central metabolic network • Unique enzyme-coding genes and EC numbers • Citric acid production: A case study • Versatile metabolic conversion centre • My opinion • Conclusion 3

4. Terminologies • Metabolism: The chemical processes occurring within a living cell or organism that are necessary for the maintenance of life. In metabolism some substances are broken down to yield energy for vital processes while other substances, necessary for life, are synthesized. • Metabolite : Organic compound that is a starting material in, an intermediate in, or an end product of metabolism. • Ortholog or orthologous genes:are genes in different species, that are similar to each other because they originated from a common ancestor. The term "ortholog" was coined in 1970. • CD`s : Coding sequences, of a gene is the portion of DNA that is transcribed into mRNA and translated into proteins. This does not include such regions as a recognition site, initiator sequence, or termination sequence, only the region that will directly code for amino acid linkage. • Enzyme Commission number (EC number) is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze. Strictly speaking, EC numbers do not specify enzymes, but enzyme-catalyzed reactions. If different enzymes (for instance from different organisms) catalyze the same reaction, then they receive the same EC number. 4

5. Background • Importance of metabolic network reconstruction. • Modern fast DNA sequencing methods & bioinformatics tools for reconstruction and cross comparison of the metabolic networks among related species and specific strains-elucidate metabolic peculiarities. • Why there is a great need for a better knowledge of genomic potential of A.niger? • Well known producer of extracellular fungal enzymes. • Citric acid is mostly exclusively produce d using A.niger nowadays. • Could be used for rational strain improvement. 5

6. BackgroundContd… • Reconstruction of a genome scale metabolic network from the annotated genome: • List of enzymes with EC numbers are extracted from the genome annotation. • It is then searched in an established biochemical reaction DB to acquire their corresponding reactions. • Biochemical reactions are then connected to each other according to certain rules. • Such information can be further interpreted as a network and analyzed by many computer programs. 6

7. Next… • Introduction • Terminologies • Background • Results and Discussion • Genomic annotation of ATCC 9029 • Comparative genomics  • Reconstruction and comparative analysis of the metabolic network • Metabolic network reconstruction • Comparative assessment of the central metabolic network • Unique enzyme-coding genes and EC numbers • Citric acid production: A case study • Versatile metabolic conversion centre • My opinion • Conclusion 7

8. Genomicannotation of ATCC 9029 • Annotated raw genome (approx 32Mb) sequence of A.niger ATCC 9029 from Integrated genomics was annotated by using a new algorithm ‘IdentiCS’ with a cutoff E-value of 10-5 . • ‘IdentiCS’ is a homology-based algorithm. • The algorithm was extended for the prediction and annotation of eukaryotic CDSs by considering the intron and extron structure of genes. 8

9. Genomic annotation of ATCC 9029 contd… • Complementation of ‘IdentiCS’ by GenScan and GeneWise for the prediction of protein-encoding genes. • Like all other homology-based methods, ‘IdentiCS’ Is unable to predict new genes for which no homologue is present in the available protein database. • Refinement of the annotation • All CDSs predicted submitted to KEGG automatic Annotation Server. • Use ‘HT-Go-FAT ‘ useful software toolkit to annotate sequences to GO, EC number, KEGG pathways and so on. • Use of text mining to assign EC number when an obvious enzyme could not be associated to an EC number or a complete EC number using above methods. 9

10. Functional annotation of predicted protein coding sequences of A. niger. Sun et al. Genome Biology 2007 8:R182   doi:10.1186/gb-2007-8-9-r182 10

11. ComparativeGenomics • Proteins predicted from the unfinished genomic sequences of A.niger ATCC 9029 and from A.niger CBS 513.88 were cross compared with proteins of 7 fungal species and 26 representative from eukaryotic organism to identify their orthologus relationships. • Results : • 88% of the CDSs can be unique to a fungus in comparison to another fungal species. • Nearly 50% of the CDSs of A. niger CBS 513.88 cannot be found in other Aspergillus species • Over 30% of the CDSs in each A. nigerstrain have homologs in another A. nigerstrain with an identity level higher than 99%. • The unique genes account for around 4% of the total number of CDSs in the two A. nigerstrains. In summary, the results from comparative genomics show that the A. nigerstrains are closely related to each other but exhibit large differences from the other fungal species compared. 11

12. Next… • Introduction • Terminologies • Background • Results and Discussion • Genomic annotation of ATCC 9029 • Comparative genomics  • Reconstruction and comparative analysis of the metabolic network • Metabolic network reconstruction • Comparative assessment of the central metabolic network • Unique enzyme-coding genes and EC numbers • Citric acid production: A case study • Versatile metabolic conversion centre • My opinion • Conclusion 12

13. Section Overview • Metabolic network reconstruction • Quick tour of KEGG • Using KEGG to reconstruct a metabolic network • Reconstruction of a simple pathway

14. Metabolic network reconstruction • Identification of missing genes in complete genomes • Search for candidates • Analysis of individual genes to assign general biochemical function: • homology • functional patterns • structural features • Comparative genomics to predict specificity: • analysis of regulation • positional clustering • gene fusions • phylogenetic patterns

15. Metabolic network reconstruction Contd…

16. Tour of KEGG • KEGG: Kyoto Encyclopedia of Genes and Genomes. • Main entry points to the KEGG web service • KEGG2 KEGG Table of Contents • PATHWAYKEGG pathway maps for biological processes • BRITE Functional hierarchies of biological systems • GENES Gene catalogs and ortholog relations in complete genomes • LIGAND Chemical compounds, drugs, glycans, and reactions

17. Information about A.niger

18. KEGG pathway database

19. Making an Organism Specific map Enzymes in A.niger are now shaded in green

20. Fungus-specific information about EC 2.7.1.1 ORF , Gene name Reaction Information Databases

21. Reaction Information

22. Enzyme Database

23. First Entry in the reconstruction • ORF : An02g14380 • GENE : hxk • Name: ATP:D-hexose 6-phosphotransferase • EC number : 2.7.1.1 • Reaction An02g14380 hxk HXK1 ATP + D-hexose = ADP + D-hexose 6-phosphate

24. Metabolic network reconstruction of A.niger • The metabolic network of A. nigerwas constructed using the EC numbers of ATCC 9029 and CBS 513.88 strains. • Methods applied: • knowledge-based method. • connection-matrix-based method. • Results: • 2443 biological reactions and 2349 metabolites. • Most of the reactions are connected to central metabolisms like carbohydrate, lipid, amino acid, energy metabolism etc. • a significant number of reactions and metabolites belong to secondary metabolism or xenobiotics biodegradation, indicating the high metabolic potential of A. niger for production of secondary metabolites or for bioremediation 24

25. The genome-scale metabolic network of A. niger. Nodes are metabolites while links are reactions. The color of the nodes represents different functional categories. The size of nodes is proportional to the number of reactions from or to that node (metabolite) in the genome-wide network. (a) The general layout of the metabolic network. (b) A zoom-in of the dashed box in 25

26. Acomparative assessment of the central metabolic network • The metabolic network reconstructed from the genomic data was compared to the network of central carbon metabolism of A. nigerreconstructed by David et al. • The network of David et al. contained 335 reactions, 284 metabolites and 129 EC numbers. • In general, there is a good agreement between these two metabolic networks regarding central metabolism. • Only 14 ECs in the metabolic network of David et al. could not be found in the genome-wide network reconstructed, most of which belong to enzymes poorly characterized in the literature in terms of protein sequences. 26

27. Uniqueness of genes or CDSs • The uniqueness of a gene or CDS from organism A is defined as : If the Ortholog of a gene from organism A is absent in organism B, it is defined that this gene is unique or specific to organism A in comparison to organism B. • This does not imply there is no homolog (namely paralog) of the gene from organism A in organism B. In some cases, this gene is just an additional copy of another gene whose orthologs are found in both organisms. • This also does not imply that this gene is found only in organism A. 27

28. Unique enzyme-coding genes and EC numbers Glycolysis and TCA cycle of A. niger: a view from the genome-scale network. Nodes represent metabolites while directional links represent metabolic reactions. The color of the nodes represents different functional categories. The size of nodes is proportional to the number of reactions from or to that node (metabolite) in the genome-wide network. The red colored links indicate that A. nigerhas additional copies of genes for these reactions • The unique enzyme-coding genes mentioned do have paralogs in other fungi or even in A. niger itself. • These paralogs were carefully verified not to be orthologs since they are orthologous to other CDSs of A. niger. • Gene redundancy or duplication has also been reported in A. niger 28

29. Next… • Introduction • Terminologies • Background • Results and Discussion • Genomic annotation of ATCC 9029 • Comparative genomics  • Reconstruction and comparative analysis of the metabolic network • Metabolic network reconstruction • Comparative assessment of the central metabolic network • Unique enzyme-coding genes and EC numbers • Citric acid production: A case study • Versatile metabolic conversion centre • My opinion • Conclusion 29

30. A versatile metabolic conversion center • Importance of citric acid production by A. niger, the metabolic reactions contributing to citric acid production are selected as an example to explore the capability of the constructed metabolic network. • The pathways related to citric acid production from glucose were extracted from the genome-wide metabolic network together with the metabolites directly connected to these pathways. • In comparison to other filamentous fungi, A. niger has redundant unique genes for the conversion of seven of (starch, sucrose, dextrin, maltose, lactose, cellulose, α,α-trehalose, sorbitol, D-glucoside, N-glycan) substrates (reactions marked as red in Figure). 30

31. Next… • Introduction • Terminologies • Background • Results and Discussion • Genomic annotation of ATCC 9029 • Comparative genomics  • Reconstruction and comparative analysis of the metabolic network • Metabolic network reconstruction • Comparative assessment of the central metabolic network • Unique enzyme-coding genes and EC numbers • Citric acid production: A case study • Versatile metabolic conversion centre • My opinion • Conclusion 31

32. My opinion • I find the paper was good as it looked certain metabolic peculiarities of A.niger which is an important industrial microorganism. • As they were first to present the genome-scale metabolic network for A. nigerand an in-depth genomic comparison of this species, I opened a huge space in front of the potential of A.niger. • The paper was not organized properly. • Many things which were said to be mentioned in the “materials and methods" sectioned was not proper. • Lot of data which they could have represented by tables were given as additional data. 32

33. Conclusion • 14,000 protein coding sequences were predicted from the raw low-coverage genome sequence of A. nigerATCC 9029 and approximately 60% of them were assigned to at least one functional category (GO, KO, COG, EC and pathways). • It is found that the genomic content of A. nigerATCC 9029 is very similar to that of A. nigerCBS 513.88; merely around 600 genes are exclusively found in each strain. • Comparative metabolic genomics revealed the high metabolic peculiarity of A. nigerby more than 1,100 unique enzyme-encoding genes. • Many unique genes are paralogsof those genes that are orthologs in the compared fungi, indicating that genetic multiplicity might be a key strategy of A. nigerto keep its versatile metabolic capacities and its robustness to adapt to different environmental conditions. • Additional copies of genes, such as the ones encoding alternative mitochondrial oxidoreductase and citrate synthases, which could have an impact on the overproduction of citric acid by this black mould. 33

34. References • Data Collection and Metabolic Network Reconstruction -Winter School in Genomics, 2006. • Metabolism of Citric Acid Production by Aspergillus niger : Model Definition, Steady-State Analysis and Constrained Optimization of Citric Acid Production Rate by Fernando Alvarez-Vasquez,1 Carlos Gonza´ lez-Alco´ n,2 Ne´ stor V. Torres1. • Metabolic peculiarities of Aspergillus niger disclosed by comparative metabolic genomics Authors : Jibin Sun , Xin Lu , Ursula Rinas and An Ping Zeng • http://www.genome.jp/kegg/ • http://www.ncbi.nlm.nih.gov/ • http://www.google.com/ • Help of Dr.Liao.

35. Questions Metabolic peculiarities ??? 35