Genomic study of Photobacterium marinum strain J15 and development of genome scale metabolic model for cellular metabolism identification
Photobacterium sp. strain J15 was originally isolated from marine water of Tanjung Pelepas, Johor. It was initially studied for its novel GDSL esterase and asparaginase production. With the production of the potential enzymes and secondary metabolites, it was realised that little is known about t...
| Main Author: | |
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| Format: | Thesis |
| Language: | English |
| Published: |
2017
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| Subjects: | |
| Online Access: | http://psasir.upm.edu.my/id/eprint/68520/1/FBSB%202018%2010%20IR.pdf |
| _version_ | 1825933542968786944 |
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| author | Roslan, Noordiyanah Nadhirah |
| author_facet | Roslan, Noordiyanah Nadhirah |
| author_sort | Roslan, Noordiyanah Nadhirah |
| collection | UPM |
| description | Photobacterium sp. strain J15 was originally isolated from marine water of Tanjung
Pelepas, Johor. It was initially studied for its novel GDSL esterase and asparaginase
production. With the production of the potential enzymes and secondary metabolites, it
was realised that little is known about the general metabolism of this Photobacterium
genus. Therefore, the aim of this study was to provide an understanding of cellular
metabolism of strain J15 through genomics and phenomics analysis and characterization
of the genome-scale properties. Genome scale metabolic model was also constructed in
order to enhance the understanding of the cell’s organization and its functionality as a
whole.
In this study, the genome sequence of Photobacterium sp. strain J15 was determined
using PacBio sequencing. The genome contained 5,684,538 base pairs comprised 3
contigs; 2 chromosomes and 1 plasmid. A total of 4,924 open reading frames (ORFs)
were predicted and 4,811 proteins were annotated against NCBI database. There are
altogether 3,238 proteins with GO assignment and 874 proteins assigned to KEGG
pathways. Phylogenomics analysis showed that Photobacterium sp. strain J15 is indeed
the same species with P. marinum AK15.
There were 535 subsystems represented in the draft genome scale metabolic model
(GEM) of P. marinum J15. The iSS1110 model consists of 1110 genes with 1495
biochemical reactions and 40 % of total number of the reaction was the sum of the three
largest subsystems; amino acid metabolism, carbohydrate metabolism, and metabolism
of cofactors as well as vitamins.
To investigate the connections between genome and phenome of P. marinum J15 and to
validate the constructed GEM, BIOLOG Phenotype Microarray was performed. Also, DuctApe program was used in order to further analyse metabolic functionality of this
bacterium. Main phenotype microarray (PM) assays showed that P. marinum J15 was
able to use: i) 93 of the 190 carbon sources tested, where 61 were used efficiently, among
which there were 16 amino acids; ii) 41 of the 95 nitrogen sources tested, where 22
compounds were used efficiently, among which were 9 amino acids and 8 peptides, and
iii) 3 of the 94 phosphorous and sulphur sources tested. Furthermore, resistance to
antibiotics, high tolerance to osmotic stress, to basic pH and to toxic compounds was
revealed by PM.
The complete genome, draft GEM and phenotypic data of P. marinum J15 in this study
would be a resource for many subsequent studies of this genus, especially since there is
only one published research on isolation of P. marinum AK15, but none on the genomic
and phenotypic characteristic. This information will be essential for discovery of unique
genes and secondary metabolite. |
| first_indexed | 2024-03-06T09:58:53Z |
| format | Thesis |
| id | upm.eprints-68520 |
| institution | Universiti Putra Malaysia |
| language | English |
| last_indexed | 2024-03-06T09:58:53Z |
| publishDate | 2017 |
| record_format | dspace |
| spelling | upm.eprints-685202019-05-14T06:46:41Z http://psasir.upm.edu.my/id/eprint/68520/ Genomic study of Photobacterium marinum strain J15 and development of genome scale metabolic model for cellular metabolism identification Roslan, Noordiyanah Nadhirah Photobacterium sp. strain J15 was originally isolated from marine water of Tanjung Pelepas, Johor. It was initially studied for its novel GDSL esterase and asparaginase production. With the production of the potential enzymes and secondary metabolites, it was realised that little is known about the general metabolism of this Photobacterium genus. Therefore, the aim of this study was to provide an understanding of cellular metabolism of strain J15 through genomics and phenomics analysis and characterization of the genome-scale properties. Genome scale metabolic model was also constructed in order to enhance the understanding of the cell’s organization and its functionality as a whole. In this study, the genome sequence of Photobacterium sp. strain J15 was determined using PacBio sequencing. The genome contained 5,684,538 base pairs comprised 3 contigs; 2 chromosomes and 1 plasmid. A total of 4,924 open reading frames (ORFs) were predicted and 4,811 proteins were annotated against NCBI database. There are altogether 3,238 proteins with GO assignment and 874 proteins assigned to KEGG pathways. Phylogenomics analysis showed that Photobacterium sp. strain J15 is indeed the same species with P. marinum AK15. There were 535 subsystems represented in the draft genome scale metabolic model (GEM) of P. marinum J15. The iSS1110 model consists of 1110 genes with 1495 biochemical reactions and 40 % of total number of the reaction was the sum of the three largest subsystems; amino acid metabolism, carbohydrate metabolism, and metabolism of cofactors as well as vitamins. To investigate the connections between genome and phenome of P. marinum J15 and to validate the constructed GEM, BIOLOG Phenotype Microarray was performed. Also, DuctApe program was used in order to further analyse metabolic functionality of this bacterium. Main phenotype microarray (PM) assays showed that P. marinum J15 was able to use: i) 93 of the 190 carbon sources tested, where 61 were used efficiently, among which there were 16 amino acids; ii) 41 of the 95 nitrogen sources tested, where 22 compounds were used efficiently, among which were 9 amino acids and 8 peptides, and iii) 3 of the 94 phosphorous and sulphur sources tested. Furthermore, resistance to antibiotics, high tolerance to osmotic stress, to basic pH and to toxic compounds was revealed by PM. The complete genome, draft GEM and phenotypic data of P. marinum J15 in this study would be a resource for many subsequent studies of this genus, especially since there is only one published research on isolation of P. marinum AK15, but none on the genomic and phenotypic characteristic. This information will be essential for discovery of unique genes and secondary metabolite. 2017-11 Thesis NonPeerReviewed text en http://psasir.upm.edu.my/id/eprint/68520/1/FBSB%202018%2010%20IR.pdf Roslan, Noordiyanah Nadhirah (2017) Genomic study of Photobacterium marinum strain J15 and development of genome scale metabolic model for cellular metabolism identification. Masters thesis, Universiti Putra Malaysia. Photobacterium marinum Bacteria |
| spellingShingle | Photobacterium marinum Bacteria Roslan, Noordiyanah Nadhirah Genomic study of Photobacterium marinum strain J15 and development of genome scale metabolic model for cellular metabolism identification |
| title | Genomic study of Photobacterium marinum strain J15 and development of genome scale metabolic model for cellular metabolism identification |
| title_full | Genomic study of Photobacterium marinum strain J15 and development of genome scale metabolic model for cellular metabolism identification |
| title_fullStr | Genomic study of Photobacterium marinum strain J15 and development of genome scale metabolic model for cellular metabolism identification |
| title_full_unstemmed | Genomic study of Photobacterium marinum strain J15 and development of genome scale metabolic model for cellular metabolism identification |
| title_short | Genomic study of Photobacterium marinum strain J15 and development of genome scale metabolic model for cellular metabolism identification |
| title_sort | genomic study of photobacterium marinum strain j15 and development of genome scale metabolic model for cellular metabolism identification |
| topic | Photobacterium marinum Bacteria |
| url | http://psasir.upm.edu.my/id/eprint/68520/1/FBSB%202018%2010%20IR.pdf |
| work_keys_str_mv | AT roslannoordiyanahnadhirah genomicstudyofphotobacteriummarinumstrainj15anddevelopmentofgenomescalemetabolicmodelforcellularmetabolismidentification |