Whole genome sequencing, comparative genomics and virulence factors analyses of Meyerozyma guilliermondii strain soexpression system
Meyerozyma guilliermondii strain SO isolated from spoiled orange has been developed as a free-inducer expression system and attains a positive impact in industrial recombinant proteins production. The comprehension on genomic features is necessitated to cater its competency to perform as an expre...
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my-upm-ir.1129522024-10-23T06:46:03Z Whole genome sequencing, comparative genomics and virulence factors analyses of Meyerozyma guilliermondii strain soexpression system 2021-12 Zainudin, Robiatul Azilah Meyerozyma guilliermondii strain SO isolated from spoiled orange has been developed as a free-inducer expression system and attains a positive impact in industrial recombinant proteins production. The comprehension on genomic features is necessitated to cater its competency to perform as an expression host. Furthermore, it may enhance the yield of production at lower cost in the absence of an inducer. Therefore, the complete genome data of M. guilliermondii strain SO representing the host system from the perspective of genome arrangement, polymorphic variants, the composition of genes and the association in metabolic pathway is prerequisite in genomic comparative and toxicity analyses. Thus, the genome data were generated from Illumina Hiseq 4000 sequencing platform and assembled into 51 scaffolds successfully accumulated into 10.63 Mbp. These enclosed 5,335 CDS genes and 5,349 protein sequences with 43.72% GC content. About 99.29% of it were annotated to public databases. These data were employed to conduct a comparison of M. guilliermondii intraspecies strains which comprises of SO, ATCC 6260, YLG18 and RP-YS-11. The study discovered 99.18% genes similarity among these strains and subsequently embarking high accuracy analysis. Besides, the evaluation of established yeast expression systems, Komagataella pastoris and Saccharomyces cerevisiae with our inhouse strain SO and the reference strain of M. guilliermondii were carried out comparatively to identify the consensus domain or subdomain that putatively responsible to perform as an expression host. A non-expression yeast species, Candida albicans was included in the investigation to structure normalization. This interspecies study revealed 666 homologous genes with 55 consensus regions of genome identified exclusively in M. guilliermondii and both expression hosts. Hence, the connectivity enzymes that played pivotal roles during carbon metabolism particularly on the utilization of methane was accessed. The study recognised an absence of alcohol oxidase (AOX) enzyme in strain SO which contributed to the factor of methanol-independency. This eventually highlighted the strength of M. guilliermondii strain SO to perform as a forthcoming freeinducer alternative host for recombinant protein expression. Additionally, the selected potential virulence factors in M. guilliermondii strain SO were determined from systemlevel insights. The algorithm of Hidden Markov Model detected in silico indication of proteases (SAP), phospholipases (PLC and PLD) and hemolysin (MAM3) motifs in the genome which possessed 85% similarity to C. albicans, a pathogenic yeast that caused candidiasis and triggering safety concerns. Hence, the investigation of apportioning virulence factors in strain SO to predict SAP, PLC, PLD and MAM3 were executed and identified the resemblance of C. albicans with the expect value 2.4e-107, 9.5e-200, 0.0e+00 and 1.2e-258, respectively. Accordingly, these significant genes possibly play roles in pathogenicity. The topology of phylogenetic analysis constructed strain SO and C. albicans branches from the same node and clustered together as a clade to signify molecular relatedness and congeneric among these species. Nevertheless, in vitro analysis in quantifying the level of expression need to be investigated from the assay to quantify the enzymatic activity which may and may not activate strain SO as an opportunistic pathogenic yeast, subsequently, certifying the toxicity status of M. guilliermondii strain SO. Comparative genomics Virulence (Microbiology) - Genetic aspects Ascomycetes 2021-12 Thesis http://psasir.upm.edu.my/id/eprint/112952/ http://psasir.upm.edu.my/id/eprint/112952/1/112952.pdf text en public masters Universiti Putra Malaysia Comparative genomics Virulence (Microbiology) - Genetic aspects Ascomycetes Oslan, Siti Nurbaya |
| institution |
Universiti Putra Malaysia |
| collection |
PSAS Institutional Repository |
| language |
English |
| advisor |
Oslan, Siti Nurbaya |
| topic |
Comparative genomics Virulence (Microbiology) - Genetic aspects Ascomycetes |
| spellingShingle |
Comparative genomics Virulence (Microbiology) - Genetic aspects Ascomycetes Zainudin, Robiatul Azilah Whole genome sequencing, comparative genomics and virulence factors analyses of Meyerozyma guilliermondii strain soexpression system |
| description |
Meyerozyma guilliermondii strain SO isolated from spoiled orange has been developed
as a free-inducer expression system and attains a positive impact in industrial
recombinant proteins production. The comprehension on genomic features is
necessitated to cater its competency to perform as an expression host. Furthermore, it
may enhance the yield of production at lower cost in the absence of an inducer.
Therefore, the complete genome data of M. guilliermondii strain SO representing the
host system from the perspective of genome arrangement, polymorphic variants, the
composition of genes and the association in metabolic pathway is prerequisite in genomic
comparative and toxicity analyses. Thus, the genome data were generated from Illumina
Hiseq 4000 sequencing platform and assembled into 51 scaffolds successfully
accumulated into 10.63 Mbp. These enclosed 5,335 CDS genes and 5,349 protein
sequences with 43.72% GC content. About 99.29% of it were annotated to public
databases. These data were employed to conduct a comparison of M. guilliermondii
intraspecies strains which comprises of SO, ATCC 6260, YLG18 and RP-YS-11. The
study discovered 99.18% genes similarity among these strains and subsequently
embarking high accuracy analysis. Besides, the evaluation of established yeast
expression systems, Komagataella pastoris and Saccharomyces cerevisiae with our inhouse
strain SO and the reference strain of M. guilliermondii were carried out
comparatively to identify the consensus domain or subdomain that putatively responsible
to perform as an expression host. A non-expression yeast species, Candida albicans was
included in the investigation to structure normalization. This interspecies study revealed
666 homologous genes with 55 consensus regions of genome identified exclusively in
M. guilliermondii and both expression hosts. Hence, the connectivity enzymes that
played pivotal roles during carbon metabolism particularly on the utilization of methane
was accessed. The study recognised an absence of alcohol oxidase (AOX) enzyme in
strain SO which contributed to the factor of methanol-independency. This eventually
highlighted the strength of M. guilliermondii strain SO to perform as a forthcoming freeinducer
alternative host for recombinant protein expression. Additionally, the selected potential virulence factors in M. guilliermondii strain SO were determined from systemlevel
insights. The algorithm of Hidden Markov Model detected in silico indication of
proteases (SAP), phospholipases (PLC and PLD) and hemolysin (MAM3) motifs in the
genome which possessed 85% similarity to C. albicans, a pathogenic yeast that caused
candidiasis and triggering safety concerns. Hence, the investigation of apportioning
virulence factors in strain SO to predict SAP, PLC, PLD and MAM3 were executed and
identified the resemblance of C. albicans with the expect value 2.4e-107, 9.5e-200, 0.0e+00
and 1.2e-258, respectively. Accordingly, these significant genes possibly play roles in
pathogenicity. The topology of phylogenetic analysis constructed strain SO and C.
albicans branches from the same node and clustered together as a clade to signify
molecular relatedness and congeneric among these species. Nevertheless, in vitro
analysis in quantifying the level of expression need to be investigated from the assay to
quantify the enzymatic activity which may and may not activate strain SO as an
opportunistic pathogenic yeast, subsequently, certifying the toxicity status of M.
guilliermondii strain SO. |
| format |
Thesis |
| qualification_level |
Master's degree |
| author |
Zainudin, Robiatul Azilah |
| author_facet |
Zainudin, Robiatul Azilah |
| author_sort |
Zainudin, Robiatul Azilah |
| title |
Whole genome sequencing, comparative genomics and virulence factors analyses of Meyerozyma guilliermondii strain soexpression system |
| title_short |
Whole genome sequencing, comparative genomics and virulence factors analyses of Meyerozyma guilliermondii strain soexpression system |
| title_full |
Whole genome sequencing, comparative genomics and virulence factors analyses of Meyerozyma guilliermondii strain soexpression system |
| title_fullStr |
Whole genome sequencing, comparative genomics and virulence factors analyses of Meyerozyma guilliermondii strain soexpression system |
| title_full_unstemmed |
Whole genome sequencing, comparative genomics and virulence factors analyses of Meyerozyma guilliermondii strain soexpression system |
| title_sort |
whole genome sequencing, comparative genomics and virulence factors analyses of meyerozyma guilliermondii strain soexpression system |
| granting_institution |
Universiti Putra Malaysia |
| publishDate |
2021 |
| url |
http://psasir.upm.edu.my/id/eprint/112952/1/112952.pdf |
| _version_ |
1818586130021351424 |