Bioinformatics study of phytase from Aspergillus niger for use as feed additive in livestock feed
Background Phytase supplementation in rations can reduce their phytic acid composition in order to enhance their nutritional value. Aspergillus niger is a fungus that can encode phytase. This study aims to determine the characteristics of its DNA sequences and amino acid composition that encode the...
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| Veröffentlicht in: | Journal of Genetic Engineering and Biotechnology 2023-12, Vol.21 (1), p.142, Article 142 |
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| creator | Maulana, Hamdan Widyastuti, Yantyati Herlina, Nina Hasbuna, Abun Al-Islahi, Aas Syiarudin Hasbi Triratna, Lita Mayasari, Novi |
| description | Background
Phytase supplementation in rations can reduce their phytic acid composition in order to enhance their nutritional value.
Aspergillus niger
is a fungus that can encode phytase. This study aims to determine the characteristics of its DNA sequences and amino acid composition that encode the phytase enzyme, as well as to determine the primer designs.
Method
This study used gene sequence data and protein-encoding phytase from
Aspergillus niger
that was collected manually from NCBI and PDB. The data was analyzed using SPDBV and then be aligned using the ClustalW Multiple Alignment features. The phylogenetic tree was built by Mega11 software. Primers were designed from selected candidate sequences that were analyzed. The designed primers were then simulated for PCR using FastPCR and SnapGene software.
Results
There are 18
Aspergillus niger
phytases in NCBI which is 14.87% of the total
Aspergillus
. There are 14
Aspergillus niger
phytases that have identity above 95%.
Aspergillus niger
110. M94550.1 is the closest strain to the PDB template. Candidate sources of phytase genes are
Aspergillus niger
110.M94550.1, 48.2.BCMY01000003.1, and 92.JQ654450.1. The primer design has 2 possibilities of self-annealing and high melting temperature on the reverse primer. PCR simulation shows that the primer design can attach completely but still has the possibility of mispriming.
Conclusion
This study suggests promising results for the future development of phytase enzyme production from
Aspergillus niger
as a feed additive using genetic engineering to enhance the quality of livestock feed in Indonesia. |
| doi_str_mv | 10.1186/s43141-023-00600-y |
| format | Article |
| fullrecord | <record><control><sourceid>gale_proqu</sourceid><recordid>TN_cdi_proquest_journals_2893681903</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A774300049</galeid><sourcerecordid>A774300049</sourcerecordid><originalsourceid>FETCH-LOGICAL-c447t-8e0b6b08294c4621d0955b3a0f4d67911442838ef0cd1883d78c0568afc536013</originalsourceid><addsrcrecordid>eNp9kU1r3DAQhk1poEuSP9CToJdenMxYH5aO29AmhUAuLeQmtPrYKrWtrWQX_O-rzRZCS6l0GJh5n-Fl3qZ5i3CFKMV1YRQZttDRFkAAtOurZtOBgparDl43GxSyb5H3j2-ay1KeoD7OJHLcNOZDTHEKKY9mjraQMi9uJSmQw7d1NsWTkNNItuXg8z4Ow1LIFPc-k0qQpY5NIcF7R4xzcY4_PYkTGWotc7Lfn0cXzVkwQ_GXv-t58_XTxy83d-39w-3nm-19axnr51Z62IkdyE4xy0SHDhTnO2ogMCd6hchYJ6n0AaxDKanrpQUupAmWUwFIz5v3p72HnH4s1YAeY7F-GMzk01I0RU5RUKp4lb77S_qUljxVd7qTigqJCuiLam8Gr49HmrOxx6V62_eM1isyVVVX_1DV7_wYbZp8iLX_B9CdAJtTKdkHfchxNHnVCPqYpz7lqWue-jlPvVaInqBSxVMN4MXxf6hfmKmgpA</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2893681903</pqid></control><display><type>article</type><title>Bioinformatics study of phytase from Aspergillus niger for use as feed additive in livestock feed</title><source>DOAJ Directory of Open Access Journals</source><source>Springer Nature OA Free Journals</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><creator>Maulana, Hamdan ; Widyastuti, Yantyati ; Herlina, Nina ; Hasbuna, Abun ; Al-Islahi, Aas Syiarudin Hasbi ; Triratna, Lita ; Mayasari, Novi</creator><creatorcontrib>Maulana, Hamdan ; Widyastuti, Yantyati ; Herlina, Nina ; Hasbuna, Abun ; Al-Islahi, Aas Syiarudin Hasbi ; Triratna, Lita ; Mayasari, Novi</creatorcontrib><description>Background
Phytase supplementation in rations can reduce their phytic acid composition in order to enhance their nutritional value.
Aspergillus niger
is a fungus that can encode phytase. This study aims to determine the characteristics of its DNA sequences and amino acid composition that encode the phytase enzyme, as well as to determine the primer designs.
Method
This study used gene sequence data and protein-encoding phytase from
Aspergillus niger
that was collected manually from NCBI and PDB. The data was analyzed using SPDBV and then be aligned using the ClustalW Multiple Alignment features. The phylogenetic tree was built by Mega11 software. Primers were designed from selected candidate sequences that were analyzed. The designed primers were then simulated for PCR using FastPCR and SnapGene software.
Results
There are 18
Aspergillus niger
phytases in NCBI which is 14.87% of the total
Aspergillus
. There are 14
Aspergillus niger
phytases that have identity above 95%.
Aspergillus niger
110. M94550.1 is the closest strain to the PDB template. Candidate sources of phytase genes are
Aspergillus niger
110.M94550.1, 48.2.BCMY01000003.1, and 92.JQ654450.1. The primer design has 2 possibilities of self-annealing and high melting temperature on the reverse primer. PCR simulation shows that the primer design can attach completely but still has the possibility of mispriming.
Conclusion
This study suggests promising results for the future development of phytase enzyme production from
Aspergillus niger
as a feed additive using genetic engineering to enhance the quality of livestock feed in Indonesia.</description><identifier>ISSN: 1687-157X</identifier><identifier>EISSN: 2090-5920</identifier><identifier>DOI: 10.1186/s43141-023-00600-y</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Amino acid composition ; Amino acid sequence ; Amino acids ; Analysis ; Animal feeding and feeds ; Animal genetic engineering ; Annealing ; Aspergillus niger ; Bioinformatics ; Biomedical Engineering and Bioengineering ; Biotechnology ; Composition ; computer software ; Data collection ; Deoxyribonucleic acid ; Design ; Dietary minerals ; DNA ; DNA sequencing ; Engineering ; Enzymes ; Feed additives ; Feeds ; Food additives ; Fungi ; Gene sequencing ; Genes ; Genetic Engineering ; Genetically modified organisms ; Genetics and Genomics ; Genomes ; Indonesia ; Livestock ; Livestock feed ; livestock feeds ; Melt temperature ; Nucleotide sequence ; nucleotide sequences ; Nucleotide sequencing ; Nutritive value ; Phosphatase ; Phosphates ; Phylogenetics ; Phylogeny ; Phytase ; phytases ; Phytic acid ; Polymerase chain reaction ; Proteins ; Proteomics ; Software ; temperature</subject><ispartof>Journal of Genetic Engineering and Biotechnology, 2023-12, Vol.21 (1), p.142, Article 142</ispartof><rights>The Author(s) 2023</rights><rights>COPYRIGHT 2023 Springer</rights><rights>The Author(s) 2023. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c447t-8e0b6b08294c4621d0955b3a0f4d67911442838ef0cd1883d78c0568afc536013</cites><orcidid>0000-0003-1017-4365 ; 0000-0002-0322-3547 ; 0000-0002-5005-3579 ; 0009-0004-4523-4131 ; 0000-0001-5437-9712 ; 0000-0001-8012-5986 ; 0009-0008-0170-2721</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,860,27903,27904</link.rule.ids></links><search><creatorcontrib>Maulana, Hamdan</creatorcontrib><creatorcontrib>Widyastuti, Yantyati</creatorcontrib><creatorcontrib>Herlina, Nina</creatorcontrib><creatorcontrib>Hasbuna, Abun</creatorcontrib><creatorcontrib>Al-Islahi, Aas Syiarudin Hasbi</creatorcontrib><creatorcontrib>Triratna, Lita</creatorcontrib><creatorcontrib>Mayasari, Novi</creatorcontrib><title>Bioinformatics study of phytase from Aspergillus niger for use as feed additive in livestock feed</title><title>Journal of Genetic Engineering and Biotechnology</title><addtitle>J Genet Eng Biotechnol</addtitle><description>Background
Phytase supplementation in rations can reduce their phytic acid composition in order to enhance their nutritional value.
Aspergillus niger
is a fungus that can encode phytase. This study aims to determine the characteristics of its DNA sequences and amino acid composition that encode the phytase enzyme, as well as to determine the primer designs.
Method
This study used gene sequence data and protein-encoding phytase from
Aspergillus niger
that was collected manually from NCBI and PDB. The data was analyzed using SPDBV and then be aligned using the ClustalW Multiple Alignment features. The phylogenetic tree was built by Mega11 software. Primers were designed from selected candidate sequences that were analyzed. The designed primers were then simulated for PCR using FastPCR and SnapGene software.
Results
There are 18
Aspergillus niger
phytases in NCBI which is 14.87% of the total
Aspergillus
. There are 14
Aspergillus niger
phytases that have identity above 95%.
Aspergillus niger
110. M94550.1 is the closest strain to the PDB template. Candidate sources of phytase genes are
Aspergillus niger
110.M94550.1, 48.2.BCMY01000003.1, and 92.JQ654450.1. The primer design has 2 possibilities of self-annealing and high melting temperature on the reverse primer. PCR simulation shows that the primer design can attach completely but still has the possibility of mispriming.
Conclusion
This study suggests promising results for the future development of phytase enzyme production from
Aspergillus niger
as a feed additive using genetic engineering to enhance the quality of livestock feed in Indonesia.</description><subject>Amino acid composition</subject><subject>Amino acid sequence</subject><subject>Amino acids</subject><subject>Analysis</subject><subject>Animal feeding and feeds</subject><subject>Animal genetic engineering</subject><subject>Annealing</subject><subject>Aspergillus niger</subject><subject>Bioinformatics</subject><subject>Biomedical Engineering and Bioengineering</subject><subject>Biotechnology</subject><subject>Composition</subject><subject>computer software</subject><subject>Data collection</subject><subject>Deoxyribonucleic acid</subject><subject>Design</subject><subject>Dietary minerals</subject><subject>DNA</subject><subject>DNA sequencing</subject><subject>Engineering</subject><subject>Enzymes</subject><subject>Feed additives</subject><subject>Feeds</subject><subject>Food additives</subject><subject>Fungi</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic Engineering</subject><subject>Genetically modified organisms</subject><subject>Genetics and Genomics</subject><subject>Genomes</subject><subject>Indonesia</subject><subject>Livestock</subject><subject>Livestock feed</subject><subject>livestock feeds</subject><subject>Melt temperature</subject><subject>Nucleotide sequence</subject><subject>nucleotide sequences</subject><subject>Nucleotide sequencing</subject><subject>Nutritive value</subject><subject>Phosphatase</subject><subject>Phosphates</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Phytase</subject><subject>phytases</subject><subject>Phytic acid</subject><subject>Polymerase chain reaction</subject><subject>Proteins</subject><subject>Proteomics</subject><subject>Software</subject><subject>temperature</subject><issn>1687-157X</issn><issn>2090-5920</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kU1r3DAQhk1poEuSP9CToJdenMxYH5aO29AmhUAuLeQmtPrYKrWtrWQX_O-rzRZCS6l0GJh5n-Fl3qZ5i3CFKMV1YRQZttDRFkAAtOurZtOBgparDl43GxSyb5H3j2-ay1KeoD7OJHLcNOZDTHEKKY9mjraQMi9uJSmQw7d1NsWTkNNItuXg8z4Ow1LIFPc-k0qQpY5NIcF7R4xzcY4_PYkTGWotc7Lfn0cXzVkwQ_GXv-t58_XTxy83d-39w-3nm-19axnr51Z62IkdyE4xy0SHDhTnO2ogMCd6hchYJ6n0AaxDKanrpQUupAmWUwFIz5v3p72HnH4s1YAeY7F-GMzk01I0RU5RUKp4lb77S_qUljxVd7qTigqJCuiLam8Gr49HmrOxx6V62_eM1isyVVVX_1DV7_wYbZp8iLX_B9CdAJtTKdkHfchxNHnVCPqYpz7lqWue-jlPvVaInqBSxVMN4MXxf6hfmKmgpA</recordid><startdate>20231201</startdate><enddate>20231201</enddate><creator>Maulana, Hamdan</creator><creator>Widyastuti, Yantyati</creator><creator>Herlina, Nina</creator><creator>Hasbuna, Abun</creator><creator>Al-Islahi, Aas Syiarudin Hasbi</creator><creator>Triratna, Lita</creator><creator>Mayasari, Novi</creator><general>Springer Berlin Heidelberg</general><general>Springer</general><general>Springer Nature B.V</general><scope>C6C</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>L6V</scope><scope>LK8</scope><scope>M7P</scope><scope>M7S</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>7S9</scope><scope>L.6</scope><orcidid>https://orcid.org/0000-0003-1017-4365</orcidid><orcidid>https://orcid.org/0000-0002-0322-3547</orcidid><orcidid>https://orcid.org/0000-0002-5005-3579</orcidid><orcidid>https://orcid.org/0009-0004-4523-4131</orcidid><orcidid>https://orcid.org/0000-0001-5437-9712</orcidid><orcidid>https://orcid.org/0000-0001-8012-5986</orcidid><orcidid>https://orcid.org/0009-0008-0170-2721</orcidid></search><sort><creationdate>20231201</creationdate><title>Bioinformatics study of phytase from Aspergillus niger for use as feed additive in livestock feed</title><author>Maulana, Hamdan ; Widyastuti, Yantyati ; Herlina, Nina ; Hasbuna, Abun ; Al-Islahi, Aas Syiarudin Hasbi ; Triratna, Lita ; Mayasari, Novi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c447t-8e0b6b08294c4621d0955b3a0f4d67911442838ef0cd1883d78c0568afc536013</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Amino acid composition</topic><topic>Amino acid sequence</topic><topic>Amino acids</topic><topic>Analysis</topic><topic>Animal feeding and feeds</topic><topic>Animal genetic engineering</topic><topic>Annealing</topic><topic>Aspergillus niger</topic><topic>Bioinformatics</topic><topic>Biomedical Engineering and Bioengineering</topic><topic>Biotechnology</topic><topic>Composition</topic><topic>computer software</topic><topic>Data collection</topic><topic>Deoxyribonucleic acid</topic><topic>Design</topic><topic>Dietary minerals</topic><topic>DNA</topic><topic>DNA sequencing</topic><topic>Engineering</topic><topic>Enzymes</topic><topic>Feed additives</topic><topic>Feeds</topic><topic>Food additives</topic><topic>Fungi</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genetic Engineering</topic><topic>Genetically modified organisms</topic><topic>Genetics and Genomics</topic><topic>Genomes</topic><topic>Indonesia</topic><topic>Livestock</topic><topic>Livestock feed</topic><topic>livestock feeds</topic><topic>Melt temperature</topic><topic>Nucleotide sequence</topic><topic>nucleotide sequences</topic><topic>Nucleotide sequencing</topic><topic>Nutritive value</topic><topic>Phosphatase</topic><topic>Phosphates</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Phytase</topic><topic>phytases</topic><topic>Phytic acid</topic><topic>Polymerase chain reaction</topic><topic>Proteins</topic><topic>Proteomics</topic><topic>Software</topic><topic>temperature</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Maulana, Hamdan</creatorcontrib><creatorcontrib>Widyastuti, Yantyati</creatorcontrib><creatorcontrib>Herlina, Nina</creatorcontrib><creatorcontrib>Hasbuna, Abun</creatorcontrib><creatorcontrib>Al-Islahi, Aas Syiarudin Hasbi</creatorcontrib><creatorcontrib>Triratna, Lita</creatorcontrib><creatorcontrib>Mayasari, Novi</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>CrossRef</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Engineering Collection</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><jtitle>Journal of Genetic Engineering and Biotechnology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Maulana, Hamdan</au><au>Widyastuti, Yantyati</au><au>Herlina, Nina</au><au>Hasbuna, Abun</au><au>Al-Islahi, Aas Syiarudin Hasbi</au><au>Triratna, Lita</au><au>Mayasari, Novi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Bioinformatics study of phytase from Aspergillus niger for use as feed additive in livestock feed</atitle><jtitle>Journal of Genetic Engineering and Biotechnology</jtitle><stitle>J Genet Eng Biotechnol</stitle><date>2023-12-01</date><risdate>2023</risdate><volume>21</volume><issue>1</issue><spage>142</spage><pages>142-</pages><artnum>142</artnum><issn>1687-157X</issn><eissn>2090-5920</eissn><abstract>Background
Phytase supplementation in rations can reduce their phytic acid composition in order to enhance their nutritional value.
Aspergillus niger
is a fungus that can encode phytase. This study aims to determine the characteristics of its DNA sequences and amino acid composition that encode the phytase enzyme, as well as to determine the primer designs.
Method
This study used gene sequence data and protein-encoding phytase from
Aspergillus niger
that was collected manually from NCBI and PDB. The data was analyzed using SPDBV and then be aligned using the ClustalW Multiple Alignment features. The phylogenetic tree was built by Mega11 software. Primers were designed from selected candidate sequences that were analyzed. The designed primers were then simulated for PCR using FastPCR and SnapGene software.
Results
There are 18
Aspergillus niger
phytases in NCBI which is 14.87% of the total
Aspergillus
. There are 14
Aspergillus niger
phytases that have identity above 95%.
Aspergillus niger
110. M94550.1 is the closest strain to the PDB template. Candidate sources of phytase genes are
Aspergillus niger
110.M94550.1, 48.2.BCMY01000003.1, and 92.JQ654450.1. The primer design has 2 possibilities of self-annealing and high melting temperature on the reverse primer. PCR simulation shows that the primer design can attach completely but still has the possibility of mispriming.
Conclusion
This study suggests promising results for the future development of phytase enzyme production from
Aspergillus niger
as a feed additive using genetic engineering to enhance the quality of livestock feed in Indonesia.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><doi>10.1186/s43141-023-00600-y</doi><orcidid>https://orcid.org/0000-0003-1017-4365</orcidid><orcidid>https://orcid.org/0000-0002-0322-3547</orcidid><orcidid>https://orcid.org/0000-0002-5005-3579</orcidid><orcidid>https://orcid.org/0009-0004-4523-4131</orcidid><orcidid>https://orcid.org/0000-0001-5437-9712</orcidid><orcidid>https://orcid.org/0000-0001-8012-5986</orcidid><orcidid>https://orcid.org/0009-0008-0170-2721</orcidid><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1687-157X |
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| issn | 1687-157X 2090-5920 |
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| source | DOAJ Directory of Open Access Journals; Springer Nature OA Free Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central |
| subjects | Amino acid composition Amino acid sequence Amino acids Analysis Animal feeding and feeds Animal genetic engineering Annealing Aspergillus niger Bioinformatics Biomedical Engineering and Bioengineering Biotechnology Composition computer software Data collection Deoxyribonucleic acid Design Dietary minerals DNA DNA sequencing Engineering Enzymes Feed additives Feeds Food additives Fungi Gene sequencing Genes Genetic Engineering Genetically modified organisms Genetics and Genomics Genomes Indonesia Livestock Livestock feed livestock feeds Melt temperature Nucleotide sequence nucleotide sequences Nucleotide sequencing Nutritive value Phosphatase Phosphates Phylogenetics Phylogeny Phytase phytases Phytic acid Polymerase chain reaction Proteins Proteomics Software temperature |
| title | Bioinformatics study of phytase from Aspergillus niger for use as feed additive in livestock feed |
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