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Liew KJ, Shahar S, Shamsir MS, Shaharuddin NB, Liang CH, Chan KG, Pointing SB, Sani RK, Goh KM. Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation. Environ Microbiome 2024; 19:29. [PMID: 38706006 PMCID: PMC11071339 DOI: 10.1186/s40793-024-00572-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 04/22/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND Hot spring biofilms provide a window into the survival strategies of microbial communities in extreme environments and offer potential for biotechnological applications. This study focused on green and brown biofilms thriving on submerged plant litter within the Sungai Klah hot spring in Malaysia, characterised by temperatures of 58-74 °C. Using Illumina shotgun metagenomics and Nanopore ligation sequencing, we investigated the microbial diversity and functional potential of metagenome-assembled genomes (MAGs) with specific focus on biofilm formation, heat stress response, and carbohydrate catabolism. RESULTS Leveraging the power of both Illumina short-reads and Nanopore long-reads, we employed an Illumina-Nanopore hybrid assembly approach to construct MAGs with enhanced quality. The dereplication process, facilitated by the dRep tool, validated the efficiency of the hybrid assembly, yielding MAGs that reflected the intricate microbial diversity of these extreme ecosystems. The comprehensive analysis of these MAGs uncovered intriguing insights into the survival strategies of thermophilic taxa in the hot spring biofilms. Moreover, we examined the plant litter degradation potential within the biofilms, shedding light on the participation of diverse microbial taxa in the breakdown of starch, cellulose, and hemicellulose. We highlight that Chloroflexota and Armatimonadota MAGs exhibited a wide array of glycosyl hydrolases targeting various carbohydrate substrates, underscoring their metabolic versatility in utilisation of carbohydrates at elevated temperatures. CONCLUSIONS This study advances understanding of microbial ecology on plant litter under elevated temperature by revealing the functional adaptation of MAGs from hot spring biofilms. In addition, our findings highlight potential for biotechnology application through identification of thermophilic lignocellulose-degrading enzymes. By demonstrating the efficiency of hybrid assembly utilising Illumina-Nanopore reads, we highlight the value of combining multiple sequencing methods for a more thorough exploration of complex microbial communities.
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Grants
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- FRGS/1/2023/STG02/UTM/02/1, FRGS/1/2019/STG03/UTM/02/1, FRGS/1/2019/STG04/UTM/02/4 Malaysia Fundamental Research Grant Scheme (FRGS)
- 4J549 UTM QuickWin grant
- 4J549 UTM QuickWin grant
- T2EP30123-0028 Singapore Ministry of Education ARC Tier 2 fund
- 1736255, 1849206, and 1920954 National Science Foundation
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Affiliation(s)
- Kok Jun Liew
- Codon Genomics, 42300 Seri Kembangan, Selangor, Malaysia
| | - Saleha Shahar
- Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Nawal Binti Shaharuddin
- School of Professional and Continuing Education, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Chee Hung Liang
- Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Stephen Brian Pointing
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA.
| | - Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
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Azemin WA, Ishak NF, Saedin MAA, Shamsir MS, Razali SA. Molecular docking and simulation studies of Chloroquine, Rimantadine and CAP-1 as potential repurposed antivirals for decapod iridescent virus 1 (DIV1). Fish Shellfish Immunol Rep 2023; 5:100120. [PMID: 37854946 PMCID: PMC10579962 DOI: 10.1016/j.fsirep.2023.100120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023] Open
Abstract
Drug repurposing is a methodology of identifying new therapeutic use for existing drugs. It is a highly efficient, time and cost-saving strategy that offers an alternative approach to the traditional drug discovery process. Past in-silico studies involving molecular docking have been successful in identifying potential repurposed drugs for the various treatment of diseases including aquaculture diseases. The emerging shrimp hemocyte iridescent virus (SHIV) or Decapod iridescent virus 1 (DIV1) is a viral pathogen that causes severe disease and high mortality (80 %) in farmed shrimps caused serious economic losses and presents a new threat to the shrimp farming industry. Therefore, effective antiviral drugs are critically needed to control DIV1 infections. The aim of this study is to investigate the interaction of potential existing antiviral drugs, Chloroquine, Rimantadine, and CAP-1 with DIV1 major capsid protein (MCP) with the intention of exploring the potential of drug repurposing. The interaction of the DIV1 MCP and three antivirals were characterised and analysed using molecular docking and molecular dynamics simulation. The results showed that CAP-1 is a more promising candidate against DIV1 with the lowest binding energy of -8.46 kcal/mol and is more stable compared to others. We speculate that CAP-1 binding may induce the conformational changes in the DIV1 MCP structure by phosphorylating multiple residues (His123, Tyr162, and Thr395) and ultimately block the viral assembly and maturation of DIV1 MCP. To the best of our knowledge, this is the first report regarding the structural characterisation of DIV1 MCP docked with repurposing drugs.
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Affiliation(s)
- Wan-Atirah Azemin
- School of Biological Sciences, Universiti Sains Malaysia, Pulau, Minden, Pinang 11800, Malaysia
| | - Nur Farahin Ishak
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Nerus, Kuala, Terengganu 21030, Malaysia
| | - Mohamad Amirul Asyraf Saedin
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Nerus, Kuala, Terengganu 21030, Malaysia
| | - Mohd Shahir Shamsir
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, UTM, Johor Bahru 81310, Malaysia
| | - Siti Aisyah Razali
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Nerus, Kuala, Terengganu 21030, Malaysia
- Biological Security and Sustainability Research Interest Group (BIOSES), Universiti Malaysia Terengganu, Nerus, Kuala, Terengganu 21030, Malaysia
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Razali SA, Shamsir MS, Ishak NF, Low CF, Azemin WA. Riding the wave of innovation: immunoinformatics in fish disease control. PeerJ 2023; 11:e16419. [PMID: 38089909 PMCID: PMC10712311 DOI: 10.7717/peerj.16419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/17/2023] [Indexed: 12/18/2023] Open
Abstract
The spread of infectious illnesses has been a significant factor restricting aquaculture production. To maximise aquatic animal health, vaccination tactics are very successful and cost-efficient for protecting fish and aquaculture animals against many disease pathogens. However, due to the increasing number of immunological cases and their complexity, it is impossible to manage, analyse, visualise, and interpret such data without the assistance of advanced computational techniques. Hence, the use of immunoinformatics tools is crucial, as they not only facilitate the management of massive amounts of data but also greatly contribute to the creation of fresh hypotheses regarding immune responses. In recent years, advances in biotechnology and immunoinformatics have opened up new research avenues for generating novel vaccines and enhancing existing vaccinations against outbreaks of infectious illnesses, thereby reducing aquaculture losses. This review focuses on understanding in silico epitope-based vaccine design, the creation of multi-epitope vaccines, the molecular interaction of immunogenic vaccines, and the application of immunoinformatics in fish disease based on the frequency of their application and reliable results. It is believed that it can bridge the gap between experimental and computational approaches and reduce the need for experimental research, so that only wet laboratory testing integrated with in silico techniques may yield highly promising results and be useful for the development of vaccines for fish.
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Affiliation(s)
- Siti Aisyah Razali
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
- Biological Security and Sustainability Research Interest Group (BIOSES), Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Mohd Shahir Shamsir
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Nur Farahin Ishak
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Chen-Fei Low
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Wan-Atirah Azemin
- School of Biological Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia
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Parvizpour S, Elengoe A, Alizadeh E, Razmara J, Shamsir MS. In silico targeting breast cancer biomarkers by applying rambutan ( Nephelium lappaceum) phytocompounds. J Biomol Struct Dyn 2023; 41:10037-10050. [PMID: 36451602 DOI: 10.1080/07391102.2022.2152868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022]
Abstract
Worldwide, breast cancer is the leading type of cancer among women. Overexpression of various prognostic indicators, including nuclear receptors, is linked to breast cancer features. To date, no effective drug has been discovered to block the proliferation of breast cancer cells. This study has been designed to discover target-based small molecular-like natural drug candidates that have anti-cancer potential without causing any serious side effects. A comprehensive substrate-based drug design was carried out to discover the potential plant compounds against the target breast cancer biomarkers including phytochemicals screening, active site identification, molecular docking, pharmacokinetic (PK) properties prediction, toxicity prediction, and molecular dynamics (MD) simulation approaches. Twenty plant compounds extracted from the rambutan (Nephelium lappaceum) were obtained from PubChem Database; and screened against the breast cancer biomarkers including estrogen receptor (ER), progesterone receptor (PR), and androgen receptor (AR). The best docking interaction was chosen based on the higher binding affinity. Analyzing the pharmacokinetic properties and toxicity prediction results indicated that the fifteen selected plant compounds have good potency without toxicity and are safe for humans. Four phytochemicals with a higher binding affinity were chosen for each breast cancer biomarker to study their stability in interaction with the target proteins using MD simulation. Among the above compounds, Ellagic acid showed the high binding affinity against all three breast cancer biomarkers.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sepideh Parvizpour
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Asita Elengoe
- Department of Biotechnology, Faculty of Science, Lincoln University College Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Effat Alizadeh
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Razmara
- Department of Computer Science, Faculty of Mathematics, Statistics, and Computer Science, University of Tabriz, Tabriz, Iran
| | - Mohd Shahir Shamsir
- Bioinformatics Research Group (BIRG), Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
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Miga M, Jahari PNS, Parimannan S, Rajandas H, Abdul-Latiff MAB, Wei YJ, Shamsir MS, Salleh FM. Characterization of the complete mitogenome data of Ischyja marapok (Lepidoptera: Noctuoidea: Erebidae) from Malaysia. Data Brief 2023; 48:109253. [PMID: 37383759 PMCID: PMC10293960 DOI: 10.1016/j.dib.2023.109253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/05/2023] [Accepted: 05/15/2023] [Indexed: 06/30/2023] Open
Abstract
Ischyja marapok is a moth species from the genus Ischyja, a member of the Lepidoptera family, Erebidae. Due to their wide variation, this family constitutes the largest described species, however, the mitogenome dataset on the genus Ischyja is scarce. Hence, the mitochondrial genome dataset of Ischyja marapok from Malaysia was completely sequenced using the next-generation sequencing technology, Illumina NovaSeq 6000 and analyzed. The mitogenome has a sequence length of 15,421 bp, consisting of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and a control region. The mitogenome is A + T biased (80.6%), with the base composition of A (39.2%), T (41.4%), C (11.9%) and G (7.5%). Among the 13 PCGs, 12 were initiated by the standard ATN codon, except for COX1 which utilizes the CGA start codon. Two PCGs were terminated with an incomplete stop codon T, while others ended with a TAA codon. Phylogenetic tree analyses showed that the sequenced I. marapok resides within the Erebinae subfamily and is closely related to Ischyja manlia (MW664367) with high bootstrap support and posterior probabilities. This dataset presented the mitogenome data of I. marapok from Malaysia, which is valuable for further research of their phylogeny and the diversification of the Ischyja genus. Also, this dataset can be implemented and used as references to assess environmental changes in the terrestrial ecosystem via environmental DNA approaches. The mitogenome of I. marapok is available in GenBank under the accession number ON165249.
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Affiliation(s)
- Marylin Miga
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia
| | - Puteri Nur Syahzanani Jahari
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia
| | - Sivachandran Parimannan
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah 08100, Malaysia
| | - Heera Rajandas
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah 08100, Malaysia
| | - Muhammad Abu Bakar Abdul-Latiff
- Environmental Management and Conservation Research Unit (ENCORE), Faculty of Applied Sciences and Technology (FAST), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Johor 84600, Malaysia
| | - Yap Jing Wei
- Centre of Research for Sustainable Uses of Natural Resources (SUNR), Faculty of Applied Sciences and Technology (FAST), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Johor 84600, Malaysia
| | - Mohd Shahir Shamsir
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah 08100, Malaysia
- Centre of Research for Sustainable Uses of Natural Resources (SUNR), Faculty of Applied Sciences and Technology (FAST), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Johor 84600, Malaysia
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Azemin WA, Alias N, Ali AM, Shamsir MS. In silico analysis prediction of HepTH1-5 as a potential therapeutic agent by targeting tumour suppressor protein networks. J Biomol Struct Dyn 2023; 41:1141-1167. [PMID: 34935583 DOI: 10.1080/07391102.2021.2017349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Many studies reported that the activation of tumour suppressor protein, p53 induced the human hepcidin expression. However, its expression decreased when p53 was silenced in human hepatoma cells. Contrary to Tilapia hepcidin TH1-5, HepTH1-5 was previously reported to trigger the p53 activation through the molecular docking approach. The INhibitor of Growth (ING) family members are also shown to directly interact with p53 and promote cell cycle arrest, senescence, apoptosis and participate in DNA replication and DNA damage responses to suppress the tumour initiation and progression. However, the interrelation between INGs and HepTH1-5 remains unknown. Therefore, this study aims to identify the mechanism and their protein interactions using in silico approaches. The finding revealed that HepTH1-5 and its ligands had interacted mostly on hotspot residues of ING proteins which involved in histone modifications via acetylation, phosphorylation, and methylation. This proves that HepTH1-5 might implicate in an apoptosis signalling pathway and preserve the protein structure and function of INGs by reducing the perturbation of histone binding upon oxidative stress response. This study would provide theoretical guidance for the design and experimental studies to decipher the role of HepTH1-5 as a potential therapeutic agent for cancer therapy. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wan-Atirah Azemin
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia.,Faculty of Science, Bioinformatics Research Group (BIRG), Department of Biosciences, Universiti Teknologi Malaysia, Skudai, Malaysia
| | - Nadiawati Alias
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia
| | - Abdul Manaf Ali
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Science, Bioinformatics Research Group (BIRG), Department of Biosciences, Universiti Teknologi Malaysia, Skudai, Malaysia.,Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
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Miga M, Jahari PNS, Parimannan S, Rajandas H, Latiff MAB, Jing Wei Y, Shamsir MS, Mohd Salleh F. Characterization of the nearly complete mitochondrial genome of ochraceous darkies, Euphaea ochracea Selys, 1859 (Odonata: Zygoptera: Euphaeidae) and phylogenetic analysis. Mitochondrial DNA B Resour 2023; 8:292-296. [PMID: 36845007 PMCID: PMC9946316 DOI: 10.1080/23802359.2023.2179355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
In the present study, the nearly complete mitochondrial genome of Euphaea ochracea was described and its phylogenetic position in the family Euphaeidae was analyzed. Here, we recovered 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and a partial control region, resulting in a mitogenome length of 15,545bp. All protein-coding genes were initiated by the typical ATN codon except nad3 and nad1, which utilizes the TTG codon. Four protein-coding genes (cox1, cox2, cox3 and nad5) are terminated by an incomplete stop codon T, while others end with either a TAA or TAG codon. The intergenic spacer region, S5, is absent in this mitogenome, supporting the lack of this region as a specific character in damselflies. Phylogenetic analysis showed that the newly sequenced E. ochracea is phylogenetically closer to E. ornata with a high support value.
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Affiliation(s)
- Marylin Miga
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | | | - Sivachandran Parimannan
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah, Malaysia
| | - Heera Rajandas
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah, Malaysia
| | - Muhammad Abu Bakar Latiff
- Environmental Management and Conservation Research Unit (ENCORE), Faculty of Applied Sciences and Technology (FAST), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Johor, Malaysia
| | - Yap Jing Wei
- Centre of Research for Sustainable Uses of Natural Resources (SUNR), Faculty of Applied Sciences and Technology (FAST), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Johor, Malaysia
| | - Mohd Shahir Shamsir
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah, Malaysia,Centre of Research for Sustainable Uses of Natural Resources (SUNR), Faculty of Applied Sciences and Technology (FAST), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Johor, Malaysia,CONTACT Faezah Mohd Salleh Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, MalaysiaCentre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah, Malaysia
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Miga M, Yap YZ, Jahari PNS, Parimannan S, Rajandas H, Abu Bakar-Latiff M, Jing Wei Y, Shamsir MS, Mohd Salleh F. Complete mitochondrial genome data and phylogenetic analysis of the Great Marquis, Bassarona dunya (Doubleday, 1848) (Lepidoptera: Nymphalidae: Limenitidinae) from Malaysia. Mitochondrial DNA B Resour 2023; 8:167-171. [PMID: 36733274 PMCID: PMC9888454 DOI: 10.1080/23802359.2023.2167476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The Great Marquis or Bassarona dunya is a butterfly species commonly found in the tropical regions of Asia, America, and Africa. This butterfly is a member of the subfamily Limenitidinae and the classification within this subfamily has been unstable. Here, we report the first complete mitochondrial genome (mitogenome) of B. dunya sampled from Malaysia. The mitogenome is 15,242 bp long, comprising a set of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and an A + T rich region. All PCGs were initiated by the typical ATN codon, except for COX1 which started with a CGA start codon. Nine PCGs were terminated with a TAA or TAG stop codon, while COX1, COX2, NAD4, and NAD5 ended with an incomplete T. The 12S and 16S rRNAs were 716 bp and 1269 bp in length, respectively. Phylogenetic analysis supported the placement of B. dunya within Limenitidinae with a high support value.
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Affiliation(s)
- Marylin Miga
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Yong Zi Yap
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | | | - Sivachandran Parimannan
- Faculty of Applied Sciences, Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Bedong, Malaysia
| | - Heera Rajandas
- Faculty of Applied Sciences, Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Bedong, Malaysia
| | - Muhammad Abu Bakar-Latiff
- Faculty of Applied Sciences and Technology (FAST), Environmental Management and Conservation Research Unit (ENCORE), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
| | - Yap Jing Wei
- Faculty of Applied Sciences and Technology (FAST), Centre of Research for Sustainable Uses of Natural Resources (SUNR), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Applied Sciences and Technology (FAST), Centre of Research for Sustainable Uses of Natural Resources (SUNR), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia,Faculty of Applied Sciences, Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Bedong, Malaysia,Faculty of Applied Sciences and Technology (FAST), Environmental Management and Conservation Research Unit (ENCORE), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia,Faculty of Applied Sciences and Technology (FAST), Centre of Research for Sustainable Uses of Natural Resources (SUNR), Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia,CONTACT Faezah Mohd Salleh Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
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Azemin WA, Alias N, Ali AM, Shamsir MS. Structural and functional characterisation of HepTH1-5 peptide as a potential hepcidin replacement. J Biomol Struct Dyn 2023; 41:681-704. [PMID: 34870559 DOI: 10.1080/07391102.2021.2011415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Hepcidin is a principal regulator of iron homeostasis and its dysregulation has been recognised as a causative factor in cancers and iron disorders. The strategy of manipulating the presence of hepcidin peptide has been used for cancer treatment. However, this has demonstrated poor efficiency and has been short-lived in patients. Many studies reported using minihepcidin therapy as an alternative way to treat hepcidin dysregulation, but this was only applied to non-cancer patients. Highly conserved fish hepcidin protein, HepTH1-5, was investigated to determine its potential use in developing a hepcidin replacement for human hepcidin (Hepc25) and as a therapeutic agent by targeting the tumour suppressor protein, p53, through structure-function analysis. The authors found that HepTH1-5 is stably bound to ferroportin, compared to Hepc25, by triggering the ferroportin internalisation via Lys42 and Lys270 ubiquitination, in a similar manner to the Hepc25 activity. Moreover, the residues Ile24 and Gly24, along with copper and zinc ligands, interacted with similar residues, Lys24 and Asp1 of Hepc25, respectively, showing that those molecules are crucial to the hepcidin replacement strategy. HepTH1-5 interacts with p53 and activates its function through phosphorylation. This finding shows that HepTH1-5 might be involved in the apoptosis signalling pathway upon a DNA damage response. This study will be very helpful for understanding the mechanism of the hepcidin replacement and providing insights into the HepTH1-5 peptide as a new target for hepcidin and cancer therapeutics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wan-Atirah Azemin
- School of Agriculture Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut, Terengganu, Malaysia.,Bioinformatics Research Group (BIRG), Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Nadiawati Alias
- School of Agriculture Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut, Terengganu, Malaysia
| | - Abdul Manaf Ali
- School of Agriculture Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, Besut, Terengganu, Malaysia
| | - Mohd Shahir Shamsir
- Bioinformatics Research Group (BIRG), Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia.,Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Johor, Malaysia
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10
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Miga M, Jahari PNS, Vei Siang C, Kamarudin KR, Shamsir MS, Tokiman L, Parimannan S, Rajandas H, Mohamed F, Salleh FM. The complete mitochondrial genome data of the Common Rose butterfly, Pachliopta aristolochiae (Lepidoptera, Papilionoidea, Papilionidae) from Malaysia. Data Brief 2022; 40:107740. [PMID: 35141362 PMCID: PMC8813591 DOI: 10.1016/j.dib.2021.107740] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/24/2022] Open
Abstract
Here, we present the complete mitochondrial genome of Pachliopta aristolochiae, a Common Rose butterfly from Malaysia. The sequence was generated using Illumina NovaSeq 6000 sequencing platform. The mitogenome is 15,235bp long, consisting of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and two D-loop regions. The total base composition was (81.6%), with A (39.3%), T (42.3%), C (11.0%) and G (7.3%). The gene order of the three tRNAs was trnM-trnI-trnQ, which differs from the ancestral insect gene order trnI-trnQ-trnM. Phylogenetic tree analysis revealed that the sequenced Pachliopta aristolochiae in this data is closely related to Losaria neptunus (NC 037868), with highly supported ML and BI analysis. The data presented in this work can provide useful resources for other researchers to study deeper into the phylogenetic relationships of Lepidoptera and the diversification of the Pachliopta species. Also, as one of the bioindicator species, this data can be used to assess environmental changes in the terrestrial and aquatic ecosystem via enviromental DNA approahes. The mitogenome of Pachliopta aristolochiae is available in GenBank under the accession number MZ781228.
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Affiliation(s)
- Marylin Miga
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia
| | - Puteri Nur Syahzanani Jahari
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia
| | - Chan Vei Siang
- School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia
| | - Kamarul Rahim Kamarudin
- Centre of Research for Sustainable Uses of Natural Resources (SUNR), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Johor 84600, Malaysia
| | - Mohd Shahir Shamsir
- Centre of Research for Sustainable Uses of Natural Resources (SUNR), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Johor 84600, Malaysia
| | - Lili Tokiman
- Johor National Parks Corporation, Kota Iskandar, Iskandar Puteri, Johor 79575, Malaysia
| | - Sivachandran Parimannan
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah 08100, Malaysia.,Deakin Genomics Centre, School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds Campus, Victoria 3216, Australia
| | - Heera Rajandas
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah 08100, Malaysia.,Deakin Genomics Centre, School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds Campus, Victoria 3216, Australia
| | - Farhan Mohamed
- School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia.,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah 08100, Malaysia
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11
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Jahari PNS, Mohd Azman S, Munian K, Ahmad Ruzman NH, Shamsir MS, Richter SR, Mohd Salleh F. Characterization of the mitogenomes of long-tailed giant rat, Leopoldamys sabanus and a comparative analysis with other Leopoldamys species. Mitochondrial DNA B Resour 2021; 6:502-504. [PMID: 33628904 PMCID: PMC7889269 DOI: 10.1080/23802359.2021.1872433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Two mitogenomes of long-tailed giant rat, Leopoldamys sabanus (Thomas, 1887), which belongs to the family Muridae were sequenced and assembled in this study. Both mitogenomes have a length of 15,973 bp and encode 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and one control region. The circular molecule of L. sabanus has a typical vertebrate gene arrangement. Phylogenetic and BLASTn analysis using 10 Leopoldamys species mitogenomes revealed sequence variation occurred within species from different time zones. Along with the taxonomic issues, this suggests a landscape change might influence genetic connectivity.
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Affiliation(s)
| | - Shahfiz Mohd Azman
- Forest Biodiversity Division, Forest Research Institute Malaysia, Selangor, Kepong, Malaysia
| | - Kaviarasu Munian
- Forest Biodiversity Division, Forest Research Institute Malaysia, Selangor, Kepong, Malaysia
| | | | - Mohd Shahir Shamsir
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Johor, Muar, Malaysia
| | - Stine R Richter
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Johor Bahru, Malaysia
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12
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Shamsir MS, Krauss SE, Ismail IA, Ab Jalil H, Johar MA, Abdul Rahman I. Development of a Haddon Matrix Framework for Higher Education Pandemic Preparedness: Scoping Review and Experiences of Malaysian Universities During the COVID-19 Pandemic. High Educ Policy 2021; 35:439-478. [PMID: 34594092 PMCID: PMC7808121 DOI: 10.1057/s41307-020-00221-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Managing education and research during pandemics has increased in importance since the onset of epidemics such as avian flu, SARS and now CoViD-19. Successful management in times of crisis ensures business continuity and institutional survival, making preparedness preceding an impending pandemic essential. Institutions of higher education (IHEs) must maintain balance between academic continuity and preventing morbidity during a pandemic crisis. To date, however, no general pandemic preparedness frameworks exist for IHEs. The aim of this paper is to report on the development of a Haddon matrix framework for IHE pandemic preparedness based on a scoping literature review of past IHE responses including pre-, during and post-pandemic phases. First, a review of previous global responses by IHEs during past pandemics was carried out. The review findings were then collated into a new IHE-centric Haddon matrix for pandemic preparedness. The content of the matrix is then illustrated through the documented responses of Malaysian universities during the early stages of the COVID-19 pandemic. The resulting IHE Haddon matrix can be used by universities as a general guide to identify preparedness gaps and intervention opportunities for business continuity during pandemics.
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Affiliation(s)
- Mohd Shahir Shamsir
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, 84600 Muar, Johor Malaysia
| | - Steven Eric Krauss
- Innovative Learning Sciences Research Centre of Excellence (INNOVATE), Faculty of Educational Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Ismi Arif Ismail
- Innovative Learning Sciences Research Centre of Excellence (INNOVATE), Faculty of Educational Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Habibah Ab Jalil
- Innovative Learning Sciences Research Centre of Excellence (INNOVATE), Faculty of Educational Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Muhammad Akmal Johar
- Faculty of Mechanical and Manufacturing Engineering, Universiti Tun Hussein Onn Malaysia, 86400 Batu Pahat, Johor Malaysia
| | - Ismail Abdul Rahman
- Faculty of Civil Engineering and Built Environment, Universiti Tun Hussein Onn Malaysia, 86400 Batu Pahat, Johor Malaysia
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13
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Lam MQ, Chen SJ, Goh KM, Abd Manan F, Yahya A, Shamsir MS, Chong CS. Genome sequence of an uncharted halophilic bacterium Robertkochia marina with deciphering its phosphate-solubilizing ability. Braz J Microbiol 2020; 52:251-256. [PMID: 33141351 DOI: 10.1007/s42770-020-00401-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/28/2020] [Indexed: 10/23/2022] Open
Abstract
The wide use of whole-genome sequencing approach in the modern genomic era has opened a great opportunity to reveal the prospective applications of halophilic bacteria. Robertkochia marina CC-AMO-30DT is one of the halophilic bacteria that was previously taxonomically identified without any inspection on its biotechnological potential from a genomic aspect. In this study, we present the whole-genome sequence of R. marina and demonstrated the ability of this bacterium in solubilizing phosphate by producing phosphatase. The genome of R. marina has 3.57 Mbp and contains 3107 predicted genes, from which 3044 are protein coding, 52 are non-coding RNAs, and 11 are pseudogenes. Several phosphatases such as alkaline phosphatases and pyrophosphatases were mined from the genome. Further genomic study (phylogenetics, sequence analysis, and functional mechanism) and experimental data suggested that the alkaline phosphatase produced by R. marina could potentially be utilized in promoting plant growth, particularly for plants on saline-based agricultural land.
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Affiliation(s)
- Ming Quan Lam
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Sye Jinn Chen
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Kian Mau Goh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Fazilah Abd Manan
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Adibah Yahya
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (UTHM), Pagoh Higher Education Hub, 84600, Muar, Johor, Malaysia
| | - Chun Shiong Chong
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
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14
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Jahari PNS, Mohd Azman S, Munian K, M Fauzi NF, Shamsir MS, Richter SR, Mohd Salleh F. The first complete mitochondrial genome data of Geoffroy's rousette, Rousettus amplexicaudatus originating from Malaysia. Mitochondrial DNA B Resour 2020; 5:3262-3264. [PMID: 33458132 PMCID: PMC7781998 DOI: 10.1080/23802359.2020.1812449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The increasing interest in understanding the evolutionary relationship between members of the Pteropodidae family has been greatly aided by genomic data from the Old World fruit bats. Here we present the complete mitogenome of Geoffroy’s rousette, Rousettus amplexicaudatus found in Peninsular Malaysia . The mitogenome constructed is 16,511bp in length containing 37 genes; 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a D-loop region. The overall base composition is estimated to be 32.28% for A, 25.64% for T, 14.09% for G and 27.98% for C, indicating a slightly AT rich feature (57.93%). A phylogenetic and BLASTn analysis against other available mitogenomes showed Malaysian R. amplexicaudatus matched 98% similarity to the same species in Cambodia and Vietnam. However, it differed considerably (92.53% similarity) with the same species in the Philippines. This suggests flexibility in Rousettus sp. with regards to adapting to mesic and dry habitats, ability for long-distance dispersal and remarkably precise lingual echolocation thus supporting its wide-range distribution and colonization. Further taxonomical and mitogenomic comparatives are required in resolving the evolutionary relationship between Rousettus spp.
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Affiliation(s)
| | - Shahfiz Mohd Azman
- Forest Biodiversity Division, Forest Research Institute Malaysia, Kepong, Malaysia
| | - Kaviarasu Munian
- Forest Biodiversity Division, Forest Research Institute Malaysia, Kepong, Malaysia
| | | | - Mohd Shahir Shamsir
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Muar, Malaysia
| | - Stine R Richter
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
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15
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Jahari PNS, Mohd Azman S, Munian K, Ahmad Ruzman NH, Shamsir MS, Richter SR, Gilbert MTP, Mohd Salleh F. Molecular identification and phylogenetic analysis of a Callosciurus notatus complete mitogenome from Peninsular Malaysia. Mitochondrial DNA B Resour 2020; 5:3004-3006. [PMID: 33458034 PMCID: PMC7782351 DOI: 10.1080/23802359.2020.1797583] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The mitogenome of a plantain squirrel, Callosciurus notatus, collected from Bukit Tarek Forest Reserve (Extension), Selangor, Malaysia was sequenced using BGISEQ-500RS technology. The 16,582 bp mitogenome consists of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. A phylogenetic and BLASTn analysis against other available datasets showed that the mitogenome matched with 99.49% similarity to a previously published C. notatus mitogenome from Peninsular Malaysia. However, it also diverged by nearly 8% (92.24% match) from a second previously published mitogenome for the same species, sampled in East Kalimantan, Indonesia. This suggests a difference in landscape features between both localities might affect its genetic connectivity.
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Affiliation(s)
| | - Shahfiz Mohd Azman
- Forest Biodiversity Division, Forest Research Institute Malaysia, Kepong, Malaysia
| | - Kaviarasu Munian
- Forest Biodiversity Division, Forest Research Institute Malaysia, Kepong, Malaysia
| | | | - Mohd Shahir Shamsir
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
| | - Stine R Richter
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
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16
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Jahari PNS, Abdul Malik NF, Shamsir MS, Gilbert MP, Mohd Salleh F. The first complete mitochondrial genome data of Hippocampus kuda originating from Malaysia. Data Brief 2020; 31:105721. [PMID: 32490085 PMCID: PMC7260291 DOI: 10.1016/j.dib.2020.105721] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 11/26/2022] Open
Abstract
The spotted seahorse, Hippocampus kuda population is exponentially decreasing globally due to habitat loss contributed by massive coastal urbanization as well as its large exploitation for Chinese herbal medicine. Genomic data would be highly useful to improve biomonitoring of seahorse populations in Malaysia via the usage of non-invasive approaches such as water environmental DNA. Here we report the first complete mitogenome of two H. kuda individuals originating from Malaysia, generated using BGISEQ-500RS sequencer. The lengths of both mitogenomes are 16,529bp, consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. The overall base composition was 32.46% for A, 29.40% for T, 14.73% for G and 23.41% for C with AT rich features (61.86%). The gene organization of Malaysian H. kuda were similar to that of most teleost species. A phylogenetic analysis of the genome against mtDNA data from other Hippocampus species showed that Malaysian H. kuda samples clustered with H. capensis, H. reidi and H. kuda. Notably however, analysis of the data using BLASTn revealed they had 99.18% similarity to H. capensis, and only 97.66% to H. kuda and H. reidi, which are all part of the unresolved H. kuda complex. The mitogenomes are deposited in Genbank under the accession number MT221436 (HK1) and MT221436 (HK2).
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Affiliation(s)
- Puteri Nur Syahzanani Jahari
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia
| | - Nur Fatihah Abdul Malik
- Johor Biotechnology & Biodiversity Corporation (J-Biotech), Level 2, Bio-XCell Malaysia, No. 2, Jalan Bioteknologi 1, SiLC Industrial Park, 79200 Iskandar Puteri, Johor, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, 84600 Muar, Johor, Malaysia
| | - M. Thomas P. Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5a, 1353, Copenhagen, Denmark
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia
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17
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Liew KJ, Bruce NC, Sani RK, Chong CS, Yaakop AS, Shamsir MS, Goh KM. Global Transcriptomic Responses of Roseithermus sacchariphilus Strain RA in Media Supplemented with Beechwood Xylan. Microorganisms 2020; 8:E976. [PMID: 32610703 PMCID: PMC7409140 DOI: 10.3390/microorganisms8070976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/23/2020] [Accepted: 06/27/2020] [Indexed: 11/17/2022] Open
Abstract
The majority of the members in order Rhodothermales are underexplored prokaryotic extremophiles. Roseithermus, a new genus within Rhodothermales, was first described in 2019. Roseithermus sacchariphilus is the only species in this genus. The current report aims to evaluate the transcriptomic responses of R. sacchariphilus strain RA when cultivated on beechwood xylan. Strain RA doubled its growth in Marine Broth (MB) containing xylan compared to Marine Broth (MB) alone. Strain RA harbors 54 potential glycosyl hydrolases (GHs) that are affiliated with 30 families, including cellulases (families GH 3, 5, 9, and 44) and hemicellulases (GH 2, 10, 16, 29, 31,43, 51, 53, 67, 78, 92, 106, 113, 130, and 154). The majority of these GHs were upregulated when the cells were grown in MB containing xylan medium and enzymatic activities for xylanase, endoglucanase, β-xylosidase, and β-glucosidase were elevated. Interestingly, with the introduction of xylan, five out of six cellulolytic genes were upregulated. Furthermore, approximately 1122 genes equivalent to one-third of the total genes for strain RA were upregulated. These upregulated genes were mostly involved in transportation, chemotaxis, and membrane components synthesis.
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Affiliation(s)
- Kok Jun Liew
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia; (K.J.L.); (C.S.C.); (M.S.S.)
| | - Neil C. Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK;
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA;
| | - Chun Shiong Chong
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia; (K.J.L.); (C.S.C.); (M.S.S.)
| | - Amira Suriaty Yaakop
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang 11800, Malaysia;
| | - Mohd Shahir Shamsir
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia; (K.J.L.); (C.S.C.); (M.S.S.)
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Johor 84600, Malaysia
| | - Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia; (K.J.L.); (C.S.C.); (M.S.S.)
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18
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Zakaria MR, Lam MQ, Chen SJ, Abdul Karim MH, Tokiman L, Yahya A, Shamsir MS, Chong CS. Genome sequence data of Mangrovimonas sp. strain CR14 isolated from mangrove forest at Tanjung Piai National Park, Malaysia. Data Brief 2020; 30:105658. [PMID: 32426431 PMCID: PMC7225383 DOI: 10.1016/j.dib.2020.105658] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/23/2020] [Accepted: 04/28/2020] [Indexed: 12/20/2022] Open
Abstract
Mangrovimonas sp. strain CR14 is a halophilic bacterium affiliated with family Flavobacteriaceae which was successfully isolated from mangrove soil samples obtained from Tanjung Piai National Park, Johor. The whole genome of strain CR14 was sequenced on an Illumina HiSeq 2500 platform (2 × 150 bp paired end). Herein, we report the genome sequence of Mangrovimonas sp. strain CR14 in which its assembled genome consisted 20 contigs with a total size of 3,590,195 bp, 3209 coding sequences, and an average 36.08% G + C content. Genome annotation and gene mining revealed that this bacterium demonstrated proteolytic activity which could be potentially applied in detergent industry. This whole-genome shotgun data of Mangrovimonas sp. strain CR14 has been deposited at DDBJ/ENA/GenBank under the accession JAAFZY000000000. The version described in this paper is version JAAFZY010000000.
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Affiliation(s)
| | - Ming Quan Lam
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Sye Jinn Chen
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | | | - Lili Tokiman
- Johor National Parks Corporation, Kota Iskandar, 79575 Iskandar Puteri, Johor, Malaysia
| | - Adibah Yahya
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, 84600 Muar, Johor, Malaysia
| | - Chun Shiong Chong
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
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19
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Razali SA, Shamsir MS. Characterisation of a catalytic triad and reaction selectivity in the dual mechanism of the catalyse hydride transfer in xylitol phosphate dehydrogenase. J Mol Graph Model 2020; 97:107548. [PMID: 32023508 DOI: 10.1016/j.jmgm.2020.107548] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/04/2020] [Accepted: 01/22/2020] [Indexed: 10/25/2022]
Abstract
Xylitol is a high-value low-calorie sweetener used as sugar substitute in food and pharmaceutical industry. Xylitol phosphate dehydrogenase (XPDH) catalyses the conversion of d-xylulose 5-phosphate (XU5P) and d-ribulose 5-phosphate (RU5P) to xylitol and ribitol respectively in the presence of nicotinamide adenine dinucleotide hydride (NADH). Although these enzymes have been shown to produce xylitol and ribitol, there is an incomplete understanding of the mechanism of the catalytic events of these reactions and the detailed mechanism has yet to be elucidated. The main goal of this work is to analyse the conformational changes of XPDH-bound ligands such as zinc, NADH, XU5P, and RU5P to elucidate the key amino acids involved in the substrate binding. In silico modelling, comparative molecular dynamics simulations, interaction analysis and conformational study were carried out on three XPDH enzymes of the Medium-chain dehydrogenase (MDR) family in order to elucidate the atomistic details of conformational transition, especially on the open and closed state of XPDH. The analysis also revealed the possible mechanism of substrate specificity that are responsible in the catalyse hydride transfer are the residues His58 and Ser39 which would act as the proton donor for reduction of XU5P and RU5P respectively. The structural comparison and MD simulations displayed a significant difference in the conformational dynamics of the catalytic and coenzyme loops between Apo and XPDH-complexes and highlight the contribution of newly found triad residues. This study would assist future mutagenesis study and enzyme modification work to increase the catalysis efficiency of xylitol production in the industry.
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Affiliation(s)
- Siti Aisyah Razali
- Bioinformatics, Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia; Bioinformatics Research Group (BIRG), Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
| | - Mohd Shahir Shamsir
- Bioinformatics Research Group (BIRG), Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia; Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, 84600 Muar, Johor, Malaysia
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20
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Shamsir MS, Abd Jamil A. Escaping the Middle Innovation Trap: Case Studies of Two Successful Spin-off Companies from a Malaysian Research University. JRMG 2019; 2:10-21. [DOI: 10.22452/jrmg.vol2no1.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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21
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Liew KJ, Ngooi CY, Shamsir MS, Sani RK, Chong CS, Goh KM. Heterologous expression, purification and biochemical characterization of a new endo-1,4-β-xylanase from Rhodothermaceae bacterium RA. Protein Expr Purif 2019; 164:105464. [DOI: 10.1016/j.pep.2019.105464] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/10/2019] [Accepted: 07/31/2019] [Indexed: 11/28/2022]
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22
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Sabetian S, Shamsir MS. Computer aided analysis of disease linked protein networks. Bioinformation 2019; 15:513-522. [PMID: 31485137 PMCID: PMC6704336 DOI: 10.6026/97320630015513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 12/26/2022] Open
Abstract
Proteins can interact in various ways, ranging from direct physical relationships to indirect interactions in a formation of protein-protein
interaction network. Diagnosis of the protein connections is critical to identify various cellular pathways. Today constructing and
analyzing the protein interaction network is being developed as a powerful approach to create network pharmacology toward detecting
unknown genes and proteins associated with diseases. Discovery drug targets regarding therapeutic decisions are exciting outcomes of
studying disease networks. Protein connections may be identified by experimental and recent new computational approaches. Due to
difficulties in analyzing in-vivo proteins interactions, many researchers have encouraged improving computational methods to design
protein interaction network. In this review, the experimental and computational approaches and also advantages and disadvantages of
these methods regarding the identification of new interactions in a molecular mechanism have been reviewed. Systematic analysis of
complex biological systems including network pharmacology and disease network has also been discussed in this review.
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Affiliation(s)
- Soudabeh Sabetian
- Department of Biological and Health Sciences, Faculty of Bioscience and Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor, Malaysia.,Infertility Research Center, Shiraz University, Shiraz 71454, Iran, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohd Shahir Shamsir
- Department of Biological and Health Sciences, Faculty of Bioscience and Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor, Malaysia
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23
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Low CF, Shamsir MS, Mohamed-Hussein ZA, Baharum SN. Evaluation of potential molecular interaction between quorum sensing receptor, LuxP and grouper fatty acids: in-silico screening and simulation. PeerJ 2019; 7:e6568. [PMID: 30984478 PMCID: PMC6452917 DOI: 10.7717/peerj.6568] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 02/05/2019] [Indexed: 11/20/2022] Open
Abstract
Pathologically relevant behaviors of Vibrio, such as the expression of virulence factors, biofilm production, and swarming motility, have been shown to be controlled by quorum sensing. The autoinducer-2 quorum sensing receptor protein LuxP is one of the target proteins for drug development to suppress the virulence of Vibrio. Here, we reported the potential molecular interaction of fatty acids identified in vibriosis-resistant grouper with LuxP. Fatty acid, 4-oxodocosahexaenoic acid (4R8) showed significant binding affinity toward LuxP (-6.0 kcal/mol) based on molecular docking analysis. The dynamic behavior of the protein-ligand complex was illustrated by molecular dynamic simulations. The fluctuation of the protein backbone, the stability of ligand binding, and hydrogen bond interactions were assessed, suggesting 4R8 possesses potential interaction with LuxP, which was supported by the low binding free energy (-29.144 kJ/mol) calculated using the molecular mechanics Poisson-Boltzmann surface area.
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Affiliation(s)
- Chen-Fei Low
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Bioscience and Bioengineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Centre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- Centre for Frontier Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Syarul Nataqain Baharum
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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24
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Parvizpour S, Razmara J, Shamsir MS. Temperature adaptation analysis of a psychrophilic mannanase through structural, functional and molecular dynamics simulation. Molecular Simulation 2018. [DOI: 10.1080/08927022.2018.1492721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Sepideh Parvizpour
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Razmara
- Department of Computer Science, Faculty of Mathematical Sciences, University of Tabriz, Tabriz, Iran
| | - Mohd Shahir Shamsir
- Bioinformatics Research Group, Faculty of Bioscience and Medical Engineering, Universiti Teknologi Malaysia, Johor, Malaysia
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25
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Liew KJ, Teo SC, Shamsir MS, Sani RK, Chong CS, Chan KG, Goh KM. Complete genome sequence of Rhodothermaceae bacterium RA with cellulolytic and xylanolytic activities. 3 Biotech 2018; 8:376. [PMID: 30105201 PMCID: PMC6087703 DOI: 10.1007/s13205-018-1391-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/06/2018] [Indexed: 11/26/2022] Open
Abstract
Rhodothermaceae bacterium RA is a halo-thermophile isolated from a saline hot spring. Previously, the genome of this bacterium was sequenced using a HiSeq 2500 platform culminating in 91 contigs. In this report, we report on the resequencing of its complete genome using a PacBio RSII platform. The genome has a GC content of 68.3%, is 4,653,222 bp in size, and encodes 3711 genes. We are interested in understanding the carbohydrate metabolic pathway, in particular the lignocellulosic biomass degradation pathway. Strain RA harbors 57 glycosyl hydrolase (GH) genes that are affiliated with 30 families. The bacterium consists of cellulose-acting (GH 3, 5, 9, and 44) and hemicellulose-acting enzymes (GH 3, 10, and 43). A crude cell-free extract of the bacterium exhibited endoglucanase, xylanase, β-glucosidase, and β-xylosidase activities. The complete genome information coupled with biochemical assays confirms that strain RA is able to degrade cellulose and xylan. Therefore, strain RA is another excellent member of family Rhodothermaceae as a repository of novel and thermostable cellulolytic and hemicellulolytic enzymes.
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Affiliation(s)
- Kok Jun Liew
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Seng Chong Teo
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, USA
| | - Chun Shiong Chong
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Kok-Gan Chan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- International Genome Centre, Jiangsu University, Zhenjiang, 212013 People’s Republic of China
| | - Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
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26
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Mohd Salleh F, Ramos-Madrigal J, Peñaloza F, Liu S, Mikkel-Holger SS, Riddhi PP, Martins R, Lenz D, Fickel J, Roos C, Shamsir MS, Azman MS, Burton KL, Stephen JR, Wilting A, Gilbert MTP. An expanded mammal mitogenome dataset from Southeast Asia. Gigascience 2018; 6:1-8. [PMID: 28873965 PMCID: PMC5737531 DOI: 10.1093/gigascience/gix053] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 07/02/2017] [Indexed: 11/24/2022] Open
Abstract
Southeast (SE) Asia is 1 of the most biodiverse regions in the world, and it holds
approximately 20% of all mammal species. Despite this, the majority of SE Asia's genetic
diversity is still poorly characterized. The growing interest in using environmental DNA
to assess and monitor SE Asian species, in particular threatened mammals—has created the
urgent need to expand the available reference database of mitochondrial barcode and
complete mitogenome sequences. We have partially addressed this need by generating 72 new
mitogenome sequences reconstructed from DNA isolated from a range of historical and modern
tissue samples. Approximately 55 gigabases of raw sequence were generated. From this data,
we assembled 72 complete mitogenome sequences, with an average depth of coverage of ×102.9
and ×55.2 for modern samples and historical samples, respectively. This dataset represents
52 species, of which 30 species had no previous mitogenome data available. The mitogenomes
were geotagged to their sampling location, where known, to display a detailed geographical
distribution of the species. Our new database of 52 taxa will strongly enhance the utility
of environmental DNA approaches for monitoring mammals in SE Asia as it greatly increases
the likelihoods that identification of metabarcoding sequencing reads can be assigned to
reference sequences. This magnifies the confidence in species detections and thus allows
more robust surveys and monitoring programmes of SE Asia's threatened mammal biodiversity.
The extensive collections of historical samples from SE Asia in western and SE Asian
museums should serve as additional valuable material to further enrich this reference
database.
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Affiliation(s)
- Faezah Mohd Salleh
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.,Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia
| | - Jazmín Ramos-Madrigal
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Fernando Peñaloza
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke Strasse 17, 10315 Berlin, Germany.,Undergraduate Program on Genomic Sciences, Universidad Nacional Autonoma de Mexico, 62210 Cuernavaca, Mexico
| | - Shanlin Liu
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.,BGI-Shenzhen, Shenzhen, GuangDong, China
| | - S Sinding Mikkel-Holger
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.,Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
| | - P Patel Riddhi
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke Strasse 17, 10315 Berlin, Germany.,Freie Universität Berlin, Kaiserswerther Str. 16-18, 14195 Berlin, Germany
| | - Renata Martins
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
| | - Dorina Lenz
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke Strasse 17, 10315 Berlin, Germany.,University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str 24-25, 14476 Potsdam, Germany
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077, Göttingen, Germany
| | - Mohd Shahir Shamsir
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor Bahru, Johor, Malaysia
| | - Mohammad Shahfiz Azman
- Forest Biodiversity Division, Forest Research Institute Malaysia, 52109 Kepong, Selangor, Malaysia
| | - K Lim Burton
- Department of Natural History, Royal Ontario Museum, Toronto, Canada
| | - J Rossiter Stephen
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Andreas Wilting
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke Strasse 17, 10315 Berlin, Germany
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen, Denmark.,NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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27
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Sadat Mohajer F, Parvizpour S, Razmara J, Shahir Shamsir M. The two mutations of actin-myosin interface and their effect on the dynamics, structures, and functions of skeletal muscle actin. J Biomol Struct Dyn 2018; 37:372-382. [PMID: 29338614 DOI: 10.1080/07391102.2018.1427630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Congenital myopathy is a broad category of muscular diseases with symptoms appearing at the time of birth. One type of congenital myopathy is Congenital Fiber Type Disproportion (CFTD), a severely debilitating disease. The G48D and G48C mutations in the D-loop and the actin-myosin interface are the two causes of CFTD. These mutations have been shown to significantly affect the structure and function of muscle fibers. To the author's knowledge, the effects of these mutations have not yet been studied. In this work, the power stroke structure of the head domain of myosin and the wild and mutated types of actin were modeled. Then, a MD simulation was run for the modeled structures to study the effects of these mutations on the structure, function, and molecular dynamics of actin. The wild and mutated actins docked with myosin showed differences in hydrogen bonding patterns, free binding energies, and hydrogen bond occupation frequencies. The G48D and G48C mutations significantly impacted the conformation of D-loops because of their larger size compared to Glycine and their ability to interfere with the polarity or hydrophobicity of this neutralized and hydrophobic loop. Therefore, the mutated loops were unable to fit properly into the hydrophobic groove of the adjacent G-actin. The abnormal structure of D-loops seems to result in the abnormal assembly of F-actins, giving rise to the symptoms of CFTD. It was also noted that G48C and G48D did not form hydrogen bonds with myosin in the residue 48 location. Nevertheless, in this case, muscles are unable to contract properly due to muscle atrophy.
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Affiliation(s)
- Faeze Sadat Mohajer
- a Bioinformatics Research Group, Faculty of Bioscience and Medical Engineering , UniversitiTeknologi Malaysia , Johor Bahru , Malaysia
| | - Sepideh Parvizpour
- b Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute , Tabriz University of Medical Sciences , Tabriz , Iran
| | - Jafar Razmara
- c Departement of Computer Science , University of Tabriz , Tabriz , Iran
| | - Mohd Shahir Shamsir
- a Bioinformatics Research Group, Faculty of Bioscience and Medical Engineering , UniversitiTeknologi Malaysia , Johor Bahru , Malaysia
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28
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Homouz D, Joyce-Tan KH, Shahir Shamsir M, Moustafa IM, Idriss H. Molecular dynamics simulations suggest changes in electrostatic interactions as a potential mechanism through which serine phosphorylation inhibits DNA Polymerase β's activity. J Mol Graph Model 2017; 79:192. [PMID: 29223917 DOI: 10.1016/j.jmgm.2017.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/31/2017] [Accepted: 11/02/2017] [Indexed: 11/27/2022]
Abstract
DNA polymerase β is a 39kDa enzyme that is a major component of Base Excision Repair in human cells. The enzyme comprises two major domains, a 31kDa domain responsible for the polymerase activity and an 8kDa domain, which bind ssDNA and has a deoxyribose phosphate (dRP) lyase activity. DNA polymerase β was shown to be phosphorylated in vitro with protein kinase C (PKC) at serines 44 and 55 (S44 and S55), resulting in loss of its polymerase enzymic activity, but not its ability to bind ssDNA. In this study, we investigate the potential phosphorylation-induced structural changes for DNA polymerase β using molecular dynamics. The simulations show drastic conformational changes of the polymerase structure as a result of S44 phosphorylation. Phosphorylation-induced conformational changes transform the closed (active) enzyme structure into an open one. Further analysis of the results points to a key hydrogen bond and newly formed salt bridges as potential drivers of these structural fluctuations. The changes observed with S44/55 and S55 phosphorylation were less dramatic than S44 and the integrity of the H-bond was not compromised. Thus the phosphorylation of S44 is likely the major contributor to structural fluctuations that lead to loss of enzymatic activity.
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Affiliation(s)
- Dirar Homouz
- Department of Physics, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, United Arab Emirates; Department of Physics, University of Houston, Houston, TX, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Kwee Hong Joyce-Tan
- Faculty of Bioscience and Bioengineering, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Bioscience and Bioengineering, Universiti Teknologi Malaysia, Johor, Malaysia
| | | | - Haitham Idriss
- Department of Biology and Biochemistry, Birzeit University, Palestine.
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29
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Shazali N, Chew TH, Shamsir MS, Tingga RCT, Mohd-Ridwan AR, Khan FAA. Assessing Bat Roosts Using the LiDAR System at Wind Cave Nature Reserve in Sarawak, Malaysian Borneo. Acta Chiropterologica 2017. [DOI: 10.3161/15081109acc2017.19.1.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Nursyafiqah Shazali
- Department of Zoology, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Teong Han Chew
- Department of Biosciences and Health Sciences, Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Mohd Shahir Shamsir
- Department of Biosciences and Health Sciences, Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | | | - A. R. Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
| | - Faisal Ali Anwarali Khan
- Department of Zoology, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia
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30
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Sabetian S, Shamsir MS. Deficiency in Sperm-Egg Protein Interaction as a Major Cause of Fertilization Failure. J Membr Biol 2017; 250:133-144. [PMID: 28280854 DOI: 10.1007/s00232-017-9954-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 02/21/2017] [Indexed: 11/29/2022]
Abstract
Complete elucidation of fertilization process at molecular level is one of the unresolved challenges in sexual reproduction studies, and understanding the molecular mechanism is crucial in overcoming difficulties in infertility and unsuccessful in vitro fertilization. Sperm-oocyte interaction is one of the most remarkable events in fertilization process, and deficiency in protein-protein interactions which mediate this interaction is a major cause of unexplained infertility. Due to detection of how the various defects of sperm-oocyte interaction can affect fertilization failure, different experimental methods have been applied. This review summarizes the current understanding of sperm-egg interaction mechanism during fertilization and also accumulates the different types of sperm-egg interaction abnormalities and their association with infertility. Several detection approaches regarding sperm-egg protein interactions and the associated defects are reviewed in this paper.
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Affiliation(s)
- Soudabeh Sabetian
- Department of Biological and Health Sciences, Faculty of Bioscience & Medical Engineering, Universiti Teknologi Malaysia, 81310, Johor, Malaysia.
| | - Mohd Shahir Shamsir
- Department of Biological and Health Sciences, Faculty of Bioscience & Medical Engineering, Universiti Teknologi Malaysia, 81310, Johor, Malaysia.
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31
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Adamu A, Shamsir MS, Wahab RA, Parvizpour S, Huyop F. Multi-template homology-based structural model of L-2-haloacid dehalogenase (DehL) from Rhizobium sp. RC1. J Biomol Struct Dyn 2016; 35:3285-3296. [DOI: 10.1080/07391102.2016.1254115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Aliyu Adamu
- Faculty of Biosciences and Medical Engineering, Department of Biotechnology and Medical Engineering, Universiti Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia
- Faculty of Science, Department of Microbiology, Kaduna State University, Tafawa Balewa way, Kaduna PMB 2339, Nigeria
| | - Mohd Shahir Shamsir
- Faculty of Biosciences and Medical Engineering, Department of Biotechnology and Medical Engineering, Universiti Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia
| | - Roswanira Abdul Wahab
- Faculty of Science, Department of Chemistry, Universiti Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia
| | - Sepideh Parvizpour
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fahrul Huyop
- Faculty of Biosciences and Medical Engineering, Department of Biotechnology and Medical Engineering, Universiti Teknologi Malaysia, Johor Bahru 81310, Johor, Malaysia
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32
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Lim JC, Thevarajoo S, Selvaratnam C, Goh KM, Shamsir MS, Ibrahim Z, Chong CS. Global transcriptomic response of Anoxybacillus sp. SK 3-4 to aluminum exposure. J Basic Microbiol 2016; 57:151-161. [PMID: 27859397 DOI: 10.1002/jobm.201600494] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/23/2016] [Indexed: 01/15/2023]
Abstract
Anoxybacillus sp. SK 3-4 is a Gram-positive, rod-shaped bacterium and a member of family Bacillaceae. We had previously reported that the strain is an aluminum resistant thermophilic bacterium. This is the first report to provide a detailed analysis of the global transcriptional response of Anoxybacillus when the cells were exposed to 600 mg L-1 of aluminum. The transcriptome was sequenced using Illumina MiSeq sequencer. Total of 708 genes were differentially expressed (fold change >2.00) with 316 genes were up-regulated while 347 genes were down-regulated, in comparing to control with no aluminum added in the culture. Based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the majority of genes encoding for cell metabolism such as glycolysis, sulfur metabolism, cysteine and methionine metabolism were up-regulated; while most of the gene associated with tricarboxylic acid cycle (TCA cycle) and valine, leucine and isoleucine metabolism were down-regulated. In addition, a significant number of the genes encoding ABC transporters, metal ions transporters, and some stress response proteins were also differentially expressed following aluminum exposure. The findings provide further insight and help us to understand on the resistance of Anoxybacillus sp. SK 3-4 toward aluminium.
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Affiliation(s)
- Jia Chun Lim
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Suganthi Thevarajoo
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Chitra Selvaratnam
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Zaharah Ibrahim
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Chun Shiong Chong
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
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33
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Sabetian S, Shamsir MS. Systematic Analysis of Protein Interaction Network Associated with Azoospermia. Int J Mol Sci 2016; 17:ijms17111857. [PMID: 27834916 PMCID: PMC5133857 DOI: 10.3390/ijms17111857] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/19/2016] [Accepted: 11/01/2016] [Indexed: 11/16/2022] Open
Abstract
Non-obstructive azoospermia is a severe infertility factor. Currently, the etiology of this condition remains elusive with several possible molecular pathway disruptions identified in the post-meiotic spermatozoa. In the presented study, in order to identify all possible candidate genes associated with azoospermia and to map their relationship, we present the first protein-protein interaction network related to azoospermia and analyze the complex effects of the related genes systematically. Using Online Mendelian Inheritance in Man, the Human Protein Reference Database and Cytoscape, we created a novel network consisting of 209 protein nodes and 737 interactions. Mathematical analysis identified three proteins, ar, dazap2, and esr1, as hub nodes and a bottleneck protein within the network. We also identified new candidate genes, CREBBP and BCAR1, which may play a role in azoospermia. The gene ontology analysis suggests a genetic link between azoospermia and liver disease. The KEGG analysis also showed 45 statistically important pathways with 31 proteins associated with colorectal, pancreatic, chronic myeloid leukemia and prostate cancer. Two new genes and associated diseases are promising for further experimental validation.
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Affiliation(s)
- Soudabeh Sabetian
- Department of Biological and Health Sciences, Faculty of Bioscience & Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor, Malaysia.
| | - Mohd Shahir Shamsir
- Department of Biological and Health Sciences, Faculty of Bioscience & Medical Engineering, Universiti Teknologi Malaysia, 81310 Johor, Malaysia.
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34
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Chan CS, Sin LL, Chan KG, Shamsir MS, Manan FA, Sani RK, Goh KM. Characterization of a glucose-tolerant β-glucosidase from Anoxybacillus sp. DT3-1. Biotechnol Biofuels 2016; 9:174. [PMID: 27555880 PMCID: PMC4994278 DOI: 10.1186/s13068-016-0587-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/15/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND In general, biofuel production involves biomass pretreatment and enzymatic saccharification, followed by the subsequent sugar conversion to biofuel via fermentation. The crucial step in the production of biofuel from biomass is the enzymatic saccharification. Many of the commercial cellulase enzyme cocktails, such as Spezyme(®) CP (Genencor), Acellerase™ 1000 (Genencor), and Celluclast(®) 1.5L (Novozymes), are ineffectively to release free glucose from the pretreated biomass without additional β-glucosidase. RESULTS In this study, for the first time, a β-glucosidase DT-Bgl gene (1359 bp) was identified in the genome of Anoxybacillus sp. DT3-1, and cloned and heterologously expressed in Escherichia coli BL21. Phylogenetic analysis indicated that DT-Bgl belonged to glycosyl hydrolase (GH) family 1. The recombinant DT-Bgl was highly active on cello-oligosaccharides and p-nitrophenyl-β-d-glucopyranoside (pNPG). The DT-Bgl was purified using an Ni-NTA column, with molecular mass of 53 kDa using an SDS-PAGE analysis. It exhibited optimum activity at 70 °C and pH 8.5, and did not require any tested co-factors for activation. The K m and V max values for DT-Bgl were 0.22 mM and 923.7 U/mg, respectively, with pNPG as substrate. The DT-Bgl displayed high glucose tolerance, and retained 93 % activity in the presence of 10 M glucose. CONCLUSIONS Anoxybacillus DT-Bgl is a novel thermostable β-glucosidase with low glucose inhibition, and converts long-chain cellodextrins to cellobiose, and further hydrolyse cellobiose to glucose. Results suggest that DT-Bgl could be useful in the development of a bioprocess for the efficient saccharification of lignocellulosic biomass.
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Affiliation(s)
- Chia Sing Chan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Lee Li Sin
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Fazilah Abd Manan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, USA
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
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35
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Parvizpour S, Razmara J, Shamsir MS, Illias RM, Abdul Murad AM. The role of alternative salt bridges in cold adaptation of a novel psychrophilic laminarinase. J Biomol Struct Dyn 2016; 35:1685-1692. [PMID: 27206405 DOI: 10.1080/07391102.2016.1191043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Sepideh Parvizpour
- a Faculty of Bioscience and Medical Engineering, Bioinformatics Research Group , Universiti Teknologi Malaysia , Johor Bahru , Malaysia
| | - Jafar Razmara
- b Faculty of Mathematical Sciences, Department of Computer Science , University of Tabriz , Tabriz , Iran
| | - Mohd Shahir Shamsir
- a Faculty of Bioscience and Medical Engineering, Bioinformatics Research Group , Universiti Teknologi Malaysia , Johor Bahru , Malaysia
| | - Rosli Md Illias
- c Faculty of Chemical Engineering, Department of Bioprocess Engineering , Universiti Teknologi Malaysia , Johor Bahru , Malaysia
| | - Abdul Munir Abdul Murad
- d Faculty of Science and Technology, School of Biosciences and Biotechnology , Universiti Kebangsaan Malaysia , Kuala Lumpur , Malaysia
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36
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Mohajer FS, Parvizpour S, Razmara J, Khoshkhooy Yazdi M, Shamsir MS. Structural, functional and molecular dynamics analysis of the native and mutated actin to study its effect on congenital myopathy. J Biomol Struct Dyn 2016; 35:1608-1614. [PMID: 27448459 DOI: 10.1080/07391102.2016.1190299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Faeze Sadat Mohajer
- a Bioinformatics Research Group, Faculty of Bioscience and Medical Engineering , UniversitiTeknologi Malaysia , Johor Bahru , Malaysia
| | - Sepideh Parvizpour
- b Biotechnology Research Center , Tabriz University of Medical Sciences , Tabriz , Iran
| | - Jafar Razmara
- c Departement of Computer Science , University of Tabriz , Tabriz , Iran
| | - Mahsa Khoshkhooy Yazdi
- d Faculty of Science, Department of Chemistry , Universiti Teknologi Malaysia , 81310 UTM, Johor , Malaysia
| | - Mohd Shahir Shamsir
- a Bioinformatics Research Group, Faculty of Bioscience and Medical Engineering , UniversitiTeknologi Malaysia , Johor Bahru , Malaysia
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Goh KM, Chan KG, Lim SW, Liew KJ, Chan CS, Shamsir MS, Ee R, Adrian TGS. Genome Analysis of a New Rhodothermaceae Strain Isolated from a Hot Spring. Front Microbiol 2016; 7:1109. [PMID: 27471502 PMCID: PMC4943939 DOI: 10.3389/fmicb.2016.01109] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/04/2016] [Indexed: 11/21/2022] Open
Abstract
A bacterial strain, designated RA, was isolated from water sample of a hot spring on Langkawi Island of Malaysia using marine agar. Strain RA is an aerophilic and thermophilic microorganism that grows optimally at 50–60°C and is capable of growing in marine broth containing 1–10% (w/v) NaCl. 16S rRNA gene sequence analysis demonstrated that this strain is most closely related (<90% sequence identity) to Rhodothermaceae, which currently comprises of six genera: Rhodothermus (two species), Salinibacter (three species), Salisaeta (one species), Rubricoccus (one species), Rubrivirga (one species), and Longimonas (one species). Notably, analysis of average nucleotide identity (ANI) values indicated that strain RA may represent the first member of a novel genus of Rhodothermaceae. The draft genome of strain RA is 4,616,094 bp with 3630 protein-coding gene sequences. Its GC content is 68.3%, which is higher than that of most other genomes of Rhodothermaceae. Strain RA has genes for sulfate permease and arylsulfatase to withstand the high sulfur and sulfate contents of the hot spring. Putative genes encoding proteins involved in adaptation to osmotic stress were identified which encode proteins namely Na+/H+ antiporters, a sodium/solute symporter, a sodium/glutamate symporter, trehalose synthase, malto-oligosyltrehalose synthase, choline-sulfatase, potassium uptake proteins (TrkA and TrkH), osmotically inducible protein C, and the K+ channel histidine kinase KdpD. Furthermore, genome description of strain RA and comparative genome studies in relation to other related genera provide an overview of the uniqueness of this bacterium.
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Affiliation(s)
- Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Soon Wee Lim
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
| | - Kok Jun Liew
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
| | - Chia Sing Chan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
| | - Robson Ee
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
| | - Tan-Guan-Sheng Adrian
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya Kuala Lumpur, Malaysia
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38
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Chai KP, Othman NFB, Teh AH, Ho KL, Chan KG, Shamsir MS, Goh KM, Ng CL. Crystal structure of Anoxybacillus α-amylase provides insights into maltose binding of a new glycosyl hydrolase subclass. Sci Rep 2016; 6:23126. [PMID: 26975884 PMCID: PMC4791539 DOI: 10.1038/srep23126] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 02/17/2016] [Indexed: 11/18/2022] Open
Abstract
A new subfamily of glycosyl hydrolase family GH13 was recently proposed for α-amylases from Anoxybacillus species (ASKA and ADTA), Geobacillus thermoleovorans (GTA, Pizzo, and GtamyII), Bacillus aquimaris (BaqA), and 95 other putative protein homologues. To understand this new GH13 subfamily, we report crystal structures of truncated ASKA (TASKA). ASKA is a thermostable enzyme capable of producing high levels of maltose. Unlike GTA, biochemical analysis showed that Ca2+ ion supplementation enhances the catalytic activities of ASKA and TASKA. The crystal structures reveal the presence of four Ca2+ ion binding sites, with three of these binding sites are highly conserved among Anoxybacillus α-amylases. This work provides structural insights into this new GH13 subfamily both in the apo form and in complex with maltose. Furthermore, structural comparison of TASKA and GTA provides an overview of the conformational changes accompanying maltose binding at each subsite.
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Affiliation(s)
- Kian Piaw Chai
- Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering, 81310 Skudai, Johor, Malaysia
| | - Noor Farhan Binti Othman
- Universiti Kebangsaan Malaysia, Institute of Systems Biology, 43600 UKM Bangi, Selangor, Malaysia
| | - Aik-Hong Teh
- Universiti Sains Malaysia, Centre for Chemical Biology, 11800 Penang, Malaysia
| | - Kok Lian Ho
- Universiti Putra Malaysia, Department of Pathology, Faculty of Medicine and Health Sciences, 43400 Serdang, Selangor, Malaysia
| | - Kok-Gan Chan
- University of Malaya, Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, 50603 Kuala Lumpur, Malaysia
| | - Mohd Shahir Shamsir
- Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering, 81310 Skudai, Johor, Malaysia
| | - Kian Mau Goh
- Universiti Teknologi Malaysia, Faculty of Biosciences and Medical Engineering, 81310 Skudai, Johor, Malaysia
| | - Chyan Leong Ng
- Universiti Kebangsaan Malaysia, Institute of Systems Biology, 43600 UKM Bangi, Selangor, Malaysia
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Mienda BS, Shamsir MS, Illias RM. Model-guided metabolic gene knockout of gnd for enhanced succinate production in Escherichia coli from glucose and glycerol substrates. Comput Biol Chem 2016; 61:130-7. [PMID: 26878126 DOI: 10.1016/j.compbiolchem.2016.01.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 11/29/2015] [Accepted: 01/26/2016] [Indexed: 01/02/2023]
Abstract
The metabolic role of 6-phosphogluconate dehydrogenase (gnd) under anaerobic conditions with respect to succinate production in Escherichia coli remained largely unspecified. Herein we report what are to our knowledge the first metabolic gene knockout of gnd to have increased succinic acid production using both glucose and glycerol substrates in E. coli. Guided by a genome scale metabolic model, we engineered the E. coli host metabolism to enhance anaerobic production of succinic acid by deleting the gnd gene, considering its location in the boundary of oxidative and non-oxidative pentose phosphate pathway. This strategy induced either the activation of malic enzyme, causing up-regulation of phosphoenolpyruvate carboxylase (ppc) and down regulation of phosphoenolpyruvate carboxykinase (ppck) and/or prevents the decarboxylation of 6 phosphogluconate to increase the pool of glyceraldehyde-3-phosphate (GAP) that is required for the formation of phosphoenolpyruvate (PEP). This approach produced a mutant strain BMS2 with succinic acid production titers of 0.35 g l(-1) and 1.40 g l(-1) from glucose and glycerol substrates respectively. This work further clearly elucidates and informs other studies that the gnd gene, is a novel deletion target for increasing succinate production in E. coli under anaerobic condition using glucose and glycerol carbon sources. The knowledge gained in this study would help in E. coli and other microbial strains development for increasing succinate production and/or other industrial chemicals.
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Affiliation(s)
- Bashir Sajo Mienda
- Bioinformatics Research Group (BIRG), Department of Biosciences and Health Sciences, Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai Johor Bahru, Malaysia.
| | - Mohd Shahir Shamsir
- Bioinformatics Research Group (BIRG), Department of Biosciences and Health Sciences, Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, 81310 Skudai Johor Bahru, Malaysia
| | - Rosli Md Illias
- Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor Bahru, Malaysia
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40
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Mienda BS, Shamsir MS, Md. Illias R. Model-assisted formate dehydrogenase-O (fdoH) gene knockout for enhanced succinate production in Escherichia coli from glucose and glycerol carbon sources. J Biomol Struct Dyn 2016; 34:2305-16. [DOI: 10.1080/07391102.2015.1113387] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Bashir Sajo Mienda
- Bioinformatics Research Group (BIRG), Faculty of Biosciences and Medical Engineering, Department of Biosciences and Health Sciences, Universiti Teknologi Malaysia, Skudai Johor Bahru 81310, Malaysia
| | - Mohd Shahir Shamsir
- Bioinformatics Research Group (BIRG), Faculty of Biosciences and Medical Engineering, Department of Biosciences and Health Sciences, Universiti Teknologi Malaysia, Skudai Johor Bahru 81310, Malaysia
| | - Rosli Md. Illias
- Faculty of Chemical Engineering, Department of Bioprocess Engineering, Universiti Teknologi Malaysia, Skudai, Johor Bahru 81310, Malaysia
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41
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Mienda BS, Shamsir MS, Md. Illias R. Model-aided atpE gene knockout strategy in Escherichia coli for enhanced succinic acid production from glycerol. J Biomol Struct Dyn 2015; 34:1705-16. [DOI: 10.1080/07391102.2015.1090341] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Bashir Sajo Mienda
- Bioinformatics Research Group (BIRG), Faculty of Biosciences and Medical Engineering, Department of Biosciences and Health Sciences, Universiti Teknologi Malaysia, 81310 Skudai, Johor Bahru, Malaysia
| | - Mohd Shahir Shamsir
- Bioinformatics Research Group (BIRG), Faculty of Biosciences and Medical Engineering, Department of Biosciences and Health Sciences, Universiti Teknologi Malaysia, 81310 Skudai, Johor Bahru, Malaysia
| | - Rosli Md. Illias
- Faculty of Chemical Engineering, Department of Bioprocess Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor Bahru, Malaysia
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42
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Habibi N, Norouzi A, Mohd Hashim SZ, Shamsir MS, Samian R. Prediction of recombinant protein overexpression in Escherichia coli using a machine learning based model (RPOLP). Comput Biol Med 2015; 66:330-6. [DOI: 10.1016/j.compbiomed.2015.09.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 09/18/2015] [Accepted: 09/19/2015] [Indexed: 01/28/2023]
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Abstract
Molecular dynamics simulations have been used extensively to model the folding and unfolding of proteins. The rates of folding and unfolding should follow the Arrhenius equation over a limited range of temperatures. This study shows that molecular dynamic simulations of the unfolding of crambin between 500K and 560K do follow the Arrhenius equation. They also show that while there is a large amount of variation between the simulations the average values for the rate show a very high degree of correlation.
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Affiliation(s)
- Andrew Dalby
- Faculty of Science and Technology, University of Westminster, London, W1W 6UW, UK
| | - Mohd Shahir Shamsir
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, 81310, Malaysia
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44
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Mienda BS, Shamsir MS. 153 Model-aided anaerobic metabolic gene knockout of malate dehydrogenase (mdh) gene predicts increased succinate production inEscherichia coli. J Biomol Struct Dyn 2015. [DOI: 10.1080/07391102.2015.1032786] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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45
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Mienda BS, Shamsir MS. In silicodeletion ofPtsGgene inEscherichia coligenome-scale model predicts increased succinate production from glycerol. J Biomol Struct Dyn 2015; 33:2380-9. [DOI: 10.1080/07391102.2015.1036461] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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46
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Sajo Mienda B, Shahir Shamsir M. Model-driven in Silico glpC Gene Knockout Predicts Increased Succinate Production from Glycerol in Escherichia Coli. AIMS Bioengineering 2015. [DOI: 10.3934/bioeng.2015.2.40] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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47
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Sajo Mienda B, Shahir Shamsir M. An overview of pathway prediction tools for synthetic design of microbial chemical factories. AIMS Bioengineering 2015. [DOI: 10.3934/bioeng.2015.1.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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48
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Lim JC, Goh KM, Shamsir MS, Ibrahim Z, Chong CS. Characterization of aluminum resistantAnoxybacillussp. SK 3-4 isolated from a hot spring. J Basic Microbiol 2014; 55:514-9. [DOI: 10.1002/jobm.201400621] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 10/21/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Jia Chun Lim
- Faculty of Biosciences and Medical Engineering; Universiti Teknologi Malaysia; Skudai Johor Malaysia
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering; Universiti Teknologi Malaysia; Skudai Johor Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Biosciences and Medical Engineering; Universiti Teknologi Malaysia; Skudai Johor Malaysia
| | - Zaharah Ibrahim
- Faculty of Biosciences and Medical Engineering; Universiti Teknologi Malaysia; Skudai Johor Malaysia
| | - Chun Shiong Chong
- Faculty of Biosciences and Medical Engineering; Universiti Teknologi Malaysia; Skudai Johor Malaysia
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Sudi IY, Shamsir MS, Jamaluddin H, Wahab RA, Huyop F. Interactions of non-natural halogenated substrates with D-specific dehalogenase (DehD) mutants using in silico studies. BIOTECHNOL BIOTEC EQ 2014; 28:949-957. [PMID: 26019583 PMCID: PMC4433833 DOI: 10.1080/13102818.2014.960663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 07/17/2014] [Indexed: 10/26/2022] Open
Abstract
The D-2-haloacid dehalogenase of D-specific dehalogenase (DehD) from Rhizobium sp. RC1 catalyses the hydrolytic dehalogenation of D-haloalkanoic acids, inverting the substrate-product configuration and thereby forming the corresponding L-hydroxyalkanoic acids. Our investigations were focused on DehD mutants: R134A and Y135A. We examined the possible interactions between these mutants with haloalkanoic acids and characterized the key catalytic residues in the wild-type dehalogenase, to design dehalogenase enzyme(s) with improved potential for dehalogenation of a wider range of substrates. Three natural substrates of wild-type DehD, specifically, monochloroacetate, monobromoacetate and D,L-2,3-dichloropropionate, and eight other non-natural haloalkanoic acids substrates of DehD, namely, L-2-chloropropionate; L-2-bromopropionate; 2,2-dichloropropionate; dichloroacetate; dibromoacetate; trichloroacetate; tribromoacetate; and 3-chloropropionate, were docked into the active site of the DehD mutants R134A and Y135A, which produced altered catalytic functions. The mutants interacted strongly with substrates that wild-type DehD does not interact with or degrade. The interaction was particularly enhanced with 3-chloropropionate, in addition to monobromoacetate, monochloroacetate and D,L-2,3-dichloropropionate. In summary, DehD variants R134A and Y135A demonstrated increased propensity for binding haloalkanoic acid and were non-stereospecific towards halogenated substrates. The improved characteristics in these mutants suggest that their functionality could be further exploited and harnessed in bioremediations and biotechnological applications.
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Affiliation(s)
- Ismaila Yada Sudi
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
| | - Mohd Shahir Shamsir
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
| | - Haryati Jamaluddin
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
| | - Fahrul Huyop
- Department of Biotechnology and Medical Engineering, Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
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50
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Sudi IY, Hamid AAA, Shamsir MS, Jamaluddin H, Wahab RA, Huyop F. Insights into the stereospecificity of the d-specific dehalogenase from Rhizobium sp. RC1 toward d- and l-2-chloropropionate. BIOTECHNOL BIOTEC EQ 2014; 28:608-615. [PMID: 26740767 PMCID: PMC4684057 DOI: 10.1080/13102818.2014.937907] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 06/06/2014] [Indexed: 11/15/2022] Open
Abstract
Halogenated compounds are recalcitrant environmental pollutants prevalent in agricultural fields, waste waters and industrial by-products, but they can be degraded by dehalogenase-containing microbes. Notably, 2-haloalkanoic acid dehalogenases are employed to resolve optically active chloropropionates, as exemplified by the d-specific dehalogenase from Rhizobium sp. RCI (DehD), which acts on d-2-chloropropionate but not on its l-enantiomer. The catalytic residues of this dehalogenase responsible for its affinity toward d-2-chloropropionate have not been experimentally determined, although its three-dimensional crystal structure has been solved. For this study, we performed in silico docking and molecular dynamic simulations of complexes formed by this dehalogenase and d- or l-2-chloropropionate. Arg134 of the enzyme plays the key role in the stereospecific binding and Arg16 is in a position that would allow it to activate a water molecule for hydrolytic attack on the d-2-chloropropionate chiral carbon for release of the halide ion to yield l-2-hydroxypropionate. We propose that within the DehD active site, the NH group of Arg134 can form a hydrogen bond with the carboxylate of d-2-chloropropionate with a strength of ∼4 kcal/mol that may act as an acid–base catalyst, whereas, when l-2-chloropropionate is present, this bond cannot be formed. The significance of the present work is vital for rational design of this dehalogenase in order to confirm the involvement of Arg16 and Arg134 residues implicated in hydrolysis and binding of d-2-chloropropionate in the active site of d-specific dehalogenase from Rhizobium sp. RC1.
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Affiliation(s)
- Ismaila Yada Sudi
- Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
| | | | - Mohd Shahir Shamsir
- Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
| | - Haryati Jamaluddin
- Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
| | | | - Fahrul Huyop
- Faculty of Biosciences and Medical Engineering (FBME), Universiti Teknologi Malaysia , Johor Bahru , Johor , Malaysia
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