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Insights Into Halophilic Microbial Adaptation: Analysis of Integrons and Associated Genomic Structures and Characterization of A American University in Cairo AUC Knowledge Fountain Theses and Dissertations Student Research Summer 8-25-2021 Insights Into Halophilic Microbial Adaptation: Analysis of Integrons and Associated Genomic Structures and Characterization of a Nitrilase in Hypersaline Environments Sarah Sonbol [email protected] Follow this and additional works at: https://fount.aucegypt.edu/etds Part of the Bacteriology Commons, Biochemistry Commons, Biodiversity Commons, Bioinformatics Commons, Biotechnology Commons, Environmental Microbiology and Microbial Ecology Commons, Genomics Commons, Marine Biology Commons, Molecular Biology Commons, and the Molecular Genetics Commons Recommended Citation APA Citation Sonbol, S. (2021).Insights Into Halophilic Microbial Adaptation: Analysis of Integrons and Associated Genomic Structures and Characterization of a Nitrilase in Hypersaline Environments [Doctoral Dissertation, the American University in Cairo]. AUC Knowledge Fountain. https://fount.aucegypt.edu/etds/1673 MLA Citation Sonbol, Sarah. Insights Into Halophilic Microbial Adaptation: Analysis of Integrons and Associated Genomic Structures and Characterization of a Nitrilase in Hypersaline Environments. 2021. American University in Cairo, Doctoral Dissertation. AUC Knowledge Fountain. https://fount.aucegypt.edu/etds/1673 This Doctoral Dissertation is brought to you for free and open access by the Student Research at AUC Knowledge Fountain. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of AUC Knowledge Fountain. For more information, please contact [email protected]. Insights into halophilic microbial adaptation: Analysis of integrons and associated genomic structures and characterization of a nitrilase in hypersaline environments School of Sciences and Engineering A Thesis Submitted by Sarah Ali Ahmed Sonbol. MSc to the Applied Sciences Graduate Program Spring, 2021 In partial fulfillment of the requirements for the degree of Doctorate in Applied Sciences (Biotechnology) Under the supervision of: Prof. Rania Siam American University in Cairo May / 2021 Insights into halophilic microbial adaptation: Analysis of integrons and associated genomic structures and characterization of a nitrilase in hypersaline environments A Thesis Submitted by Sarah Ali Ahmed Sonbol to the Applied Sciences Graduate Program (Biotechnology) Has been approved by Dr. Rania Siam (Thesis committee Chair/Advisor) ____________________ Affiliation ____________________ Dr. (Thesis committee Reader/Internal Examiner) ____________________ Affiliation ____________________ Dr. (Thesis committee Reader/Internal Examiner) ____________________ Affiliation ____________________ Dr. (Thesis committee Reader/External Examiner) ____________________ Affiliation ____________________ Dr. (Thesis committee Reader/External Examiner) ____________________ Affiliation ____________________ Dr. ____________________ (Moderator) ____________________ Affiliation Graduate Program Director Date School Dean Date ii Dedication To my beloved family Words cannot express how grateful I am for your presence in my life, your endless support and your continuous encouragements iii Acknowledgements I am really thankful to Dr. Rania Siam for her support, guidance and supervision of this thesis. I am also grateful to Dr. Karim Seddik the Associate Dean of graduate studies for his support and help throughout many logistics. My appreciation towards Dr. Ari Ferreira for his critical revision and participation in writing the nitrilase manuscript. My deep thanks to Mr. Amged Oaf for his great efforts and help throughout my PhD especially in my lab work. Thanks to Mr. Ahmed El Hosseiny for his help in my bioinformatics work. I am also deeply indeted to Dr. Nahla Hussein and Dr. Laila Ziko for their great help and support, fruitful lab discussions, revising manuscripts, providing suggestions and feeedback and for their continuous encouragement. I would also like to express my thanks towards Dr. Rehab Abdullah for her support and help in the lab and in providing some of the used reagents. Mr. Saifullah Soliman was a great assistant in LCL library screening, thus I owe him my thanks. Moreover, E. coli B548 and C319 were kindly provided from Dr. D. Mazel lab at Pasteur’s Institute, Paris, France. Special Thanks to Dr. Céline Loot in Dr. Mazel’s lab for the useful insights and tips concerning integron recombination assays. I acknowledge Dr. H. El Saied and his lab members for providing the Aghormy Lake filtered water sample, guidance through PCR screening of metagenomic DNA, and providing 16S rRNA sequencing results. Acknowledgments to Dr. T. Soliman for performing the Qiime analysis on the 16S rRNA sequences. Special thanks to Mr. Osama Ali for his help in ordering needed reagents. I am really thankful to Dr. Ghada Moustafa, Dr. Ali El Behery, Dr. Emanbellah Ramadan and Dr. Mohamed Maged for their help, advice and useful discussions at the beginning of my PhD. I am also indeted to Salma El Shafie, Shaimaa Farag and Marina Nabil for their help, support and encouragement. I would like to thank all biology department and biotechnology graduate program professors those whom I have TAed with or have taken courses with because I have learned a lot from them all. In addition, I am really thankful to the the biology department technical lab aides Mr. Zien and Mohamed El-Bagoury for their help during lab work. Finally, this work could have never been done without th generous PhD fellowship that I have received from Youssef Jameel foundation. Thank you very much. I would also like to thank the AUC for funding my practical lab work by the AUC student research grant and for the AUC conference grant which allowed me to participate in ISME17 in Leipzig, Germany. iv Abstract Hypersaline environments are unique habitats in which residing microorganisms show distinctive adaptive measures that allow their survival under these stress conditions. Hence, halophiles are considered a unique resource of enzymes and gene cassettes with characteristics that could be exploited in different biotechnological applications. Here, due to the attention directed towards finding more stable nitrilases that has a great potential in green bioremediation processes and in different industries; we have biochemically characterized a nitrilase (NitraS-ATII) that we have previously isolated from the hypersaline and thermophilic Atlantis II Deep brine pool lower convective layer (LCL). Nitrilases can hydrolyze nitriles in a one-step reaction into their corresponding carboxylic acid and ammonia. NitraS-ATII showed higher thermal stability compared to a closely related nitrilase, and tolerance towards high concentrations of some heavy metals. We have also focused on analyzing integrons and their associated genetic structures in hypersaline environments because of their presumed adaptive role. Integrons are genetic platforms in which an integron integrase (IntI) mediates the excision and integration of gene cassettes within the integron at specific recombination sites. We constructed a fosmid library from the metagenome of hypersaline Aghormy Lake in Siwa Oasis. This library and the library of the Atlantis II Deep brine pool lower convective layer (LCL) were screened using pre-designed degenerate primers to amplify intI genes. However, we only detected two positive clones in the Aghormy lake library from which one (AGH-1G10) was further sequenced and analyzed and its integron components were all detected. The AGH-1G10 intI in addition to another identified IntI from Kebrit Deep brine pool Upper interface (KD UIN360) were synthesised and expressed in pBAD18 plasmid to test their in vivo excision activity. However, no activity was observed for both proteins. This could be attributed to using a deletion assay in which the used recombination sites cannot be identified by newly identified IntIs. In addition, we used IntegronFinder software to analyze 80 halophilic bacterial genomes and 141 halophilic archaeal genomes. Our results revealed the presence of 19 new complete integrons and 44 clusters of attC sites lacking a neighboring integron-integrase (CALINs) in bacterial genomes and 1 complete integron in an archaeal genome. We also analyzed 28 hypersaline metagenomic assemblies in which we have identified eight complete integrons, 18 solitary integron integrases and 92 CALINs. Toxin-antitoxin (TA) gene cassettes were abundant in most detected integrons and CALINs, regardless of the length of the gene cassette array. Moreover, as expected, we have found different classes of insertion sequences (ISs) within and nearby integrons and CALINs. Surprisingly, this was only observed within analyzed genomes rather than assembled metagenomes which could be due to frequent concurrence of transposable elements’ repetitive sequences with the peripheries of contigs. Some IS types were v more frequent than others such as IS1182 elements and different ISs that are presumably able to mobilize adjacent genetic structures in presence of one copy of the IS element. Mining for group II introns revealed the presence of not only group IIC-attC, previously found embedded within different studied integrons, but also full and truncated group IIB introns (UHB.I2, H.ha.F1 and H.ha.F2) in CALINs within the extreme halophile Halorhodospira halochloris and a hypersaline metagenome. In addition, we have observed a relative abundance in arginine repressor (ArgR) binding sites within or overlapping with IntI promoters (PintI) raising questions
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