Deanship of Graduate Studies Al-Quds University Phylogenetic
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Deanship of Graduate Studies Al-Quds University Phylogenetic Typing of Streptomyces Species Using Multilocus PCR Analysis Mohammad Ahmad Al-Qadi M.Sc. Thesis Jerusalem-Palestine 1434Hijri/2013 Phylogenetic Typing of Streptomyces Species Using Multilocus PCR Analysis Prepared By: Mohammad Ahmad Al-Qadi B.Sc. Arab American University, Palestine Supervisor: Dr. Sameer A. Barghouthi A thesis submitted in partial fulfillment of requirements for the degree of Master of Medical Laboratory Sciences / Microbiology and Immunology Track, Department of Medical Laboratory Sciences, Faculty of Health Professions, Al-Quds University. 1434Hijri/2013 Al-Quds University Deanship of Graduate Studies Department of Medical Laboratory Sciences Thesis Approval Phylogenetic Typing of Streptomyces Species Using Multilocus PCR Analysis Prepared By: Mohammad Ahmad Al-Qadi Registration No. 20913084 Supervisor: Dr. Sameer A. Barghouthi Master Thesis submitted and accepted, Date: 06/01/2013 The names and signatures of the examining committee members are as follows: 1- Head of committee: Dr. Sameer A. Barghouthi 2- Internal Examiner: Dr. Ibrahim Abbasi 3- External Examiner: Dr. Walid Basha Jerusalem-Palestine 1434/2013 Dedication: I dedicate my work to those dearest to me, my dear mother who faced a great deal of time and difficulties for the sake of my success and wellbeing, my kind father whose advice have guided my path through difficult times, my lovely sisters who supported my efforts, my late brother with whom I had the best companionship, my supportive uncle Ali who helped me in my duties, my loving wife whose affection and efforts made this possible. Mohammad Ahmad Al-Qadi Declaration I certify that this thesis submitted for the degree of master, is the result of my own research, except where otherwise acknowledged, and that this study (or any part of the same) has not been submitted for a higher degree to any other university or institution. Signed------------ Mohammad Ahmad Al-Qadi Date: 14/12/2012 i Acknowledgments I offer my deepest feelings of gratitude and acknowledgment to my supervisor Dr. Sameer A. Barghouthi for his sincere efforts in my training, supervision, and guidance. The study was conducted in the research lab of the faculty of health professions in Al-Quds University. ii Abstract: Streptomyces species are important bacteria; they produce several bioactive metabolites such as antibiotics including antibacterial, antifungal, antiviral, anticancer, and other secondary metabolites that are important for human health, veterinary medicine, soil and plants. Classification of Streptomyces using classical methods; morphological, microscopic, and biochemical, suffers from major weaknesses and confusion. Classical methods are difficult to apply to the large number of available Streptomyces spp. (>570), cumbersome, expensive, time consuming, and most importantly are not applicable for routine work, require extensive experience which hinder their application and bacterial identification. With the development of molecular biology, a possible solution to most problems is in sight. 16S ribotyping is being applied, yet it failed to identify species. This study was designed to categorize Streptomyces spp (known and unknown) into smaller and manageable subgroups and simplify identification and classification of the genus Streptomyces , the multi-locus gene analysis in addition to the 16S rRNA gene was deemed the method of choice; the selected genes were Superoxide dismutase (SOD), Pyruvate phosphate dikinase (PPD), Sigma Factor (σf), Amino acid adenylation domain protein (aaa), [2Fe-2S] protein (IS), and Transcriptional regulator (TR). Based on available DNA sequences, BLAST search with published sequences, 17 primers were designed under the following criteria: amplicon sizes must be distinguishable by agarose gels, all primers should have similar melting temperatures (Tm) (60ºC), and that no any primer pair will react with all Streptomyces species. Worldwide collected soil samples were cultured on citrate-glycerol medium or ISP4, suspected isolates were subjected to PCR in a multiplex setting. SOD amplicon was sequenced for a limited number of isolates in order to validate and confirm the ability of the proposed Multilocus typing to separate species into subgroups. Theoretically, Streptomyces spp. can be subdivided into genetic subgroups based on the presence or absence of selected loci. The sequential arrangement of loci had generated a flow chart which placed a given isolate in one of 192 possible subgroups rendering its accurate identification highly possible. iii ﻤﻠﺨص Abstract in Arabic ﺘﻌد اﻝﺒﻜﺘﻴرﻴﺎ ﻤن ﻓﺼﻴﻠﺔ ﺴﺘرﻴﺒﺘوﻤﺎﻴﺴز (.Streptomyces spp) ذات أﻫﻤﻴﻪ ﻜﺒﻴرة، إذ ﺘﻨﺘﺞ ﻋدة ﻤواد ذات ﺨﺼﺎﺌص ﺤﻴوﻴﺔ ﻫﺎﻤﺔ ﻜﺎﻝﻤﻀﺎدات اﻝﺤﻴوﻴﺔ ﺒﻤﺎ ﻓﻴﻬﺎ ﻤن ﻤواد ﻤﻀﺎدة ﻝﻠﺒﻜﺘﻴرﻴﺎ، اﻝﻔﻴروﺴﺎت، اﻝﻔطرﻴﺎت، وﻤواد ﻤﻀﺎدة ﻝﻠﺨﻼﻴﺎ اﻝﺴرطﺎﻨﻴﺔ، ﺒﺎﻹﻀﺎﻓﺔ إﻝﻰ ﻤﻨﺘﺠﺎت ﺜﺎﻨوﻴﺔ أﺨرى ﻝﻬﺎ اﺴﺘﺨداﻤﺎت و ﺘطﺒﻴﻘﺎت ﻤﻬﻤﺔ ﻓﻲ ﻤﺠﺎل اﻝﺼﺤﺔ، اﻝطب اﻝﺒﻴطري، واﻝزارﻋﺔ . إن ﺘﺼﻨﻴف اﻝﺴﺘرﻴﺒﺘوﻤﺎﻴﺴز ( Streptomyces) ﺒﺎﺴﺘﺨدام اﻝطرق اﻝﺘﻘﻠﻴدﻴﺔ، ﺒﻨﺎءا ﻋﻠﻰ اﻝطارز اﻝﺸﻜﻠﻲ ، أو اﻝﻤﺠﻬري، وﺒﻨﺎءا ﻋﻠﻰ ﺨﺼﺎﺌص اﻝﻜﻴﻤﻴﺎء اﻝﺤﻴوﻴﺔ ﻴﻌﺎﻨﻲ ﻤن ﻝﺒس وﻨﻘﺎط ﻀﻌف واﻀﺤﺔ . ﻓﺎﻝطرق اﻝﺘﻘﻠﻴدﻴﺔ ﺼﻌﺒﺔ اﻝﺘطﺒﻴق ﺒﺴﺒب وﺠود ﻋدد ﻜﺒﻴر ﻤن أﻨواع اﻝﺴﺘرﻴﺒﺘوﻤﺎﻴﺴز (S. species) ( > 570 ) ، ﻨﺎﻫﻴك ﻋن ﺘﻌﻘﻴد ﻫذﻩ اﻝطرق وا رﺘﻔﺎع ﻜﻠﻔﺘﻬﺎ . ﻜﻤﺎ أﻨﻬﺎ ﺒﺤﺎﺠﺔ إﻝﻰ وﻗت طوﻴل، وﻫﻲ ﻏﻴر ﻗﺎﺒﻠﺔ ﻝﻠﺘطﺒﻴق ﺒﺸﻜل روﺘﻴﻨﻲ، وﻫذا ﻷﻨﻬﺎ ﺘﺤﺘﺎج إﻝﻰ ﺨﺒرة ﻋﺎﻝﻴﺔ، ﻤﻤﺎ ﻴﻌﻴق ﺘطﺒﻴﻘﻬﺎ واﺴﺘﺨداﻤﻬﺎ ﻓﻲ اﻝﺘﺸﺨﻴص . واﻵن، ﻤﻊ ﺘطور ﻋﻠم اﻷﺤﻴﺎء اﻝﺠزﻴﺌﻲ ﻫﻨﺎك ﺒدﻴل ﻤﺤﺘﻤل ﻴﻠوح ﻓﻲ اﻷﻓق . وﺒﺎﻝرﻏم ﻤن اﺴﺘﺨدام اﻝﻌﺎﻤل اﻝارﻴﺒوﺴوﻤﻲ ( 16S rRNA) ﻓﻲ اﻝﺘﺼﻨﻴف إﻻ أﻨﻪ ﻤﺎ ازل ﻗﺎﺼار ﻓﻲ اﻝﺘﺼﻨﻴف ﻋﻠﻰ ﻤﺴﺘوى اﻝﻨوع (Species) . ﻫذﻩ اﻝدارﺴﺔ ﺘﻬدف إﻝﻰ ﺘﻘﺴﻴم أﻨواع اﻝﺴﺘرﻴﺒﺘوﻤﺎﻴﺴز ( اﻝﻤﻌروﻓﺔ ﻤﻨﻬﺎ وﻏﻴر اﻝﻤﻌروﻓﺔ ) إﻝﻰ ﻤﺠﻤوﻋﺎت ﺼﻐﻴرة ﻴﺴﻬل اﻝﺘﻌرف ﻋﻠﻴﻬﺎ وﺘﺼﻨﻴﻔﻬﺎ ﻀﻤن ﺠﻨس اﻝﺴﺘرﻴﺒﺘوﻤﺎﻴﺴز Streptomyces) (Genus . إن اﺴﺘﺨدام ﺠﻴﻨﺎت ﻤﺘﻌددة (multilocus) ﺒﺎﻹﻀﺎﻓﺔ إﻝﻰ ﺠﻴن 16S rRNA ﻫﻲ اﻝوﺴﻴﻠﺔ اﻝﻤﺘﺒﻌﺔ ﻓﻲ ﻫذﻩ اﻝدارﺴﺔ، أﻤﺎ ﺒﺎﻝﻨﺴﺒﺔ ﻝﻠﺠﻴﻨﺎت اﻝﻤﺨﺘﺎرة ﻝﻠدارﺴﺔ ﻓﻬﻲ Superoxide dismutase (SOD), Pyruvate phosphate dikinase (PPD), Sigma Factor (σf), Amino acid iv adenylation domain protein (aaa), [2Fe-2S] protein (IS), and Transcriptional regulator (TR). و ﻗد اﺨﺘﻴرت ﺒﻨﺎءا ﻋﻠﻰ اﻝﻤﻌﻠوﻤﺎت اﻝﻤﺘﺎﺤﺔ ﻋن ﺘﺴﻠﺴل اﻝﻘواﻋد اﻝﻨﻴﺘروﺠﻴﻨﻴﺔ ﻝﻠﺤﻤض اﻝﻨووي DNA ﻓﻲ ﻗواﻋد اﻝﺒﻴﺎﻨﺎت اﻝﻤﻨﺸورة ﻋﻠﻰ اﻻﻨﺘرﻨت (Data base)، وﻤﻘﺎرﻨﺔ ﺴﻠﺴﻠﺔ اﻝﻘواﻋد اﻝﻨﻴﺘروﺠﻴﻨﻴﺔ اﻝﻤﺨﺘﺎرة ﺒ ﻤﺘﺴﻠﺴﻼت اﻝﻘواﻋد اﻝﻨﻴﺘروﺠﻴﻨﻴﺔ اﻝﻤﻨﺸورة ﻋﻠﻰ ﻗواﻋد اﻝﺒﻴﺎﻨﺎت . ﻝﻘد اﺴﺘﺨدﻤت 17 ﺒﺎدﺌﺔ (primer) ﻓﻲ ﻫذﻩ اﻝدارﺴﺔ ﺼﻤﻤت وﻓق اﻝﻤﻌﺎﻴﻴر اﻝﺘﺎﻝﻴﺔ : ان ﻴﻜون ﺤﺠم اﻝﻨﺎﺘﺞ (amplicon) ﻝﻜل ﻤﻨﻬﺎ ﻤﻤﻴاز ﻋن ﻏﻴرﻩ ﻋﻨد ﻋرﻀﻪ ﻋﻠﻰ ﺠل اﻻﺠروز (agrose gel) ، أن ﺘﻜون ﺠﻤﻴﻊ اﻝﺒﺎدﺌﺎت ﻝﻬﺎ ﻨﻔس درﺠﺔ اﻻﻨ ﻔﺼﺎل (Tm) وﻫﻲ 60 درﺠﺔ ﻤﺌوﻴﺔ، وأﻴﻀﺎ أن ﻻ ﻴﺘﻔﺎﻋل أي زوج ﻤن ﻫذﻩ اﻝﺒﺎدﺌﺎت ﻤﻊ ﺠﻤﻴﻊ أﻨواع اﻝﺴﺘرﻴﺒﺘوﻤﺎﻴﺴز . ﺘم ﺠﻤﻊ ﻋﻴﻨﺎت اﻝﺘرﺒﺔ ﻤن ﻤﻨﺎطق ﻤﺨﺘﻠﻔﺔ ﻤن اﻝﻌﺎﻝم وزرﻋت ﻋﻠﻰ وﺴط ﺒﻜﺘﻴري ﻤﺤﺘوي ﻋﻠﻰ ﻤﻠﺢ اﻝﺴﺘارت ﺒﺎﻹﻀﺎﻓﺔ إﻝﻰ اﻝﺠﻠﻴﺴﻴرول (citrate-glycerol) وﻋﻠﻰ وﺴط ﺒﻜﺘﻴري آﺨر ﻤﻌروف و ﻤﻌد ﺨﺼﻴﺼﺎ ﻝﻬذﻩ اﻝﺒﻜﺘﻴرﻴﺎ (ISP4) . ﺠﻬزت اﻷﺤﻤﺎض اﻝﻨووﻴﺔ اﻝﻤﺴﺘﺨرﺠﺔ ﻤن ﻫذﻩ اﻝﺒﻜﺘﻴرﻴﺎ ﻝﺘﻔﺎﻋل اﻷﻨزﻴم اﻝﻤﺒﻠﻤر (PCR) ﺒﺎﺴﺘﺨدام ﺘﻘﻨﻴﺔ اﻝﺨﻠط ﺒﻴن اﻝﺒﺎدﺌﺎت (multiplex PCR) . ﻝﻘد ﺘم اﺴﺘﺨدام ﺘﻘﻨﻴﺔ ﺘﺤﻠﻴل اﻝﻘواﻋد اﻝﻨﻴﺘروﺠﻴﻨﻴﺔ (sequencing) ﻋﻠﻰ ﻋدد ﻤﻌﻴن ﻤن اﻝﻌزﻻت ﺒﺎﺴﺘﺨدام ﺠﻴن SOD ﻝﺘﺄﻜﻴد ٕواﺜﺒﺎت ﻗدرة ﻫذﻩ اﻝطرﻴﻘﺔ ﻋﻠﻰ ﻓﺼل أﻨواع ﺒﻜﺘﻴرﻴﺎ ﺴﺘرﻴﺒﺘوﻤﺎﻴﺴز إﻝﻰ ﻤﺠﻤوﻋﺎت ﺼﻐﻴرة ﺒﻨﺎءا ﻋﻠﻰ وﺠود أو ﻏﻴﺎب اﻝﻤواﻗﻊ اﻝﻤﺨﺘﺎرة (loci) ﻤن اﻝﺠﻴﻨﺎت. ﻝﻘد أﻨﺘﺠت ﻫذﻩ اﻝدارﺴﺔ ﻤﺨططﺎ ﻴﻀﻊ ﻫذﻩ اﻝﺒﻜﺘﻴرﻴﺎ وﻴﻘﺴﻤﻬﺎ إﻝﻰ 192 ﻤﺠﻤوﻋﺔ (Cluster) ﻤﻤﺎ ﻴزﻴد ﻤن ﻓرص اﻝﺘﻌرف ﻋﻠﻴﻬﺎ . v Table of abbreviation Abbreviation Full word aaa Amino acid adenylation domain protein BLAST Basic Local Alignment Search Tool bp Base pair CCG media Sodium Citrate Casaminoacids Glycerol media ELISA Enzyme-Linked Immunosorbent Assay G7 Golden mixture 7 IE Indirect ELISA IS [2Fe-2S] protein ISP4 International Streptomyces project 4 LFRFA Low-frequency restriction fragment analysis MLEE Multilocus enzyme electrophoresis MLSA Multilocus sequence analysis SIMCA Soft independent modeling by class analogy Tm Melting temperature PAGE Polyacrylamide gel electrophoresis RAPD Random amplification of polymorphic DNA PCR Polymerase chain reaction PFGE Pulsed-field gel electrophoresis vi Abbreviation Full word QUBC Al-Quds University Bacterial Collection QUGP Al-Quds University General Primers SDS Sodium dodecyl sulfate σf Sigma Factor SOD Superoxide dismutase spp. Species TR Transcriptional regulator vii Table of Contents Declaration .................................................................................................................................. i Acknowledgment ....................................................................................................................... ii Abstract ..................................................................................................................................... iii iv .......................................................................................................... ا Abstract in Arabic Table of abbreviation ................................................................................................................ vi Table of contents ..................................................................................................................... viii List of tables .............................................................................................................................. xi List of figures ........................................................................................................................... xii Chapter 1: Introduction .............................................................................................................1 1. literature review ......................................................................................................................2