FACULTY OF APPLIED SCIENCE BACHELOR IN SCIENCE (HONOURS) BIOLOGY GENETICS (BIO511)

GENETIC RECOMBINATION

PREPARED BY: FARIDAH SAING MATRIX NO: 2010517591 PREPARED FOR: MR ABDUL MANAP BIN MAHMUD

DATE OF SUBMISSION: 21st MAY 2012

ABSTRACT Although genetic recombination was discovered following the formation of Darwin's theories of evolution, it is still claimed that mutations are the source of any natural variability. It has however, now been known for decades that the variety of characteristics found among offspring from the same parent, or between the various breeds of plants and animal are the result of recombination events during meiotic cell division (crossing over and independent assortment of homologues). We know the variations isolated by breeders are the result of recombination and not mutation due to the short period of time involved with the isolation of the varieties, and the fact that the features segregate out in the offspring based on classic Mendelian predictions. However, actually there still a lack of evidence of the genetic recombination and the type of cell or organism that always used this process also the important for them. Thus, this finding will explain for the genetic recombination evidences according to some current studies.

INTRODUCTION Genetic recombination is a process combination of genes from parent cells that leads to the new generation of cell variants possessing characteristic phenotypically distinct cell types (Gajanan, 2011). The DNA or RNA is broke and rejoined with other DNA or RNA. The idea for recombinant DNA was first proposed by Peter Lobban. He is a graduate student of Prof. Dale Kaiser in the Biochemistry Department at Stanford University Medical School. The first publications describing the successful production and intracellular replication of recombinant DNA was in 1972 and 1973. Stanford University applied for a US patent on recombinant DNA in 1974, listing the inventors as Stanley N. Cohen and Herbert W. Boyer; this patent was awarded in 1980. The first licensed drug generated using recombinant DNA technology was human insulin, developed by Genentech and Licensed by Eli Lilly and Company. According to Nieminena, M., et. al.( 2010), genetic recombination can occur between two different DNA molecules (intermolecular recombination) or between two regions of a single DNA molecule

(intramolecular recombination). There are two types of common genetic recombination which are homologous recombination and non-homologous recombination which non-homologous recombination requires no or little sequence homology between two DNA that will be joined in the process (Nieminena, M. et. al., 2010). Homologous recombination (HR) is a process by which DNA double strand breaks are repaired through the alignment of homologous sequences of DNA (Cerbinkaite, A. et al., 2011). CURRENT STUDIES In this finding, there are five current studies that explained about the evidences of genetic recombination in various types of cell or organism. Hepatitis C virus RNA recombination in cell culture Through this study, Reither and his colleagues conducting an experiment to analyze and characterize recombination events during Hepatitis C virus replication. The Hepatitis C virus (HCV) is an enveloped, positive strand RNA virus of the family of Flaviviridae. Infection was occurs primarily through the exposure to

HCV-contaminated blood and remains persistent and frequently causes chronic hepatitis that can progress to liver cirrhosis and liver cell carcinoma. This experiment is conducted with HCV plasmid generation by using PCR, in vitro transcription, sequence analysis of recombination and calculating the recombination frequency. From the result obtained, it shows that recombinants were readily detected with frequencies correlating to the distance between the mutations in the HCV. The observed HCV recombinant frequency was dependent on the cross-over length. They indicate that the greater cross-over length, the recombinant frequency increased. Evidence of recombination in the Banana bunchy top virus genome In this study, Muhammad Zeeshan Hyder and his other group members were carried an experiment to find the evidence of recombination in the Banana bunchy top virus (BBTV) genome. BBTV is a significant subject being multicomponent circular single stranded DNA virus belongs to family Nanoviridae. This experiment is conducted by identifying the DNA sequence of plant infected BBTV from five areas in Pakistan. Then it compared with the DNA sequence from BBTV from other countries from GenBank such as from Taiwan, China, Australia, India and Egypt. From the analysis, it indicates that a recombination occurs between the two subgroups of BBTV from Taiwan and China. The isolates are recombination involved isolates from Pakistan and other South Pacific isolates (minor parents) with isolates from Taiwan (major parents). Evidence for inter- and intra-clade recombination in rabies virus

Rabies is a fatal disease caused by infection of rabies virus that is usually transmitted to humans through bites by rabid animals. Rabies virus is the prototype virus of the lyssa virus genus of the Rhabdoviridae family. It has a singlestranded, negative-sense RNA Genome. Domestic and wild mammals such as dogs, cats, foxes, bats and ferret badgers are major natural hosts and vectors of rabies virus infection. Homologous recombination is considered rare in negative-strand RNA viruses and has not been reported for rabies virus. Based on study conducted by Wei, L. et.al. (2011), full-length genomes of 44 rabies virus strains were analyzed for potential homologous recombination events. Phylogenetic analysis classified these strains into three clades. By applying six different recombination detection methods, one inter-clade and one intra-clade potential recombination events were identified with high confidence values. Software-predicted recombination break points of the two events were all located within the polymerase gene. From the result, they have determined that recombination is occurred in between the lineage represented by isolate gene from a dog (major patent) with isolate gene from a sika deer (minor parent) forming gene that they found in isolate virus of rabies patient (recombinant) from China. Recombination in Avian GammaCoronavirus Infectious Bronchitis Virus According to Thor, S. W., (2011), avian infectious bronchitis virus (IBV) is a gamma-coronavirus in the family Coronaviridae, the order Nidovirales, and the genus Coronavirus that causes a highly contagious upper-respiratory disease of domestic chickens. In layer type birds it can cause a drop in egg production and some strains are nephropathogenic. Infectious bronchitis remains one of the

most widely reported respiratory diseases of chickens worldwide despite the routine usage of attenuated live vaccines to control the disease. Control of IBV is difficult because there is little to no crossprotection between the numerous different serotypes of the virus. In this study, they sequenced and analyzed the full-length genomes of eight avian gamma-coronavirus infectious bronchitis virus (IBV) isolates that represent different serotypes that have not been previously sequenced, and we compared these sequences with other gamma-coronavirus full-length genome sequences available in GenBank for evidence of recombination. Evidence of recombination was found in every sequence analyzed and was distributed throughout the entire genome. Areas that have the highest occurrence of recombination are located in regions of the genome that code for non-structural proteins 2, 3 and 16, and the structural spike glycoprotein. The extent of the recombination observed, suggests that this may be one of the principal mechanisms for generating genetic and antigenic diversity within IBV. These data indicate that reticulate evolutionary change due to recombination in IBV, likely plays a major role in the origin and adaptation of the virus leading to new genetic types and strains of the virus. Recombination microRNA rates of human

microRNAs that could help in understanding the function, evolution, and disease-related roles of microRNAs. In this study, they performed a comprehensive analysis of gene recombination rates and human miRNAs and discovered that miRNA genes that have lower recombination rates tend to have lower tissue specificity, greater numbers of associated diseases and lower expression levels. miRNAs that are expressed in a variety of tissues are likely to be important for the proper regulation of various genes in a number of tissues. This may have caused selective pressure that slowed the evolution of these miRNA genes leading to relatively low recombination rates. DISCUSSION . From the previous current studies, recombination has been shown to be a significant factor in generating genetic diversity in most microorganisms such viruses, for example in HCV, IBV, BBTV and rabies viruses. The recombination is a common feature of DNA viruses, and that viruses evolve not only by the accumulation of point mutations but also by genetic recombination. Reiter et al., (2011), mentioned that due to the rapid virus turnover and the large number of HCV-infected liver cells in vivo, it is expected that recombination will be of biological importance when strong selection pressures are operative. Beside that the study that presents the first evidence suggesting the possibility of homologous recombination in rabies virus by Wei, L. et al. (2011), have provided valuable insights for understanding the diversity and evolution of rabies virus as well as other negative-strand RNA viruses. The species are doing the genetic recombination and evolved to cope with the new environment. When the species disperse to other places with new

MicroRNAs (miRNAs) are important gene regulators at the post-transcriptional level in nearly all critical biological processes, such as cell growth, proliferation, differentiation, development, and apoptosis and human signalling network. However, the association between microRNAs and recombination remains largely unknown. According to Huizhi, Z. et al. (2009), they conduct this study to reveal patterns in recombination rates of

environment, they have to evolve and the way they could choose to evolve is by recombined their genetic either intrarecombination or interrecombination. This genetic recombination not only benefits for the diversification of species by produce new species but also increase the ability to survive in new environment. During recombination, there are certain factors that will influence the quality of recombination. As mention earlier from the study by Huizhi, Z. et al. (2009), the recombination rate is one of the factors that can affect the evolution process. The increased of rate of effective recombination caused by an increase in the rate of recombination occur. Lower the rate of recombination, evolutionary process will become slowed. Effective recombination events, defined as events that have a measurable effect on genetic material. Non-effective recombination, for example when imported DNA replaces an identical fragment in the recipient genome, cannot be directly observed. Besides give benefits for viruses and bacteria species diversification, genetic recombination also very important to human body system. For example in the Huizhi, Z. et al., (2009) study explained that recombination is essential to microRNA in play their role in almost all biological processes in human. The recombination rate also becomes the factor that will influence the tissue specificity, number of associated disease and expression level in human body. CONCLUSION Through the previous studies, the genetic recombination is very important process that need by certain organism such viruses and bacteria for widen their species diversification and ability to survive in the new habitat or environment. This genetic

recombination process also gives beneficial to human through miRNA as regulators to the some critical biological process such growth and development. There also some factors that will affect the quality of the recombination. One of the factors is the rate of the recombination where higher the rate of recombination, more effective the recombination and more efficient the evolutionary process. While lower the rate of recombination, slower the evolutionary process. REFERENCES Cerbinskaite, A., Mukhopadhyay, A., Plummer, E.R., Curtin, N.J., and Edmondson, R.J. 2012. Defective homologous recombination in human cancers. Cancer Treatment Reviews, 38, 89-100 Didelot, X. and Maiden, M.C.J. 2010. Impact of recombination on bacterial evolution, Trend in Microbiology, 18, 315- 322 Huizhi Zhao, Dong Wang, Bing Liu, Xingpeng Jiang, Jing Zhang, Ming Fan, Zhengjie Fan, Ying Chen, Sonya Wei Song, Wei Gao, Tianzi Jiang and Qinghua Cui. 2009. Recombination rates of human microRNA. Biochemical and Biophysical Research Communications, 379, 702-705 Joseph Borg, J., Georgitsi, M., Vassiliki Marinou, V.A., Kollia, P., and George P. Patrinos, G.P. 2009. Genetic recombination as a major cause of mutagenesis in the human globin gene clusters, Clinical Biochemistry, 42, 1839-1850 Muhammad Zeeshan Hyder, Shahzad Hussain Shah, Shahid Hameed, and Syed Muhammad Saqlan Naqvi.2011. Evidence of recombination in the Banana bunchy top virus genome.

Infection, Genetics and Evolution, 11, 1293-1300 Nieminena, M., Tuuri, T., and Savilahti, H. 2010. Genetic recombination pathways and their application for genome modification of human embryonic stem cells, Expeimental Cell Research, 316, 2578-2586 Reiter, J., Vilaro, G.P., Scheller, N., Mina, L.B., Dez, J., and Meyerhans, A. 2011. Hepatitis C virus RNA recombination in cell culture. Journal of Hepatology, 55, 777783 Thor, S. W., Hilt, D. A., Kissinger , J.C., Paterson, A.H. and Jackwood, M.W. (2011). Recombination in Avian Gamma-Coronavirus Infectious Bronchitis Virus. Viruses, 3, 17771799 Wei Liu, Yanfeng Liu, Jing Liu, Jianwei Zhai and Youhua Xie. 2011. Evidence for interand intra-clade recombinations in rabies virus. Infection, Genetics and Evolution, 11, 1906-1922