In silico Vaccine designing for Lyme disease

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Abstract

The vaccine designing project for Lyme disease involves various Bio-informatics tools and techniques for Insilico designing of a vaccine. Lyme disease is caused by the bacterium Borrelia Burgdorferi also called as Lyme Borreliosis or Lyme Arthritis. The bacterium uses ‘Ticks’ as vectors and infects Humans through tick bites. The symptoms can start from simple skin rashes to arthritis or paralysis or even memory loss if untreated. Borrelia Burgdorferi is a Gram Negative bacterium of Spirochaetaceae family. In the vaccine designing procedure all the protein sequences available for the bacterium are retrieved from NCBI and performed a primary screening to eliminate hypothetical or putative or unnamed sequences from the list and  secondary screening to eliminate sequences that shows more than 30% of similarity with Human genome. As a vaccine is needed to be given to a human host it’s very important to check for the maximum foreignness to humans, bio-informatics tools like BLAST and TFASTy were used for this purpose to eliminate similar and identical sequences. Using the TFASTy tool, (which compares our protein query against translated genome sequences of humans) the sequences that shows zero similarity are chosen for further steps. Surface Accessibility Area is another aspect to be considered and the sequence with highest SAA value is taken and it’s antigenic sites were found using protein variability server and the sequence with highest SAA value among them was chosen as the potential vaccine candidate and further modelling was done using the software ‘ARGUS LAB’.

Introduction

Lyme disease is transmitted to humans by the bite of infected ticks of the Ixodes genus. Usually, the tick must be attached for 36 to 48 hours before the bacteria can spread. In North America, the only bacterium involved is Borrelia burgdorferi sensu stricto, while in Europe and Asia, the bacteria Borrelia afzelii and Borrelia garinii are also causes of the disease. The disease does not appear to be transmissible between people, by other animals, or through food. Diagnosis is based upon a combination of symptoms, history of tick exposure,and possibly testing for specific antibodies in the blood. Blood tests are often negative in the early stages of the disease. Testing of individual ticks is not typically useful.

Lyme disease was clinically described as an infectious illness by Dr. Alan Steere and colleagues in 1977 and is currently the leading vector-borne disease in the United States. Steere et al. suggested that the epidemiology of Lyme disease indicated transmission by an arthropod vector due to the geographic clustering of patients in rural areas and the seasonal occurrence of the symptoms. Subsequently, Dr. Willy Burgdorfer and co-workers observed spirochetes in the mid-gut tissues from ticks collected in a Lyme disease endemic area. These spirochetes produced a skin rash resembling erythema migrans when injected into rabbits, and sera from Lyme disease patients reacted with the bacteria in indirect immune-fluorescence assays. In recognition of this discovery, the bacterium was named Borrelia Burgdorferi.

The bacteria, known as spirochetes for their unique corkscrew shape and twisting propulsion, are slow to replicate and one of few bacteria that have learned to survive without iron, instead relying on a supply of manganese for their survival (lending to potential treatment strategies intending to starve the bacteria of manganese).Unlike most disease-causing bacteria, Borrelia burgdorferi do not appear to emit a toxin. Instead, the bacterium seems to have a direct interaction with the cell tissues it infects. Also interesting is the bacteria’s slow replication rate, meaning that the number of bacteria found in a host remains quite small even after active infection.

  1. burgdorferi has a very unique genome. It consists of one large linear chromosome that is 910,725 base pairs long. This chromosome contains approximately 853 genes coding for basic functions such as DNA replication, transcription, translation as well as transport and metabolic systems. However, in addition to this chromosome, the bacterium also contains 21 other linear and circular plasmids that add an additional 533,000 base pairs of DNA. The genomic organization of B. burgdorferi is unique due to the high number of plasmids. Research has shown that some bacteria lacking a complete set of plasmids are unable to successfully infect their host, leading researchers to believe that the plasmids may encode virulent DNA (Fraser). One plasmid named lp25 has been found to be necessary for Borrelia infection. An lp25 gene named BBE22 has been discovered to encode for a nicotinamidase which by itself can maintain the ability for the bacteria to infect the host even when the plasmid is removed (Purser). However, in general, the sequenced genome does not contain any obvious genes coding for pathogenesis, and therefore, the mechanisms of B. burgdorferi infections are still a hot topic of research.

Conclusion

From the Insilico project it’s been concluded that the protein undeccaprenyl diphosphate has the antigenic sequence ‘QGLGALPG’ which is a potential vaccine candidate made using immuno-informatics approach and could be taken for further synthesis in lab and tests on clinical trials. Even though the sequence retrieval gave 50 thousand and more sequences, there were only few sequences that are completely foreign to human genome.   These Insilico works can save much of time and cost in designing a vaccine molecule also the Bio-informatics tools are greatly helpful in screening or designing processes. Through the Insilico designing all possible risks are eliminated and also unwanted sequences are easily removed and our time will be saved in finding a potential vaccine candidate. As our approaches are sequence and structure based the molecular designing works are also made easier with designing software like Argus lab. Still there are lots of diseases in need of drugs and vaccines to be created; hopefully these Insilico works will make the task easier for researchers to design vaccines or drugs in future.

References

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