cluster classification of mycobacteriophages isolated from tropical soils of puerto rico 1
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Cluster Classification of Mycobacteriophages Isolated from Tropical Soils of Puerto Rico
Nicole Colón¹, Alberto Cintron¹, Carolina Montañez¹, Luzmarie Reyes¹
University of Puerto Rico, Cayey campus¹
Abstract
Mycobacteriophages have been studied through time for a number of reasons. They have been
used as model systems for the study of biological processes, such as phage infection and the dogma
central. This study aims to analyze different unsequenced mycobacteriophages and classify them into
their respective clusters using PCR and Gel Electrophoresis. Each group of researchers received a specific
Mycobacteriophage. The bacteriophages’ DNA were amplified using the PCR method, and were later
analyzed by running an electrophoresis gel.
Introduction
For many decades bacteriophages have
been know as viruses that infect bacteria. Each
Bacteriophage is composed of a head and a tail
(figure 1.1). The head, stores the genetic
material, while the tail is used to inject the
genetic material into the host bacterial cell.
Phages can be classified according to their
morphology and nucleic acids. The International
Comittee on Taxonomy on Viruses has study
and classified over 2,475 species in 2011.
“Mycobacteriophages are viruses that
infect bacteria belonging to the mycobacteria
genus”(Rubin 2012). Mycobacteriophages can
be found in a variety of soils. They can be
classified as harmless bacteria or disease causing
agents, such as tuberculosis. The size of a phage
depends on the average number of phage
particles liberated when an infected bacterium is
lysed.
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Bacteriophages can be isolated by enriching soil
samples in a nutrient media containing the
bacterial host. Doing this will let the phage
reproduce, increase in number, and form
plaques. The plaques represent the cycles of
infection and cell lysis, which identify the
phage. After identification, the plaques are
purified for further characterization.
The Mycobacteriophages are classified into
clustesr using specific primers. Table 1 shows
the Mycobacteriophage Clusters in Phages data
base. For this experiment we only used from
cluster A to cluster I because the rest of the
cluster didn’t have design primers.
For many years, Mycobacteriophages
have been studied and analyzed in order to
understand biological processes. Around 2,400
Mycobacteriophages have been analyzed and
characterized. “Over 70 universities and collages
around the United States, have isolated, purified,
and characterized Mycobacteriophages from soil
samples” (Rubin 2012). This experiment
analyzes and examines specific phages in order
to assign them into clusters.
Figure 1.1 Shows the structure of a bacteriophage.
Table 1 Shows the Mycobacteriophage Clusters In Phagesdb.
Materials and Methods
During this experiment, four specific
Mycobacteriophages genomic DNA were
assigned. Different Genomic DNA were
designated from Mycobacteriophages classified
as Phagus_Maximus, Suave, Bloo and Wilie.
The preparation of the phage DNA’s and the
Head
Tail
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forward and reverse primers were previously
made. Test tubes were labeled from 1 to 15. To
each tube a certain amount of each reagent was
added. First, 5l of Nano Pure PCR Grade
Water (H2O) was added. Later, 5l of each
Mycobacteriophage genomic DNA was added to
each tube. Following this step, 1l of the
specific forward and reverse primers were also
incorporated. In addition, 12l of the PCR
Master Mix, which contained Taq Polymerase,
Buffer, Nucleotides, Mg2+, were added. The
tubes were placed in a thermocycler for
amplification. Once amplified, the
electrophoresis method was performed. The
agarose gel was prepared using 200mL of TAE
buffer and 4g of agarose. After that, 2l of
loading dye were added to the reagents. The
wells of the agarose gel were loaded and they
were left to run for one hour at 80 volts. This
whole procedure was repeated with five gels of
different Mycobacteriophages, including the
control gel.
Results
The gel was analyzed and photographs
were taken using a gel documentation system.
The bands of some of the Mycobacteriophages
indicated that they were part of a specific
cluster. The thicker upper bands are bright,
because they contain the genome, and the ones
that ran towards the bottom of the wells are
the primer replications of a specific region of the
genome. Figure 1.2 shows the controls on an
agarose gel. In the control gel amplification of
Colbert and Puhltonio genomic DNAs resulted
in PCR products using B1 cluster specific
primers. Thus these phages are verified as
belonging to Cluster B1 and their size pair base
is 700. As well, Ghost and LRRHood resulted in
PCR products as belonging to Cluster C1. And
their size is 400 base pair. Also for Pumpkin,
which DNA resulted, as being part of Cluster E
and its size was 800 base pair. Figure 1.3 the
middle contains the results of the experimental
agarose gels. It contains the
Mycobacteriophages known as Bloo and Suave.
In the experimental gel neither Wilie nor Bloo
showed an amplified PCR product. The final gel
was named as class gel containing two
Mycobactheriophage. Figure 1.3 left bottom
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contains the Mycobactheriophage Suave, which
did not show any amplified PCR product. While
in Figure 1.3, top left, contains the
Mycobactheriophage Phagus_Maximus, whose
amplification of its genomic DNA resulted in a
PCR product about 500 base pair using B2
clusters specific primers.
Figure 1.2 Shows the Control Gel.
Figure 1.3 Shows the three gels made during this Research Experience. From left to right are the Class Gel #4, Experimental Gel and Control Gel.
Discussion
This study provides information about
the classification of each Mycobacteriophage.
The conclusion during this experiment was that
only Phagus_Maximus could be classified as
belonging to cluster B2. The results of the other
Mycobactheriophages were not clear; therefore
we cannot arrive to any conclusions. The
Mycobacteriophage named Wilie had ambiguous
results, because it did not show any bands. Wilie
had a low amount of DNA, that’s the reason
why there weren’t any amplify products on the
gel. In order to classify this Mycobacteriophage
it will be necessary to prepare the phage with a
greater amount of DNA and if is necessary test
the phage with a new set of designed cluster
primers. The Mycobacteriophages classified as
Wilie, Suave and Bloo did not showed any
amplified PCR product. In order for them to be
classified is
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necessary to design new PCR cluster primers from J trough Q to test on them.
Acknowledgements
Special thanks to: our mentor Dr.Rubin, the TA’s, Melisa Medina and Valeria Rivera, Yadira Ortiz and RISE. Also to Dr. Eneida Díaz, and Dr. Elena González.
References
Hatfull, Graham F., Cresawn, Steven E., Hendrix, Roger, W. 2008. Comparative Genomics of the Mycobacteriophages: Insights into Bacteriophage Evolution. Research in Microbiology Volume 159, Issue 5. P. 332-339.
Mycobacteriophage Database. [unknown]. http://phagesdb.org/
Ross, Robert. 2012. General Botany Study Guide. Department of Biology UPR Cayey. Puerto Rico pp xxvii, xxviii, xxix.
Rubin. M, 2012. Experimental Classification of Mycobacteriophages: Theoretical Background on Important Concepts and Techniques.
Simmons, Michael J., Snustad, D. Peter. 2012. Principles of Genetics. John Wiley & Sons, Inc. New Jersey pp. 165, 167, 168.