Investigation of Newly-explored Species

 We should obtain the pure culture of those new bacteria species. Firstly, we should identify the
method that would allow us to make evidence of the proper bacterial types isolation. We could
use methods of DNA staining in order to visualize the ovoid structure inside the cells. It would help
us to identify the proper colonies after the application of selection. Secondly, selective medium
must be applied to favor the growth of our bacteria only. Selective medium must provide all
required nutrients in accordance to our bacterium carbon and energy sources, and electron
donors. To avoid heterogeneity of bacterium population spread-plate and streak-plate techniques
should be used. A solid colony represents a pure culture, so can be proceed to further
investigation after staining and microscopy.
Specimen prepared from our bacteria should viewed under transmission electron microscope to
investigate ultrathin structure of our new structure.
To identify the type of proteins and nucleic acid we have to extract them out the cells and purified.
Nucleic-acid binding proteins should be positively charged. Therefore they can be purified by ionexchange chromatography. A negatively-charged support (cation exchanger) will bind proteins
with an overall positive charge.
Proteome of our new species can be analyzed by two-dimensional electrophoresis. Moreover, we
can take bacterium, which is morphologically similar to our bacteria, or bacterium from the same
habitat, but without discovered new structure. Proteins in this known bacterium can be resolved
by two-dimensional electrophoresis to compare with our unknown bacterium proteome. In this
way we can discriminate proteins unique to our bacterium. Particular attention should be paid to
proteins with high isoelectric point, which mean high content of basic amino acids.
Further we can extract protein of interest from the gel and determine its mass with mass
spectrometry. With the help of peptide mass fingerprinting it could be possible to identify our
protein, if this protein is in fingerprint databases of course. If our protein was not found in
databases, we can sequence it. Primary structure then can be align with primary structures of
known proteins from databases with help of bioinformatics tools. Such bioinformatics analyses
provides us with information about our proteins’ orthologs. Thus it can help us to clarify place of
our species in taxonomy.
The main group of DNA-binding proteins in eukaryotic cells are histones. Histones are very
conservative proteins. That’s why we have a chance that our proteins will be recognizable by
commercially available antibodies to histones. So immunoprecipitation can be applied to extract
proteins. Purity of such protein sample is very high. We have to rid of antibodies and protein can
be sequenced. Commercially available fluorescent tag antibodies can applied to visualized new
structure in our bacteria.
Description of nucleic acid as long chains give me reasons to assume that this is DNA. RNA has
more complex secondary and tertiary structure. Thus, we should extract DNA from bacteria and
sequenced it. And similarly to protein sequences analysis – bioinformatics tools can provide us
with helpful information to define the closest relatives and origin of our species.
Besides, knowing of nucleic acid sequence make possible to manipulate with bacterium genome
with the help of gene engineering tools. Gene that encode our protein can be inserted into vector,
so a lot of pure protein of interest can be obtained. From pure protein crystals can be grown to
undergo x-ray crystallography to provide us with data about protein’s tertiary structure. Nuclear
magnetic resonance (NMR) spectroscopy is another one method for elucidating three-dimensional
structure.
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“Long chains of nucleic acid” – this is description of DNA molecule, thus this is genetic material of
the cell. “Nucleic acid wrapped around a protein” – a description of the nucleosome – the basic
unit of DNA packaging in nucleus of eukaryotic cells. Thus, we can speculate, that found new
species is a transitional form between prokaryotic and eukaryotic organisms. And found new
structure is the new way of packaging of genetic material, different from the arranging of bacterial
genetic material and closer to eukaryotic DNA packaging.
References
Lansing M. Prescott (2002). Microbiology. (L. M. Prescott, J. P. Harley, D. A. Klein). McGraw-Hill
Higher Education
J.M. Berg, J. L. Tymoczko, L. Stryer (2002) Biochemistry (Fifth ed.) New York: W. H. Freeman
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