Kanazawa University Research: Genetic Typing of a Bacterium with Biotechnological Potential

KANAZAWA, Japan, Dec. 4, 2019 /PRNewswire/ -- Researchers at Kanazawa University describe in Scientific Reports the genetic typing of the bacterium Pseudomonas putida. The bacterium is normally not highly infectious but isolated from several clinical sites.

Pseudomonas putida is a bacterium occurring in soil, aquatic environments and plants. Although the virulence of Pseudomonas p. — the ability of the bacterium to infect its host and inflict a disease — is considered to be low, infection in severely ill patients can be lethal. P. putida strains (also called isolates) have been found in hospitals, e.g. in urine, blood or wound discharge from patients, and such clinical isolates have been found to display resistance to drugs. Now, Kohei Ogura from Kanazawa University and colleagues have performed gene sequencing for various P. putida isolates originating from both environmental and clinical sites.

Genetic typing of different P. putida strains enables to determine which are the more virulent ones.  This is important because P. putida has high biotechnological value. Indeed, P. putida is a perfect microbiological platform for 'metabolic engineering', in which selected biochemical processes within the cells of an organism are stimulated so that the cells produce more of a particular substance.  (Examples of metabolic engineering include the industrial production of beer, wine and cheese.)

The researchers applied a technique known as multilocus sequence typing (MLST), a method used in molecular biology for the genetic typing of more than one locus — a locus refers to the position on a chromosome where a specific gene is located.

The MLST technique is based on obtaining DNA sequences of several so-called 'housekeeping genes': genes that are needed for the maintenance of the basic functioning of a cell. In order to arrive at a valid MLST scheme, typically 100 isolates are required. Ogura and colleagues used 106 isolates, with 16 having an environmental origin and 90 coming from clinical sites.  For the MLST scheme, the scientists used 8 housekeeping genes.

The scientists not only obtained the first MLST scheme for P. putida, they also were able to deduce that the studied bacterium isolates are clonal, meaning that they share common ancestry. At the same time, the researchers found that "our MLST scheme reflects the genetic diversity of P. putida group isolated from both clinical and environmental sites".

Background

Genotyping

Genetic typing (genotyping) refers to detecting small genetic differences (i.e., differences in DNA) that can correspond to big changes in phenotype. These changes include both differences in physical appearance and differences associated with the origin of diseases.

Genotyping applies to all organisms, from humans to viruses and bacteria. Genotyping viruses and bacteria are helpful for understanding and controlling pathogens causing diseases. 

Many methods exist to perform (partial) genotyping. Kohei Ogura from Kanazawa University used the multilocus sequence typing (MLST) method to obtain the genotype of the bacterium P. putida.

Reference

Kohei Ogura, Kayo Shimada, and Tohru Miyoshi-Akiyama. A multilocus sequence typing scheme of Pseudomonas putida for clinical and environmental isolates, Scientific Reports 9, 13980 (2019).

DOI: 10.1038/s41598-019-50299-6

URL: https://doi.org/10.1038/s41598-019-50299-6

About Nano Life Science Institute (WPI-NanoLSI)

https://nanolsi.kanazawa-u.ac.jp/en/

Nano Life Science Institute (NanoLSI), Kanazawa University is a research center established in 2017 as part of the World Premier International Research Center Initiative of the Ministry of Education, Culture, Sports, Science and Technology. The objective of this initiative is to form world-tier research centers. NanoLSI combines the foremost knowledge of bio-scanning probe microscopy to establish 'nano-endoscopic techniques' to directly image, analyze, and manipulate biomolecules for insights into mechanisms governing life phenomena such as diseases.

About Kanazawa University

http://www.kanazawa-u.ac.jp/e/

As the leading comprehensive university on the Sea of Japan coast, Kanazawa University has contributed greatly to higher education and academic research in Japan since it was founded in 1949. The University has three colleges and 17 schools offering courses in subjects that include medicine, computer engineering, and humanities.

The University is located on the coast of the Sea of Japan in Kanazawa – a city rich in history and culture. The city of Kanazawa has a highly respected intellectual profile since the time of the fiefdom (1598-1867). Kanazawa University is divided into two main campuses: Kakuma and Takaramachi for its approximately 10,200 students including 600 from overseas.

Further information

Hiroe Yoneda
Vice Director of Public Affairs
WPI Nano Life Science Institute (WPI-NanoLSI)
Kanazawa University
Kakuma-machi, Kanazawa 920-1192, Japan
Email: nanolsi-office@adm.kanazawa-u.ac.jp  
Tel: +81-(76)-234-4550