Thermotoga petrophila explained

Thermotoga petrophila is a hyperthermophilic, anaerobic, non-spore-forming, rod-shaped, fermentative heterotroph, with type strain RKU-1^T.^[1] T. petrophila was first discovered and isolated from an oil reservoir off of the coast of Japan and was deemed genetically distinct from its sister clades. Because these organism are found in deep, hot aquatic settings, they have become of great interest for biotechnology due to their enzymes functioning at high temperatures and pressures.

Description

T. petrophila strain RKU-1 belongs to one of the deepest branching bacteria phyla, Thermotogota, but it is a member of a later branching clade within its genus Thermotoga.^[2] T. petrophila was first isolated from an oil reserve off the coast of Japan in 2001. This was the first time that this novel organism was morphologically and genetically described.

Morphological Characteristic

T. petrophila are rod shaped bacteria containing a sheath like structure that balloons at both ends called a toga. Typically, the cells size ranged from 2-7 μm long to 0.7-1.0 μm wide, and have flagella at the subpolar and lateral regions of the cell. The optimal growth rate occurs at 80 °C, but growth is observed from 47-88 °C. Growth occurs between pH 5.2-9.0 with optimum growth occurring at a pH 7. Ionic strength as well as oxygen availability affects the growth of T. petrophila negatively. It can grow and obtain carbon from the majority of sugars, excluding mannitol and xylose. While it cannot reduce sulfate to hydrogen sulfide, it reduces sulfur to thiosulfate which is further reduced to hydrogen sulfide.

Genotypic Characteristics

T. petrophila shares more than 99% of its 16S rRNA genetic sequence with its sister clade, T. maritima, T. neapolitana, and T. naphthophila, but each of these are distinct species as they share less than 30% similarity shown by DNA-DNA hybridization experiments. The G+C base content of the DNA is 46.6%.  T. petrophila is also known to contain one of the smallest plasmids. Thermotoga petrophila RKU1 plasmid (pRKU1) is negatively supercoiled, contains 846 base pairs, and carries only the rep gene.^[3] Due to T. Petrophila being part of the deep branching bacterial lineages, some horizontal genetic transfer has occurred with the maltose transporter gene (mal3) and the archaeal lineage Thermococcales, while the mal1 and mal2 genes are more closely related to bacterial maltose transporter genes.^[4]

Metabolism

The majority of the Thermotogota species use the Embden–Meyerhof–Parnas pathway to catabolize glucose, however, during the tricarboxylic acid pathway,T. petrophila, uses the malic enzyme to create a pyruvate intermediate. They oxidatively catabolize malate to succinyl-CoA and reductively produce succinate from malate.^[5]

Applications

Because these organisms are found near hyperthermophic deep sea oil rigs, their enzymes tend to be thermostable. Recently, the textile industry was investigating the fermentative scale up strategy of cloning the α – amylase gene from T. petrophila into E. coli. Their results indicate that the efficiency of this enzyme helps with the desizing of cotton cloth.^[6]

For the biofuel industry, cellulase enzyme genes from T. petrophila have been cloned and put into E. coli for an enhanced saccharification reaction from softwood dust. With nitric acid treatment and the transformed enzymes, the results revealed that lignin degradation was more efficiently optimized and that the recombinant cellulases actively hydrolyzed cellulose indicating that this method could potentially be used for better lignocellulosic based bioethanol manufacturing.^[7]

For medical purposes, T. petrophila K4 genetically engineered strain used its DNA polymerase (K4pol_L329A) for a detection method of acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) detection kit.^[8]

Further reading

• Book: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E . The Prokaryotes: Volume 7: Proteobacteria: Delta, Epsilon Subclass. Deeply Rooting Bacteria . Springer . New York . 2006 . 978-0-387-30747-3 .
• Book: Priest F, Goodfellow M . Applied Microbial Systematics . Springer Science & Business Media . November 2000 . 978-0-412-71660-7 .
• Haq IU, Khan MA, Muneer B, Hussain Z, Afzal S, Majeed S, Rashid N, Javed MM, Ahmad I . 6 . Cloning, characterization and molecular docking of a highly thermostable β-1,4-glucosidase from Thermotoga petrophila . Biotechnology Letters . 34 . 9 . 1703–1709 . September 2012 . 22714267 . 10.1007/s10529-012-0953-0 . 17477338 .
• Souza TA, Santos CR, Souza AR, Oldiges DP, Ruller R, Prade RA, Squina FM, Murakami MT . 6 . Structure of a novel thermostable GH51 α-L-arabinofuranosidase from Thermotoga petrophila RKU-1 . Protein Science . 20 . 9 . 1632–1637 . September 2011 . 21796714 . 3190157 . 10.1002/pro.693 .
• Sano S, Yamada Y, Shinkawa T, Kato S, Okada T, Higashibata H, Fujiwara S . Mutations to create thermostable reverse transcriptase with bacterial family A DNA polymerase from Thermotoga petrophila K4 . Journal of Bioscience and Bioengineering . 113 . 3 . 315–321 . March 2012 . 22143068 . 10.1016/j.jbiosc.2011.11.001 .

External links

• • LPSN
• Type strain of Thermotoga petrophila at BacDive - the Bacterial Diversity Metadatabase

Notes and References

1. Takahata Y, Nishijima M, Hoaki T, Maruyama T . Thermotoga petrophila sp. nov. and Thermotoga naphthophila sp. nov., two hyperthermophilic bacteria from the Kubiki oil reservoir in Niigata, Japan . International Journal of Systematic and Evolutionary Microbiology . 51 . Pt 5 . 1901–1909 . September 2001 . 11594624 . 10.1099/00207713-51-5-1901 . free .
2. Book: Bhandari V, Gupta RS . The Phylum Thermotogae . 2014 . Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F . The Prokaryotes: Other Major Lineages of Bacteria and The Archaea . 989–1015 . Berlin, Heidelberg . Springer . en . 10.1007/978-3-642-38954-2_118 . 978-3-642-38954-2 .
3. Smillie C, Garcillán-Barcia MP, Francia MV, Rocha EP, de la Cruz F . Mobility of plasmids . Microbiology and Molecular Biology Reviews . 74 . 3 . 434–452 . September 2010 . 20805406 . 2937521 . 10.1128/MMBR.00020-10 .
4. Noll KM, Lapierre P, Gogarten JP, Nanavati DM . Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales . BMC Evolutionary Biology . 8 . 1 . 7 . January 2008 . 18197971 . 2246101 . 10.1186/1471-2148-8-7 . free .
5. Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM, DeBoy RT, Nelson KE, Nesbø CL, Doolittle WF, Gogarten JP, Noll KM . 6 . On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales . Proceedings of the National Academy of Sciences of the United States of America . 106 . 14 . 5865–5870 . April 2009 . 19307556 . 2667022 . 10.1073/pnas.0901260106 . 2009PNAS..106.5865Z . free .
6. Zafar A, Aftab MN, Iqbal I, Din ZU, Saleem MA . Pilot-scale production of a highly thermostable α-amylase enzyme from Thermotoga petrophila cloned into E. coli and its application as a desizer in textile industry . RSC Advances . 9 . 2 . 984–992 . January 2019 . 35517638 . 9059537 . 10.1039/C8RA06554C . 2019RSCAd...9..984Z .
7. Haq I, Mustafa Z, Nawaz A, Mukhtar H, Zhou X, Xu Y . 2020-07-23 . Comparative assessment of acids and alkali based pretreatment on sawdust for enhanced saccharification with thermophilic cellulases . Revista Mexicana de Ingeniería Química . en . 19 . Sup. 1 . 305–314 . 10.24275/rmiq/Bio1702 . 225313585 . 2395-8472. free .
8. Summer S, Schmidt R, Herdina AN, Krickl I, Madner J, Greiner G, Mayer FJ, Perkmann-Nagele N, Strassl R . High stability of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA under minimal storage conditions for detection by Real-Time PCR. . July 2020 . 1–9 . 10.1101/2020.07.21.20158154.