Insight into thermophiles and their wide-spectrum applications

Mehta, Ridhi; Singhal, Paavan; Singh, Hardeep; Damle, Dhanashree; Sharma, Anil Kumar

doi:10.1007/s13205-016-0368-z

Cited by 91 publications

(49 citation statements)

References 79 publications

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“…Instead, each biomolecule inside microorganisms must be adapted to the temperatures in which they grow. This makes proteins and metabolites from microbes growing at hot temperatures particularly interesting for biotechnological and industrial applications [ 8 ]. Organisms can be generally categorized based on the temperature range of their optimal growth.…”

Section: Introductionmentioning

confidence: 99%

Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures

Engqvist

2018

BMC Microbiol

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BackgroundThe ambient temperature of all habitats is a key physical property that shapes the biology of microbes inhabiting them. The optimal growth temperature (OGT) of a microbe, is therefore a key piece of data needed to understand evolutionary adaptations manifested in their genome sequence. Unfortunately there is no growth temperature database or easily downloadable dataset encompassing the majority of cultured microorganisms. We are thus limited in interpreting genomic data to identify temperature adaptations in microbes.ResultsIn this work I significantly contribute to closing this gap by mining data from major culture collection centres to obtain growth temperature data for a nonredundant set of 21,498 microbes. The dataset (10.5281/zenodo.1175608) contains mainly bacteria and archaea and spans psychrophiles, mesophiles, thermophiles and hyperthermophiles. Using this data a full 43% of all protein entries in the UniProt database can be annotated with the growth temperature of the species from which they originate. I validate the dataset by showing a Pearson correlation of up to 0.89 between growth temperature and mean enzyme optima, a physiological property directly influenced by the growth temperature. Using the temperature dataset I correlate the genomic occurance of enzyme functional annotations with growth temperature. I identify 319 enzyme functions that either increase or decrease in occurrence with temperature. Eight metabolic pathways were statistically enriched for these enzyme functions. Furthermore, I establish a correlation between 33 domains of unknown function (DUFs) with growth temperature in microbes, four of which (DUF438, DUF1524, DUF1957 and DUF3458_C) were significant in both archaea and bacteria.ConclusionsThe growth temperature dataset enables large-scale correlation analysis with enzyme function- and domain-level annotations. Growth-temperature dependent changes in their occurrence highlight potential evolutionary adaptations. A few of the identified changes are previously known, such as the preference for menaquinone biosynthesis through the futalosine pathway in bacteria growing at high temperatures. Others represent important starting points for future studies, such as DUFs where their occurrence change with temperature. The growth temperature dataset should become a valuable community resource and will find additional, important, uses in correlating genomic, transcriptomic, proteomic, metabolomic, phenotypic or taxonomic properties with temperature in future studies.Electronic supplementary materialThe online version of this article (10.1186/s12866-018-1320-7) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures

Engqvist

2018

BMC Microbiol

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“…Instead, each biomolecule inside microorganisms must be adapted to the temperatures in which they grow. This makes proteins and metabolites from microbes growing at hot temperatures particularly interesting for biotechnological and industrial applications (Mehta et al 2016) . Organisms can be generally categorized based on the temperature range of their optimal growth.…”

Section: Introductionmentioning

confidence: 99%

Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures

Engqvist

2018

Preprint

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Interpreting genomic data to identify temperature adaptations is challenging due to limited accessibility of growth temperature data. In this work I mine public culture collection websites to obtain growth temperature data for 21,498 organisms. Leveraging this unique dataset I identify 319 enzyme activities that either increase or decrease in abundance with temperature. This is a striking result showing that up to 9% of enzyme activities may represent metabolic changes important for adapting to growth at differing temperatures in microbes. Eight metabolic pathways were statistically enriched for these enzyme activities, further highlighting specific areas of metabolism that may be particularly important for such adaptations. Furthermore, I establish a correlation between 33 domains of unknown function (DUFs) with growth temperature in microbes, four of which (DUF438, DUF1524, DUF1957 and DUF3458_C) were significant in both archaea and bacteria. These DUFs may represent novel, as yet undiscovered, functions relating to temperature adaptation.

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“…Also, there are many factors affecting the tolerance level of thermophilic bacteria, these include; permeability, chemical stability of membrane lipids and GC contents. Similarly, there are more hydrogen bonds in GC base pair compared with AT base pair (Mehta et al 2016). In addition, the pH observation showed that the sampling locations have neutral pH.…”

Section: Discussionmentioning

confidence: 95%

Isolation and molecular identification of carbohydrase and protease producing Bacillus subtilis JCM 1465 isolated from Penen Hot Springs in North Sumatra, Indonesia

Fachrial¹,

Anggraini²,

Harmileni³

et al. 2019

Biodiversitas

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Abstract. Fachrial E, Anggraini S, Harmileni, Nugroho TT, Saryono. 2019. Isolation and molecular identification of carbohydrase and protease producing Bacillus subtilis JCM 1465 isolated from Penen Hot Springs in North Sumatra, Indonesia. Biodiversitas 20: 3493-3498. The application of enzymes industrially is increasing every year and thermophilic microbes are a promising source of these enzymes for industrial use due to their temperature stability. The aim of this study, therefore, was to isolate, characterize and identify the enzyme producer-thermophilic bacteria from the Penen Hot Spring in Deli Serdang, North Sumatra, Indonesia. In the experimental setup, carbohydrase activities including inulinase and amylase were determined by the formation of clear zone around the colonies after soaking with Lugol on the TSA medium supplemented with 1% inulin powder and 1% starch. Similarly, the protease activities were determined by the formation of clear zone around the colonies on Skim Milk Agar Medium. Then, of the 11 isolates, only one known as UTMP 12 showed maximum enzyme activity. The isolate was then characterized based on morphology and biochemistry and found to be Bacillus subtilis strain JCM 1465 (accession number NR_113265, homolog 99.72%). Furthermore, this is the first study on carbohydrase and protease activities of Bacillus subtilis strain JCM 1465 and the result shows that the thermophilic bacteria are needed in the production of carbohydrase and protease.

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Insight into thermophiles and their wide-spectrum applications

Cited by 91 publications

References 79 publications

Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures

Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures

Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures

Isolation and molecular identification of carbohydrase and protease producing Bacillus subtilis JCM 1465 isolated from Penen Hot Springs in North Sumatra, Indonesia

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