Amino acid composition in endothermic vertebrates is biased in the same direction as in thermophilic prokaryotes

Wang, Guang-Zhong; Lercher, Martin J.

doi:10.1186/1471-2148-10-263

Cited by 25 publications

(35 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Among thermophilic fungi, M. thermophila and T. terrestris are two of the best characterized in 9 terms of thermostable enzymes and cellulolytic activity [1][2][3][4] . The fermentation characteristics of 10 these two organisms have been examined and found to be suitable for large-scale production 5,6 .…”

Section: Genomes Summarymentioning

confidence: 99%

“…They can also potentially be developed into cell factories to support production of 26 chemicals and materials at elevated temperatures. Enzymes from thermophilic fungi often 27 tolerate higher temperatures than enzymes from mesophilic species, and some show stability at 28 70-80 °C 1,2 . Notably, it has been reported the cellulolytic activity of some thermophilic species 29 was several times higher than that of the most active cellulolytic mesophiles 3 .…”

mentioning

confidence: 99%

“…8). When comparing the GC content of M. 1 thermophila and T. terrestris with C. globusum and other species within the class 2 Sordariomycetes, it appears that although the genomes of the thermophilic species have a slightly 3 lower genome-level GC content than C. globosum, they have a higher GC content in coding 4 regions, which is reflected in the third position of codons (Supplementary Table 10 T. terrestris codons have a higher GC3. This is in contrast to thermophilic prokaryotes, where 10 analysis of large numbers of sequenced thermophiles and hyperthermophiles did not reveal a 11 correlation of higher GC (and GC3) with thermal adaptability 18 .…”

mentioning

confidence: 99%

“…Selection from natural population 29 variability or from mutagenized strains remains a useful tool for strain development. With a 30 finished genome as a scaffold and modern sequencing technologies, resequencing these strains 1 and identifying mutations becomes relatively simple but very helpful for identifying beneficial 2 and deleterious genetic changes. 3 Thermostability alone does not explain why the enzymes from the thermophilic fungi 4 display higher hydrolytic power than enzymes produced by mesophiles.…”

mentioning

confidence: 99%

See 3 more Smart Citations

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

et al. 2011

View full text Add to dashboard Cite

Thermostable enzymes and thermophilic cell factories may afford economic advantages inFurthermore, we present evidence suggesting that aside from representing a potential 9 reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using 10 classical and molecular genetics. 11Rapid, efficient and robust enzymatic degradation of biomass-derived polysaccharides is 12 currently a major challenge for biofuel production. A prerequisite is the availability of enzymes 13 that hydrolyze cellulose, hemicellulose and other polysaccharides into fermentable sugars at 14 conditions suitable for industrial use. The best studied and most widely used cellulases and to overcome these obstacles is to raise the reaction temperature, thereby increasing hydrolytic 20 rates and reducing contamination risks. AT-rich repetitive regions (Fig. 1) To examine the strategy used by these thermophiles for decomposition of plant cell wall 9 polysaccharides, we used RNA-Seq to compare transcript profiles during growth on barley straw 10 or alfalfa straw to growth on glucose. Alfalfa was chosen to represent dicotyledonous plants, 11 whereas barley was used to represent monocotyledon plants. The major difference between these 12 materials is that the carbohydrates from barley cell wall are mainly cellulose and hemicellulose 13 with a negligible amount of pectin 11 , whereas alfalfa cell wall contains pectin and xylan in 14 roughly similar proportions, each consisting of 15-20% of total carbohydrates 12, . 15 We observed notable differences between the transcriptional profiles of genes encoding conditions. For example, the orthologs in Clades A, B, E, G and P of GH61 are upregulated 8 under growth in complex substrates for both thermophiles (Fig. 2b). An even more striking 9 correlation between transcript levels and orthologs is evident for the GH6 and GH7 cellulases 10 ( Supplementary Fig. 7) where the transcript profiles for the orthologs of the two organisms are Table 7). Thermophilic fungi are major components of the microflora in self-heating composts. They 9 break down cellulose at a faster rate than prodigious, mesophilic cellulase producers such as T. Tables 11-14). On the basis of 24 our comparative analyses of the genomes from two thermophilic fungi, we conclude that their 25 nucleotide and protein features are different from those observed in thermophilic prokaryotes. 26 We also investigated the possibility that thermophilic fungi possess major differences in 27 processes mediating thermophily including heat shock, oxidative stress, membrane biosynthesis, 28 chromatin structure and modification, and fungal cell wall metabolism. We compared the 29 proteins predicted to be involved in these processes in C. globosum, M. thermophila and T. 30 terrestris, but were unable to find differences that can convincingly be interpreted as the Fig. 9). Within the Sordiariales, thermophily 6 is restricted to subgroups of the family Chaetomiaceae. Among fungi more broadly, thermophily 7 also exists in the Zygomycota, but it ...

show abstract

Section: Genomes Summarymentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

et al. 2011

View full text Add to dashboard Cite

show abstract

“…The different design strategies introduced to the protein structure are increasing the disulfide bonds, salt bridges and stabilizing the loop regions either by introducing residues such as proline or removing glycine. Similarly, another common strategy is finding the most flexible region of the target proteins from the experimental B-factors and then to focus mutagenesis on this aspect (Farias and Bonato, 2003;Kumar et al, 2000;Wang and Lercher, 2010;Anbarasan et al, 2010). One of the direct method in case of proteins of interest having enhanced thermal stability may be obtained either by protein engineering or by searching for homologs in thermophiles Radestock and Gohlke, 2011).…”

Section: Introductionmentioning

confidence: 99%

<i>In-silico</i> Rational Protein Engineering and Design Approach to Improve Thermostability of a Haloalkane Dehalogenase Enzyme

Satpathy¹,

Konkimalla²,

Ratha³

2015

American Journal of Bioinformatics

View full text Add to dashboard Cite

Thermostability of enzymes is a major prerequisite for use in industrial enzymology. There are as such no simple general principles for achieving thermostability in case of enzymes as many factors are required to fulfil for different enzymes. The present study describes computational methods to design thermostable haloalkane dehalogenase enzyme using the crystal structure available Protein Data Bank (PDB ID: 1EDE). In in silico design strategy rule-based approaches such as disulfide bond geometry, new hydrophobic pocket design, new salt bridge construction and multiple mutations (combination of the above approaches) were introduced to the original enzyme. After each design strategy the functional effect was confirmed in terms of enzyme substrate binding by molecular docking using Autodock vina tool. Best design strategy was evaluated by comparative molecular dynamics simulation applying simulated annealing method at 8 ns using GROMACS tool. The surface hydrophobicity which is the key factor for thermostability in haloalkane dehalogenase was obtained from the simulation result. Upon optimizing the parameters, thermostability of mutant enzyme under consideration was also confirmed by the 5 ns molecular dynamics simulation at 400, 500 and 600 K.

show abstract

A proteome‐scale analysis of vertebrate protein amino acid occurrence: Thermoadaptation shows a correlation with protein solvation but less so with dynamics

Buck

2022

Proteins

View full text Add to dashboard Cite

Despite differences in behaviors and living conditions, vertebrate organisms share the great majority of proteins, often with subtle differences in amino acid sequence.Here, we present a simple way to analyze the difference in amino acid occurrence by comparing highly homologous proteins on a subproteome level between several vertebrate model organisms. Specifically, we use this method to identify a pattern of amino acid conservation as well as a shift in amino acid occurrence between homeotherms (warm-blooded species) and poikilotherms (cold-blooded species). Importantly, this general analysis and a specific example further establish a broad correlation, if not likely connection between the thermal adaptation of protein sequences and two of their physical features: on average a change in their protein dynamics and, even more strongly, in their solvation. For poikilotherms, such as frog and fish, the lower body temperature is expected to increase the protein-protein interaction due to a decrease in protein internal dynamics. In order to counteract the tendency for enhanced binding caused by low temperatures, poikilotherms enhance the solvation of their proteins by favoring polar amino acids. This feature appears to dominate over possible changes in dynamics for some proteins. The results suggest that a general trend for amino acid choice is part of the mechanism for thermoadaptation of vertebrate organisms at the molecular level.

show abstract

Amino acid composition in endothermic vertebrates is biased in the same direction as in thermophilic prokaryotes

Cited by 25 publications

References 29 publications

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

<i>In-silico</i> Rational Protein Engineering and Design Approach to Improve Thermostability of a Haloalkane Dehalogenase Enzyme

A proteome‐scale analysis of vertebrate protein amino acid occurrence: Thermoadaptation shows a correlation with protein solvation but less so with dynamics

Contact Info

Product

Resources

About