1
|
Li W, Jacobsen MT, Park C, Jung JU, Lin NP, Huang PS, Lal RA, Chou DHC. A cysteine-specific solubilizing tag strategy enables efficient chemical protein synthesis of difficult targets. Chem Sci 2024; 15:3214-3222. [PMID: 38425513 PMCID: PMC10901488 DOI: 10.1039/d3sc06032b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/18/2024] [Indexed: 03/02/2024] Open
Abstract
We developed a new cysteine-specific solubilizing tag strategy via a cysteine-conjugated succinimide. This solubilizing tag remains stable under common native chemical ligation conditions and can be efficiently removed with palladium-based catalysts. Utilizing this approach, we synthesized two proteins containing notably difficult peptide segments: interleukin-2 (IL-2) and insulin. This IL-2 chemical synthesis represents the simplest and most efficient approach to date, which is enabled by the cysteine-specific solubilizing tag to synthesize and ligate long peptide segments. Additionally, we synthesized a T8P insulin variant, previously identified in an infant with neonatal diabetes. We show that T8P insulin exhibits reduced bioactivity (a 30-fold decrease compared to standard insulin), potentially contributing to the onset of diabetes in these patients. In summary, our work provides an efficient tool to synthesize challenging proteins and opens new avenues for exploring research directions in understanding their biological functions.
Collapse
Affiliation(s)
- Wenchao Li
- División of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University Palo Alto CA 94305 USA
| | - Michael T Jacobsen
- División of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University Palo Alto CA 94305 USA
| | - Claire Park
- División of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University Palo Alto CA 94305 USA
| | - Jae Un Jung
- División of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University Palo Alto CA 94305 USA
| | - Nai-Pin Lin
- División of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University Palo Alto CA 94305 USA
| | - Po-Ssu Huang
- Department of Bioengineering, Stanford University Palo Alto CA 94305 USA
| | - Rayhan A Lal
- Division of Endocrinology, Department of Medicine, School of Medicine, Stanford University Palo Alto CA 94305 USA
| | - Danny Hung-Chieh Chou
- División of Endocrinology and Diabetes, Department of Pediatrics, School of Medicine, Stanford University Palo Alto CA 94305 USA
| |
Collapse
|
2
|
Bai X, Li D, Ma F, Deng X, Luo M, Feng Y, Yang G. Improved thermostability of creatinase from Alcaligenes Faecalis through non-biased phylogenetic consensus-guided mutagenesis. Microb Cell Fact 2020; 19:194. [PMID: 33069232 PMCID: PMC7568399 DOI: 10.1186/s12934-020-01451-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 10/07/2020] [Indexed: 02/06/2023] Open
Abstract
Background Enzymatic quantification of creatinine has become an essential method for clinical evaluation of renal function. Although creatinase (CR) is frequently used for this purpose, its poor thermostability severely limits industrial applications. Herein, we report a novel creatinase from Alcaligenes faecalis (afCR) with higher catalytic activity and lower KM value, than currently used creatinases. Furthermore, we developed a non-biased phylogenetic consensus method to improve the thermostability of afCR. Results We applied a non-biased phylogenetic consensus method to identify 59 candidate consensus residues from 24 creatinase family homologs for screening afCR mutants with improved thermostability. Twenty-one amino acids of afCR were selected to mutagenesis and 11 of them exhibited improved thermostability compared to the parent enzyme (afCR-M0). Combination of single-site mutations in sequential screens resulted in a quadruple mutant D17V/T199S/L6P/T251C (M4-2) which showed ~ 1700-fold enhanced half-life at 57 °C and a 4.2 °C higher T5015 than that of afCR-M0. The mutant retained catalytic activity equivalent to afCR-M0, and thus showed strong promise for application in creatinine detection. Structural homology modeling revealed a wide range of potential molecular interactions associated with individual mutations that contributed to improving afCR thermostability. Conclusions Results of this study clearly demonstrated that the non-biased-phylogenetic consensus design for improvement of thermostability in afCR is effective and promising in improving the thermostability of more enzymes.
Collapse
Affiliation(s)
- Xue Bai
- Institute of Biothermal Science and Technology, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China
| | - Daixi Li
- Institute of Biothermal Science and Technology, University of Shanghai for Science and Technology, Shanghai, 200093, People's Republic of China.
| | - Fuqiang Ma
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, Jiangsu, People's Republic of China
| | - Xi Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China
| | - Manjie Luo
- Wuhan Hzymes Biotechnology Co., Ltd., Wuhan, 430000, Hubei, People's Republic of China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China
| | - Guangyu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd., Shanghai, 200240, People's Republic of China.
| |
Collapse
|
3
|
Thermostabilization of VPR, a kinetically stable cold adapted subtilase, via multiple proline substitutions into surface loops. Sci Rep 2020; 10:1045. [PMID: 31974391 PMCID: PMC6978356 DOI: 10.1038/s41598-020-57873-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/27/2019] [Indexed: 11/24/2022] Open
Abstract
Protein stability is a widely studied topic, there are still aspects however that need addressing. In this paper we examined the effects of multiple proline substitutions into loop regions of the kinetically stable proteinase K-like serine protease VPR, using the thermostable structural homologue AQUI as a template. Four locations for proline substitutions were chosen to imitate the structure of AQUI. Variants were produced and characterized using differential scanning calorimetry (DSC), circular dichroism (CD), steady state fluorescence, acrylamide fluorescence quenching and thermal inactivation experiments. The final product VPRΔC_N3P/I5P/N238P/T265P was greatly stabilized which was achieved without any noticeable detrimental effects to the catalytic efficiency of the enzyme. This stabilization seems to be derived from the conformation restrictive properties of the proline residue in its ability to act as an anchor point and strengthen pre-existing interactions within the protein and allowing for these interactions to prevail when thermal energy is applied to the system. In addition, the results underline the importance of the synergy between distant local protein motions needed to result in stabilizing effects and thus giving an insight into the nature of the stability of VPR, its unfolding landscape and how proline residues can infer kinetic stability onto protein structures.
Collapse
|
4
|
Óskarsson KR, Kristjánsson MM. Improved expression, purification and characterization of VPR, a cold active subtilisin-like serine proteinase and the effects of calcium on expression and stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:152-162. [PMID: 30502512 DOI: 10.1016/j.bbapap.2018.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 01/21/2023]
Abstract
Cloning into a pET 11a vector, followed by high-level expression of the cold adapted subtilase, VPR, utilizing the rhamnose titratable T7 system of Lemo21, resulted in a dramatic increase of soluble protein compared to the older system used. Expression optimization clearly shows the importance of calcium in the medium after induction, both for stability of the proteinase and cell health. Characterization of the purified enzyme obtained in a redesigned purification protocol which removed apparent RNA contaminants, resulted in a significantly higher value for kcat than previously reported. The new recombinant protein exhibited slightly lower stability against thermal denaturation and thermal inactivation. Our results also indicate that two of the calcium binding sites have apparent binding constants in the mM range. Binding of calcium to the weaker of those two sites only affects resistance of the enzyme against irreversible thermal inactivation. Differential scanning calorimetry revealed a non-two-state denaturation process, with indication of presence of intermediates caused by unfolding of calcium binding motifs.
Collapse
Affiliation(s)
- Kristinn R Óskarsson
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland
| | - Magnús M Kristjánsson
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland.
| |
Collapse
|
5
|
Zhao HY, Feng H. Engineering Bacillus pumilus alkaline serine protease to increase its low-temperature proteolytic activity by directed evolution. BMC Biotechnol 2018; 18:34. [PMID: 29859069 PMCID: PMC5984802 DOI: 10.1186/s12896-018-0451-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 05/25/2018] [Indexed: 02/07/2023] Open
Abstract
Background Mesophilic alkaline serine proteases from various bacteria have been commercially applied in a range of industries owing to their high catalytic efficiency and wide substrate specificity. However, these proteases have an optimal catalytic temperature of approximately 50 °C, and their activity decreases significantly at low temperature. Therefore, to enhance their cold activity, it is necessary to improve the catalytic performance of these proteases at low temperature. The alkaline serine protease (DHAP) from Bacillus pumilus BA06 is a typical mesophilic enzyme, which has demonstrated great potential in various industrial applications. Here we attempted to improve the cold activity of DHAP via directed evolution. Results Seven variants (P9S, A1G/K27Q, A38V, A116T, T162I, S182R, and T243S) of DHAP from B. pumilus were obtained via directed evolution. The results showed that all of the variants had increased proteolytic activity at 15 °C towards both the casein and synthetic peptide substrates. With the exception of variant T243S, the thermostability of these variants did not decrease in comparison with the wild-type enzyme. Kinetic analysis indicated that the increase in catalytic efficiency was largely attributed to the increase in turnover number (kcat). Furthermore, the combined variants generated by site-directed mutagenesis showed a further increase in specific caseinolytic activity and the kcat value for hydrolysis of the synthetic peptide. The combined variants of P9S/K27Q and P9S/T162I exhibited an approximate 5-fold increase in caseinolytic activity at 15 °C and almost no loss of thermostability. Finally, the possible mechanism responsible for the change in catalytic properties for these variants was interpreted based on structural modeling. Conclusions Directed evolution and site-directed mutagenesis were combined to engineer variants of the DHAP from B. pumilus. All of the variants exhibited an increase in hydrolytic efficiency at low temperature towards both of the substrates, casein and synthetic peptide, without any loss of thermostability compared with the wild-type. These data suggest that engineering low-temperature activity for a bacterial protease is not always associated with the loss of thermostability. Furthermore, our findings demonstrate that enhanced cold activity and thermostability could be integrated into a single variant. Electronic supplementary material The online version of this article (10.1186/s12896-018-0451-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hong-Yan Zhao
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, People's Republic of China.,Laboratory of Molecular Target Therapy of Cancer, Institute of Basic Medical Sciences, Hubei University of Medicine, Shiyan, 442000, Hubei, People's Republic of China
| | - Hong Feng
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, People's Republic of China.
| |
Collapse
|
6
|
A single mutation Gln142Lys doubles the catalytic activity of VPR, a cold adapted subtilisin-like serine proteinase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1436-43. [PMID: 27456266 DOI: 10.1016/j.bbapap.2016.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 07/11/2016] [Accepted: 07/15/2016] [Indexed: 11/20/2022]
Abstract
Structural comparisons of the cold adapted subtilase VPR and its thermophilic homologue, aqualysin I (AQUI) indicated the presence of additional salt bridges in the latter. Few of those appear to contribute significantly to thermal stability of AQUI. This includes a putative salt bridge between residues Lys142 and Glu172 as its deletion did not have any significant effect on its stability or activity (Jónsdóttir et al. (2014)). Insertion of this putative salt bridge into the structure of VPR, in a double mutant (VPRΔC_Q142K/S172E), however was detrimental to the stability of the enzyme. Incorporation of either the Q142K or S172E mutations into VPR, were found to significantly affect the catalytic properties of the enzyme. The single mutation Q142K was highly effective, as it increased the kcat and kcat/Km more than twofold. When the Q142K mutation was inserted into a thermostabilized, but a low activity mutant of VPR (VPRΔC_N3P/I5P), the activity increased about tenfold in terms of kcat and kcat/Km, while retaining the stability of the mutant. Molecular dynamics simulations of the single mutants were carried out to provide structural rationale for these experimental observations. Based on root mean square fluctuation (RMSF) profiles, the two mutants were more flexible in certain regions of the structure and the Q142K mutant had the highest overall flexibility of the three enzymes. The results suggest that weakening of specific H-bonds resulting from the mutations may be propagated over some distance giving rise to higher flexibility in the active site regions of the enzyme, causing higher catalytic activity in the mutants.
Collapse
|
7
|
Wang Q, Cen Z, Zhao J. The survival mechanisms of thermophiles at high temperatures: an angle of omics. Physiology (Bethesda) 2015; 30:97-106. [PMID: 25729055 DOI: 10.1152/physiol.00066.2013] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Thermophiles are referred to as microorganisms with optimal growth temperatures of >60 °C. Over the past few years, a number of studies have been conducted regarding thermophiles, especially using the omics strategies. This review provides a systematic view of the survival physiology of thermophiles from an "omics" perspective, which suggests that the adaptive ability of thermophiles is based on a cooperative mode with multi-dimensional regulations integrating genomics, transcriptomics, and proteomics.
Collapse
Affiliation(s)
- Quanhui Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; and BGI-Shenzhen, Shenzhen, China
| | - Zhen Cen
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; and
| | - Jingjing Zhao
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; and
| |
Collapse
|
8
|
Sakaguchi M, Osaku K, Maejima S, Ohno N, Sugahara Y, Oyama F, Kawakita M. Highly conserved salt bridge stabilizes a proteinase K subfamily enzyme, Aqualysin I, from Thermus aquaticus YT-1. AMB Express 2014; 4:59. [PMID: 25136511 PMCID: PMC4131155 DOI: 10.1186/s13568-014-0059-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 07/02/2014] [Indexed: 11/10/2022] Open
Abstract
The proteinase K subfamily enzymes, thermophilic Aqualysin I (AQN) from Thermus aquaticus YT-1 and psychrophilic serine protease (VPR) from Vibrio sp. PA-44, have six and seven salt bridges, respectively. To understand the possible significance of salt bridges in the thermal stability of AQN, we prepared mutant proteins in which amino acid residues participating in salt bridges common to proteinase K subfamily members and intrinsic to AQN were replaced to disrupt the bridges one at a time. Disruption of a salt bridge common to proteinase K subfamily enzymes in the D183N mutant resulted in a significant reduction in thermal stability, and a massive change in the content of the secondary structure was observed, even at 70°C, in the circular dichroism (CD) analysis. These results indicate that the common salt bridge Asp183-Arg12 is important in maintaining the conformation of proteinase K subfamily enzymes and suggest the importance of proximity between the regions around Asp183 and the N-terminal region around Arg12. Of the three mutants that lack an AQN intrinsic salt bridge, D212N was more prone to unfolding at 80°C than the wild-type enzyme. Similarly, D17N and E237Q were less thermostable than the wild-type enzyme, although this may be partially due to increased autolysis. The AQN intrinsic salt bridges appear to confer additional thermal stability to this enzyme. These findings will further our understanding of the factors involved in stabilizing protein structure.
Collapse
|
9
|
Sigtryggsdóttir ÁR, Papaleo E, Thorbjarnardóttir SH, Kristjánsson MM. Flexibility of cold- and heat-adapted subtilisin-like serine proteinases evaluated with fluorescence quenching and molecular dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:705-12. [DOI: 10.1016/j.bbapap.2014.02.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 02/04/2014] [Accepted: 02/12/2014] [Indexed: 11/24/2022]
|
10
|
Zhang S, He Y, Yu H, Dong Z. Seven N-terminal residues of a thermophilic xylanase are sufficient to confer hyperthermostability on its mesophilic counterpart. PLoS One 2014; 9:e87632. [PMID: 24498158 PMCID: PMC3907472 DOI: 10.1371/journal.pone.0087632] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 12/27/2013] [Indexed: 11/18/2022] Open
Abstract
Xylanases, and especially thermostable xylanases, are increasingly of interest for the deconstruction of lignocellulosic biomass. In this paper, the termini of a pair of xylanases, mesophilic SoxB and thermophilic TfxA, were studied. Two regions in the N-terminus of TfxA were discovered to be potentially important for the thermostability. By focusing on Region 4, it was demonstrated that only two mutations, N32G and S33P cooperated to improve the thermostability of mesophilic SoxB. By introducing two potential regions into SoxB in combination, the most thermostable mutant, M2-N32G-S33P, was obtained. The M2-N32G-S33P had a melting temperature (Tm) that was 25.6°C higher than the Tm of SoxB. Moreover, M2-N32G-S33P was even three-fold more stable than TfxA and had a Tm value that was 9°C higher than the Tm of TfxA. Thus, for the first time, the mesophilic SoxB "pupil" outperformed its thermophilic TfxA "master" and acquired hyperthermostability simply by introducing seven thermostabilizing residues from the extreme N-terminus of TfxA. This work suggested that mutations in the extreme N-terminus were sufficient for the mesophilic xylanase SoxB to acquire hyperthermostability.
Collapse
Affiliation(s)
- Shan Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Yongzhi He
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Haiying Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Zhiyang Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
- * E-mail:
| |
Collapse
|
11
|
Chen Z, Wen B, Wang Q, Tong W, Guo J, Bai X, Zhao J, Sun Y, Tang Q, Lin Z, Lin L, Liu S. Quantitative proteomics reveals the temperature-dependent proteins encoded by a series of cluster genes in thermoanaerobacter tengcongensis. Mol Cell Proteomics 2013; 12:2266-77. [PMID: 23665590 DOI: 10.1074/mcp.m112.025817] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Comprehensive and quantitative information of the thermophile proteome is an important source for understanding of the survival mechanism under high growth temperature. Thermoanaerobacter tengcongensis (T. tengcongensis), a typical anaerobic thermophilic eubacterium, was selected to quantitatively evaluate its protein abundance changes in response to four different temperatures. With optimized procedures of isobaric tags for relative and absolute quantitation quantitative proteomics (iTRAQ), such as peptide fractionation with high-pH reverse phase (RP) high performance liquid chromatography (HPLC), tandem MS acquisition mode in LTQ Orbitrap Velos MS, and evaluation of the quantification algorithms, high quality of the quantitative information of the peptides identified were acquired. In total, 1589 unique proteins were identified and defined 251 as the temperature-dependent proteins. Analysis of genomic locations toward the correspondent genes of these temperature-dependent proteins revealed that more than 30% were contiguous units with relevant biological functions, which are likely to form the operon structures in T. tengcongensis. The RNA sequencing (RNA-seq) data further demonstrated that these cluster genes were cotranscribed, and their mRNA abundance changes responding to temperature exhibited the similar trends as the proteomic results, suggesting that the temperature-dependent proteins are highly associated with the correspondent transcription status. Hence, the operon regulation is likely an energy-efficient mode for T. tengcongensis survival. In addition, evaluation to the functions of differential proteomes indicated that the abundance of the proteins participating in sulfur-respiration on the plasma membrane was decreased as the temperature increased, whereas the glycolysis-related protein abundance was increased. The energy supply in T. tengcongensis at high temperature is, therefore, speculated not mainly through the respiration chain reactions.
Collapse
Affiliation(s)
- Zhen Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China 101318
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
van Noort V, Bradatsch B, Arumugam M, Amlacher S, Bange G, Creevey C, Falk S, Mende DR, Sinning I, Hurt E, Bork P. Consistent mutational paths predict eukaryotic thermostability. BMC Evol Biol 2013; 13:7. [PMID: 23305080 PMCID: PMC3546890 DOI: 10.1186/1471-2148-13-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 01/07/2013] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Proteomes of thermophilic prokaryotes have been instrumental in structural biology and successfully exploited in biotechnology, however many proteins required for eukaryotic cell function are absent from bacteria or archaea. With Chaetomium thermophilum, Thielavia terrestris and Thielavia heterothallica three genome sequences of thermophilic eukaryotes have been published. RESULTS Studying the genomes and proteomes of these thermophilic fungi, we found common strategies of thermal adaptation across the different kingdoms of Life, including amino acid biases and a reduced genome size. A phylogenetics-guided comparison of thermophilic proteomes with those of other, mesophilic Sordariomycetes revealed consistent amino acid substitutions associated to thermophily that were also present in an independent lineage of thermophilic fungi. The most consistent pattern is the substitution of lysine by arginine, which we could find in almost all lineages but has not been extensively used in protein stability engineering. By exploiting mutational paths towards the thermophiles, we could predict particular amino acid residues in individual proteins that contribute to thermostability and validated some of them experimentally. By determining the three-dimensional structure of an exemplar protein from C. thermophilum (Arx1), we could also characterise the molecular consequences of some of these mutations. CONCLUSIONS The comparative analysis of these three genomes not only enhances our understanding of the evolution of thermophily, but also provides new ways to engineer protein stability.
Collapse
Affiliation(s)
- Vera van Noort
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg 69117, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Blum JK, Ricketts MD, Bommarius AS. Improved thermostability of AEH by combining B-FIT analysis and structure-guided consensus method. J Biotechnol 2012; 160:214-21. [DOI: 10.1016/j.jbiotec.2012.02.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 02/19/2012] [Accepted: 02/24/2012] [Indexed: 10/28/2022]
|
14
|
Tattersall GJ, Sinclair BJ, Withers PC, Fields PA, Seebacher F, Cooper CE, Maloney SK. Coping with Thermal Challenges: Physiological Adaptations to Environmental Temperatures. Compr Physiol 2012; 2:2151-202. [DOI: 10.1002/cphy.c110055] [Citation(s) in RCA: 184] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
15
|
Structural and functional properties of glycerol-3-phosphate dehydrogenase from a mammalian hibernator. Protein J 2012; 31:109-19. [PMID: 22180227 DOI: 10.1007/s10930-011-9376-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Glycerol-3-phosphate dehydrogenase (G3PDH; E.C.1.1.1.8) was purified from liver and skeletal muscle of black-tailed prairie dogs (Cynomys ludivicianus), a hibernating species. Native and subunit molecular masses of the dimeric enzyme were 77 and 40 kD, respectively, and both tissues contained a single isozyme with a pI of 6.4. Kinetic parameters of purified G3PDH from prairie dog liver and muscle were characterized at 22 and 5 °C and compared with rabbit muscle G3PDH. Substrate affinities for hibernator muscle G3PDH were stable (NAD) or increased significantly (K(m) G3P and DHAP decreased) at low temperature whereas K(m) NAD and DHAP of rabbit G3PDH increased. Prairie dog G3PDH showed greater conservation of K(m) G3P over a wide temperature range as well as greater thermal stability and resistance to chemical denaturation by guanidine hydrochloride than the rabbit enzyme. In addition, using the protein sequence of the hibernating thirteen-lined ground squirrel (Ictidomys tridecemlineatus) and bioinformatics tools, the deduced protein structure of G3PDH was compared between heterothermic and homeothermic mammals. Structural and functional characteristics of G3PDH from the hibernating species would support enzyme function over a wide range of core body temperatures over cycles of torpor and arousal.
Collapse
|
16
|
Liang X, Bian Y, Tang XF, Xiao G, Tang B. Enhancement of keratinolytic activity of a thermophilic subtilase by improving its autolysis resistance and thermostability under reducing conditions. Appl Microbiol Biotechnol 2010; 87:999-1006. [DOI: 10.1007/s00253-010-2534-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 02/27/2010] [Accepted: 03/01/2010] [Indexed: 11/29/2022]
|