Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum

Bargiela, Rafael; Lanthaler, Karin; Potter, Colin M.; Ferrer, Manuel; Yakunin, Alexander F.; Paizs, Béla; Golyshin, Peter N.; Golyshina, Olga V.

doi:10.3390/microorganisms8050759

Cited by 4 publications

(5 citation statements)

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“…It revealed high confidence interactions with other subunits of DNA polymerase III (dnaE, dnaQ, holA) and proteins that have been described to be involved in replicative synthesis in bacteria. These interactions confirm the role of AUB74781.1 in DNA replication ( Bargiela et al, 2020 ). The protein AUB74810.1 explained as pyrimidine/purine nucleoside phosphorylase showed strong interactions with proteins associated with the purine salvage pathway.…”

Section: Resultssupporting

confidence: 81%

“…Additionally, cold adaptation in psychrophiles is attributed to membrane proteins, chaperones, RNA helicases, cold shock proteins, carotenoids, short- and branched-chain fatty acids, and antioxidative enzymes. Furthermore, an increase in the expression of proteins related to replication, transport, and folding was reported as a mechanism of cold adaptation ( De Maayer et al, 2014 ; Bargiela et al, 2020 ). Likewise, changes in the catalytic activity of the enzymes, changes in central metabolic activities, post-translational modifications, synthesis of storage polymers, like polyhydroxyalkanoates (PHAs) were reported to be advantageous for bacterial adaptation to cold temperatures ( Tribelli and Lopez, 2018 ; Bargiela et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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Investigating the Functional Role of Hypothetical Proteins From an Antarctic Bacterium Pseudomonas sp. Lz4W: Emphasis on Identifying Proteins Involved in Cold Adaptation

et al. 2022

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Exploring the molecular mechanisms behind bacterial adaptation to extreme temperatures has potential biotechnological applications. In the present study, Pseudomonas sp. Lz4W, a Gram-negative psychrophilic bacterium adapted to survive in Antarctica, was selected to decipher the molecular mechanism underlying the cold adaptation. Proteome analysis of the isolates grown at 4°C was performed to identify the proteins and pathways that are responsible for the adaptation. However, many proteins from the expressed proteome were found to be hypothetical proteins (HPs), whose function is unknown. Investigating the functional roles of these proteins may provide additional information in the biological understanding of the bacterial cold adaptation. Thus, our study aimed to assign functions to these HPs and understand their role at the molecular level. We used a structured insilico workflow combining different bioinformatics tools and databases for functional annotation. Pseudomonas sp. Lz4W genome (CP017432, version 1) contains 4493 genes and 4412 coding sequences (CDS), of which 743 CDS were annotated as HPs. Of these, from the proteome analysis, 61 HPs were found to be expressed consistently at the protein level. The amino acid sequences of these 61 HPs were submitted to our workflow and we could successfully assign a function to 18 HPs. Most of these proteins were predicted to be involved in biological mechanisms of cold adaptations such as peptidoglycan metabolism, cell wall organization, ATP hydrolysis, outer membrane fluidity, catalysis, and others. This study provided a better understanding of the functional significance of HPs in cold adaptation of Pseudomonas sp. Lz4W. Our approach emphasizes the importance of addressing the “hypothetical protein problem” for a thorough understanding of mechanisms at the cellular level, as well as, provided the assessment of integrating proteomics methods with various annotation and curation approaches to characterize hypothetical or uncharacterized protein data. The MS proteomics data generated from this study has been deposited to the ProteomeXchange through PRIDE with the dataset identifier–PXD029741.

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Section: Resultssupporting

confidence: 81%

Section: Introductionmentioning

confidence: 99%

Investigating the Functional Role of Hypothetical Proteins From an Antarctic Bacterium Pseudomonas sp. Lz4W: Emphasis on Identifying Proteins Involved in Cold Adaptation

et al. 2022

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“…The study of Subbiah et.al on the classification rules for psychrophilic and mesophilic proteins showed that when the percentage of Ser and Thr is higher than certain values, the proteins would be classified as psychrophilic proteins ( Nath et al, 2012 ). Meanwhile, a pairwise comparison of proteins from cold-adapted archaea revealed that there was higher content of non-charged polar residues, especially threonine ( Berthelot et al, 2019 ; Bargiela et al, 2020 ). Ser and Thr are uncharged polar amino acids and prefer to reside on the surface of the psychrophilic proteins ( Jahandideh et al, 2007 ), therefore they tend to have more interactions with water molecules around proteins ( Sun et al, 2020 ).…”

Section: Resultsmentioning

confidence: 99%

Discrimination of psychrophilic enzymes using machine learning algorithms with amino acid composition descriptor

Huang

Liu

2023

Front. Microbiol.

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IntroductionPsychrophilic enzymes are a class of macromolecules with high catalytic activity at low temperatures. Cold-active enzymes possessing eco-friendly and cost-effective properties, are of huge potential application in detergent, textiles, environmental remediation, pharmaceutical as well as food industry. Compared with the time-consuming and labor-intensive experiments, computational modeling especially the machine learning (ML) algorithm is a high-throughput screening tool to identify psychrophilic enzymes efficiently.MethodsIn this study, the influence of 4 ML methods (support vector machines, K-nearest neighbor, random forest, and naïve Bayes), and three descriptors, i.e., amino acid composition (AAC), dipeptide combinations (DPC), and AAC + DPC on the model performance were systematically analyzed.Results and discussionAmong the 4 ML methods, the support vector machine model based on the AAC descriptor using 5-fold cross-validation achieved the best prediction accuracy with 80.6%. The AAC outperformed than the DPC and AAC + DPC descriptors regardless of the ML methods used. In addition, amino acid frequencies between psychrophilic and non-psychrophilic proteins revealed that higher frequencies of Ala, Gly, Ser, and Thr, and lower frequencies of Glu, Lys, Arg, Ile,Val, and Leu could be related to the protein psychrophilicity. Further, ternary models were also developed that could classify psychrophilic, mesophilic, and thermophilic proteins effectively. The predictive accuracy of the ternary classification model using AAC descriptor via the support vector machine algorithm was 75.8%. These findings would enhance our insight into the cold-adaption mechanisms of psychrophilic proteins and aid in the design of engineered cold-active enzymes. Moreover, the proposed model could be used as a screening tool to identify novel cold-adapted proteins.

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“…Furthermore, Lon proteases and serine proteases of S46 superfamily were detected, which are membrane-bound enzymes (Additional file 3 : Table S2) hydrolysing extracellular proteins for their assimilation and are very common in Thermoplasmatales [ 51 , 53 , 54 ].…”

Section: Resultsmentioning

confidence: 99%

Evolutionary patterns of archaea predominant in acidic environment

Bargiela

Korzhenkov

McIntosh

et al. 2023

Environmental Microbiome

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Background Archaea of the order Thermoplasmatales are widely distributed in natural acidic areas and are amongst the most acidophilic prokaryotic organisms known so far. These organisms are difficult to culture, with currently only six genera validly published since the discovery of Thermoplasma acidophilum in 1970. Moreover, known great diversity of uncultured Thermoplasmatales represents microbial dark matter and underlines the necessity of efforts in cultivation and study of these archaea. Organisms from the order Thermoplasmatales affiliated with the so-called “alphabet-plasmas”, and collectively dubbed “E-plasma”, were the focus of this study. These archaea were found predominantly in the hyperacidic site PM4 of Parys Mountain, Wales, UK, making up to 58% of total metagenomic reads. However, these archaea escaped all cultivation attempts. Results Their genome-based metabolism revealed its peptidolytic potential, in line with the physiology of the previously studied Thermoplasmatales isolates. Analyses of the genome and evolutionary history reconstruction have shown both the gain and loss of genes, that may have contributed to the success of the “E-plasma” in hyperacidic environment compared to their community neighbours. Notable genes among them are involved in the following molecular processes: signal transduction, stress response and glyoxylate shunt, as well as multiple copies of genes associated with various cellular functions; from energy production and conversion, replication, recombination, and repair, to cell wall/membrane/envelope biogenesis and archaella production. History events reconstruction shows that these genes, acquired by putative common ancestors, may determine the evolutionary and functional divergences of “E-plasma”, which is much more developed than other representatives of the order Thermoplasmatales. In addition, the ancestral hereditary reconstruction strongly indicates the placement of Thermogymnomonas acidicola close to the root of the Thermoplasmatales. Conclusions This study has analysed the metagenome-assembled genome of “E-plasma”, which denotes the basis of their predominance in Parys Mountain environmental microbiome, their global ubiquity, and points into the right direction of further cultivation attempts. The results suggest distinct evolutionary trajectories of organisms comprising the order Thermoplasmatales, which is important for the understanding of their evolution and lifestyle.

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Proteome Cold-Shock Response in the Extremely Acidophilic Archaeon, Cuniculiplasma divulgatum

Cited by 4 publications

References 50 publications

Investigating the Functional Role of Hypothetical Proteins From an Antarctic Bacterium Pseudomonas sp. Lz4W: Emphasis on Identifying Proteins Involved in Cold Adaptation

Investigating the Functional Role of Hypothetical Proteins From an Antarctic Bacterium Pseudomonas sp. Lz4W: Emphasis on Identifying Proteins Involved in Cold Adaptation

Discrimination of psychrophilic enzymes using machine learning algorithms with amino acid composition descriptor

Evolutionary patterns of archaea predominant in acidic environment

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