Protein adaptations in extremophiles: An insight into extremophilic connection of mycobacterial proteome

Dynamic structure of the cytoplasm

The cytoplasm is a dense and complex milieu in which a plethora of biochemical reactions occur. Its structure is not understood so far, albeit being central to cellular functioning. In this review, we highlight a novel perspective in which the physical properties of the cytoplasm are regulated in space and time and actively contribute to cellular function. Furthermore, we underscore recent findings that the dynamic formation of local assemblies within the cytoplasm, such as condensates and polysomes, serves as a key regulator of mesoscale cytoplasmic dynamics.

Tolerance to NSAIDs in Actinobacteria From a Mexican Volcano Crater: Genomics and Bioremediation Potential

Non-steroidal anti-inflammatory drugs (NSAIDs) are emerging contaminants that pose significant health and environmental risks due to their persistence, including their presence in drinking water. Bioremediation, particularly through microorganisms such as actinobacteria, offers a sustainable approach to mitigate these pollutants. Actinobacteria from poly-extreme environments exhibit unique genetic and metabolic adaptations, enabling resistance to and degradation of various contaminants. This study aimed to evaluate the tolerance of actinobacteria to NSAIDs and conduct a genomic analysis of a selected strain. Actinobacteria were isolated from the crater of the Chichonal volcano [Chiapas, Mexico), resulting in 16 isolates. Among these, Micrococcus luteus P8SUE1, Micrococcus yunnanensis P9AGU1, and Kocuria rhizophila P1AGU3 demonstrated tolerance to diclofenac, ibuprofen, and paracetamol at concentrations of 1 ppm, 10 ppm, and 100 ppm, respectively. Whole-genome sequencing of M. yunnanensis P9AGU1 identified genes linked to the degradation of aromatic compounds and adaptations to extreme environmental conditions, highlighting its potential for bioremediation applications.

Genome wide screening to discover novel toxin-antitoxin modules in Mycobacterium indicus pranii; perspective on gene acquisition during mycobacterial evolution

Mycobacterium indicus pranii (MIP), a benign saprophyte with potent immunomodulatory attributes, holds a pivotal position in mycobacterial evolution, potentially serving as the precursor to the pathogenic Mycobacterium avium complex (MAC). Despite its established immunotherapeutic efficacy against leprosy and notable outcomes in gram-negative sepsis and COVID-19 cases, the genomic and biochemical features of MIP remain largely elusive. This study explores the uncharted territory of toxin-antitoxin (TA) systems within MIP, hypothesizing their role in mycobacterial pathogenicity regulation. Genome-wide screening, employing diverse databases, unveils putative TA modules in MIP, setting the stage for a comparative analysis with known modules in Mycobacterium tuberculosis, Mycobacterium smegmatis, Escherichia coli, and Vibrio cholerae. The study further delves into the TA network of MAC and Mycobacterium intracellulare, unraveling interactive properties and family characteristics of identified TA modules in MIP. This comprehensive exploration seeks to illuminate the contribution of TA modules in regulating virulence, habitat diversification, and the evolutionary pathogenicity of mycobacteria. The insights garnered from this investigation not only enhance our understanding of MIP's potential as a vaccine candidate but also hold promise in optimizing tuberculosis drug regimens for expedited recovery.

Beyond protein folding: The pleiotropic functions of PPIases in cellular processes and microbial virulence

Peptidyl prolyl cis/trans isomerases (PPIases), a ubiquitously distributed superfamily of enzymes, associated with signal transduction, trafficking, assembly, biofilm formation, stress tolerance, cell cycle regulation, gene expression and tissue regeneration, is a key regulator of metabolic disorders and microbial virulence. This review assumes an integrative approach, to provide a holistic overview of the structural and functional diversity of PPIases, examining their conformational dynamics, cellular distribution, and physiological significance. We explore their intricate involvement in cellular processes and virulence modulation in both eukaryotic and prokaryotic systems. Additionally, we evaluate the potential of these molecular chaperones as drug targets and vaccine candidates, emphasizing their relevance in therapeutic development. By synthesizing recent findings and providing a broader perspective on these proteins, this review aims to enhance our understanding of their multifaceted roles in biology and their potential applications in medicine.

Deciphering the enigmatic PilY1 of Acidithiobacillus thiooxidans: An in silico analysis

Thirty years since the first report on the PilY1 protein in bacteria, only the C-terminal domain has been crystallized; there is no study in which the N-terminal domain, let alone the complete protein, has been crystallized. In our laboratory, we are interested in characterizing the Type IV Pili (T4P) of Acidithiobacillus thiooxidans. We performed an in silico characterization of PilY1 and other pilins of the T4P of this acidophilic bacterium. In silico characterization is crucial for understanding how proteins adapt and function under extreme conditions. By analyzing the primary and secondary structures of proteins through computational methods, researchers can gain valuable insights into protein stability, key structural features, and unique amino acid compositions that contribute to resilience in harsh environments. Here, it is presented a description of the particularities of At. thiooxidans PilY1 through predictor software and homology data. Our results suggest that PilY1 from At. thiooxidans may have the same role as has been described for other PilY1 associated with T4P in neutrophilic bacteria; also, its C-terminal interacts (interface interaction) with the minor pilins PilX, PilW and PilV. The N-terminal region comprises domains such as the vWA and the MIDAS, involved in signaling, ligand-binding, and protein-protein interaction. In fact, the vWA domain has intrinsically disordered regions that enable it to maintain its structure over a wide pH range, not only at extreme acidity to which At. thiooxidans is adapted. The results obtained helped us design the correct methodology for its heterologous expression. This allowed us partially experimentally characterize it by obtaining the N-terminal domain recombinantly and evaluating its acid stability through fluorescence spectroscopy. The data suggest that it remains stable across pH changes. This work thus provides guidance for the characterization of extracellular proteins from extremophilic organisms.

Halo-alkaliphilic microbes as an effective tool for heavy metal pollution abatement and resource recovery: challenges and future prospects

The current study presents an overview of heavy metals bioremediation from halo-alkaline conditions by using extremophilic microorganisms. Heavy metal remediation from the extreme environment with high pH and elevated salt concentration is a challenge as mesophilic microorganisms are unable to thrive under these polyextremophilic conditions. Thus, for effective bioremediation of extreme systems, specialized microbes (extremophiles) are projected as potential bioremediating agents, that not only thrive under such extreme conditions but are also capable of remediating heavy metals from these environments. The physiological versatility of extremophiles especially halophiles and alkaliphiles and their enzymes (extremozymes) could conveniently be harnessed to remediate and detoxify heavy metals from the high alkaline saline environment. Bibliometric analysis has shown that research in this direction has found pace in recent years and thus this review is a timely attempt to highlight the importance of halo-alkaliphiles for effective contaminant removal in extreme conditions. Also, this review systematically presents insights on adaptive measures utilized by extremophiles to cope with harsh environments and outlines the role of extremophilic microbes in industrial wastewater treatment and recovery of metals from waste with relevant examples. Further, the major challenges and way forward for the effective applicability of halo-alkaliphilic microbes in heavy metals bioremediation from extremophilic conditions are also highlighted.

Insects, Plants, and Microorganisms from Dry Lands as Novel Sources of Proteins and Peptides for Human Consumption

Protein malnutrition is present in developing countries but also in developed ones due to actual eating habits involving insufficient protein intake. In addition to this, it is estimated by the Food and Agricultural Organization of the United Nations that the world's population will increase to 9.1 billion people in less than 30 years. This poses a significant challenge in terms of nourishing the population. Different strategies have been proposed to address this challenge, including exploring novel protein sources such as plants. For instance, Prosopis alba pods have an 85.5% protein content. Other examples are microorganisms, such as Halobacillus adaensis which produces 571 U/mL of protease, and insects such as those belonging to the Orthoptera order, like grasshoppers, which have a protein content of 65.96%. These sources have been found in dry lands and are being explored to address this challenge.

Environmental Adaptation of Psychrophilic Bacteria Subtercola spp. Isolated from Various Cryospheric Habitats

Subtercola boreus K300T is a novel psychrophilic strain that was isolated from permanently cold groundwater in Finland and has also been found in several places in Antarctica including lake, soil, and rocks. We performed genomic and transcriptomic analyses of 5 strains from Antarctica and a type strain to understand their adaptation to different environments. Interestingly, the isolates from rocks showed a low growth rate and smaller genome size than strains from the other isolation sources (lake, soil, and groundwater). Based on these habitat-dependent characteristics, the strains could be classified into two ecotypes, which showed differences in energy production, signal transduction, and transcription in the clusters of orthologous groups of proteins (COGs) functional category. In addition, expression pattern changes revealed differences in metabolic processes, including uric acid metabolism, DNA repair, major facilitator superfamily (MFS) transporters, and xylose degradation, depending on the nutritional status of their habitats. These findings provide crucial insights into the environmental adaptation of bacteria, highlighting genetic diversity and regulatory mechanisms that enable them to thrive in the cryosphere.

The exploitation of host autophagy and ubiquitin machinery by Mycobacterium tuberculosis in shaping immune responses and host defense during infection

Intracellular pathogens have evolved various efficient molecular armaments to subvert innate defenses. Cellular ubiquitination, a normal physiological process to maintain homeostasis, is emerging one such exploited mechanism. Ubiquitin (Ub), a small protein modifier, is conjugated to diverse protein substrates to regulate many functions. Structurally diverse linkages of poly-Ub to target proteins allow enormous functional diversity with specificity being governed by evolutionarily conserved enzymes (E3-Ub ligases). The Ub-binding domain (UBD) and LC3-interacting region (LIR) are critical features of macroautophagy/autophagy receptors that recognize Ub-conjugated on protein substrates. Emerging evidence suggests that E3-Ub ligases unexpectedly protect against intracellular pathogens by tagging poly-Ub on their surfaces and targeting them to phagophores. Two E3-Ub ligases, PRKN and SMURF1, provide immunity against Mycobacterium tuberculosis (M. tb). Both enzymes conjugate K63 and K48-linked poly-Ub to M. tb for successful delivery to phagophores. Intriguingly, M. tb exploits virulence factors to effectively dampen host-directed autophagy utilizing diverse mechanisms. Autophagy receptors contain LIR-motifs that interact with conserved Atg8-family proteins to modulate phagophore biogenesis and fusion to the lysosome. Intracellular pathogens have evolved a vast repertoire of virulence effectors to subdue host-immunity via hijacking the host ubiquitination process. This review highlights the xenophagy-mediated clearance of M. tb involving host E3-Ub ligases and counter-strategy of autophagy inhibition by M. tb using virulence factors. The role of Ub-binding receptors and their mode of autophagy regulation is also explained. We also discuss the co-opting and utilization of the host Ub system by M. tb for its survival and virulence.Abbreviations: APC: anaphase promoting complex/cyclosome; ATG5: autophagy related 5; BCG: bacille Calmette-Guerin; C2: Ca²⁺-binding motif; CALCOCO2: calcium binding and coiled-coil domain 2; CUE: coupling of ubiquitin conjugation to ER degradation domains; DUB: deubiquitinating enzyme; GABARAP: GABA type A receptor-associated protein; HECT: homologous to the E6-AP carboxyl terminus; IBR: in-between-ring fingers; IFN: interferon; IL1B: interleukin 1 beta; KEAP1: kelch like ECH associated protein 1; LAMP1: lysosomal associated membrane protein 1; LGALS: galectin; LIR: LC3-interacting region; MAPK11/p38: mitogen-activated protein kinase 11; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAP3K7/TAK1: mitogen-activated protein kinase kinase kinase 7; MAPK8/JNK: mitogen-activated protein kinase 8; MHC-II: major histocompatibility complex-II; MTOR: mechanistic target of rapamycin kinase; NBR1: NBR1 autophagy cargo receptor; NFKB1/p50: nuclear factor kappa B subunit 1; OPTN: optineurin; PB1: phox and bem 1; PE/PPE: proline-glutamic acid/proline-proline-glutamic acid; PknG: serine/threonine-protein kinase PknG; PRKN: parkin RBR E3 ubiquitin protein ligase; RBR: RING-in between RING; RING: really interesting new gene; RNF166: RING finger protein 166; ROS: reactive oxygen species; SMURF1: SMAD specific E3 ubiquitin protein ligase 1; SQSTM1: sequestosome 1; STING1: stimulator of interferon response cGAMP interactor 1; TAX1BP1: Tax1 binding protein 1; TBK1: TANK binding kinase 1; TNF: tumor necrosis factor; TRAF6: TNF receptor associated factor 6; Ub: ubiquitin; UBA: ubiquitin-associated; UBAN: ubiquitin-binding domain in ABIN proteins and NEMO; UBD: ubiquitin-binding domain; UBL: ubiquitin-like; ULK1: unc-51 like autophagy activating kinase 1.

Recovery of bacterioruberin and proteins using aqueous solutions of surface-active compounds

Haloarchaea microorganisms are little explored marine resources that can be a promising source of valuable compounds with unique characteristics, due to their adaptation to extreme environments. In this work, the extraction of bacterioruberin and proteins from Haloferax mediterranei ATCC 33500 was investigated using aqueous solutions of ionic liquids and surfactants, which were further compared with ethanol. Despite the good performance of ethanol in the extraction of bacterioruberin, the use of aqueous solutions of surface-active compounds allowed the simultaneous release of bacterioruberin and proteins in a multi-product process, with the non-ionic surfactants being identified as the most promising. The optimum operational conditions allowed a maximum extraction yield of 0.37 ± 0.01 mgbacterioruberin gwet biomass -1 and 352 ± 9 mgprotein gwet biomass -1 with an aqueous solution of Tween® 20 (at 182.4 mM) as the extraction solvent. In addition, high purities of bacterioruberin were obtained, after performing a simple induced precipitation using ethanol as an antisolvent to recover the proteins present in the initial extract. Finally, a step for polishing the bacterioruberin was performed, to enable solvent recycling, further closing the process to maximize its circularity.

Modeled microgravity alters apoptotic gene expression and caspase activity in the squid-vibrio symbiosis

Background

Spaceflight is a novel and profoundly stressful environment for life. One aspect of spaceflight, microgravity, has been shown to perturb animal physiology thereby posing numerous health risks, including dysregulation of normal developmental pathways. Microgravity can also negatively impact the interactions between animals and their microbiomes. However, the effects of microgravity on developmental processes influenced by beneficial microbes, such as apoptosis, remains poorly understood. Here, the binary mutualism between the bobtail squid, Euprymna scolopes, and the gram-negative bacterium, Vibrio fischeri, was studied under modeled microgravity conditions to elucidate how this unique stressor alters apoptotic cell death induced by beneficial microbes.

Results

Analysis of the host genome and transcriptome revealed a complex network of apoptosis genes affiliated with extrinsic/receptor-mediated and intrinsic/stress-induced apoptosis. Expression of apoptosis genes under modeled microgravity conditions occurred earlier and at high levels compared to gravity controls, in particular the expression of genes encoding initiator and executioner caspases. Functional assays of these apoptotic proteases revealed heightened activity under modeled microgravity; however, these increases could be mitigated using caspase inhibitors.

Conclusions

The outcomes of this study indicated that modeled microgravity alters the expression of both extrinsic and intrinsic apoptosis gene expression and that this process is mediated in part by caspases. Modeled microgravity-associated increases of caspase activity can be pharmacologically inhibited suggesting that perturbations to the normal apoptosis signaling cascade can be mitigated, which may have broader implications for maintaining animal-microbial homeostasis in spaceflight.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02614-x.

Perspectives on the microorganism of extreme environments and their applications

Extremophiles are organisms that can survive and thrive in conditions termed as "extreme" by human beings. Conventional methods cannot be applied under extreme conditions like temperature and pH fluctuations, high salinity, etc. for a variety of reasons. Extremophiles can function and are adapted to thrive in these environments and are sustainable, cheaper, and efficient, therefore, they serve as better alternatives to the traditional methods. They adapt to these environments with biochemical and physiological changes and produce products like extremolytes, extremozymes, biosurfactants, etc., which are found to be useful in a wide range of industries like sustainable agriculture, food, cosmetics, and pharmaceuticals. These products also play a crucial role in bioremediation, production of biofuels, biorefinery, and astrobiology. This review paper comprehensively lists out the current applications of extremophiles and their products in various industries and explores the prospects of the same. They help us understand the underlying basis of biological mechanisms exploring the boundaries of life and thus help us understand the origin and evolution of life on Earth. This helps us in the research for extra-terrestrial life and space exploration. The structure and biochemical properties of extremophiles along with any possible long-term effects of their applications need to be investigated further.

Structural and functional adaptation in extremophilic microbial α-amylases

Maintaining stable native conformation of a protein under a given ecological condition is the prerequisite for survival of organisms. Extremophilic bacteria and archaea have evolved to adapt under extreme conditions of temperature, pH, salt, and pressure. Molecular adaptations of proteins under these conditions are essential for their survival. These organisms have the capability to maintain stable, native conformations of proteins under extreme conditions. The enzymes produced by the extremophiles are also known as extremozyme, which are used in several industries. Stability and functionality of extremozymes under varying temperature, pH, and solvent conditions are the most desirable requirement of industry. α-Amylase is one of the most important enzymes used in food, pharmaceutical, textile, and detergent industries. This enzyme is produced by diverse microorganisms including various extremophiles. Therefore, understanding its stability is important from fundamental as well as an applied point of view. Each class of extremophiles has a distinctive set of dominant non-covalent interactions which are important for their stability. Static information obtained by comparative analysis of amino acid sequence and atomic resolution structure provides information on the prevalence of particular amino acids or a group of non-covalent interactions. Protein folding studies give the information about thermodynamic and kinetic stability in order to understand dynamic aspect of molecular adaptations. In this review, we have summarized information on amino acid sequence, structure, stability, and adaptability of α-amylases from different classes of extremophiles.

First Insight into the Diversity and Antibacterial Potential of Psychrophilic and Psychotrophic Microbial Communities of Abandoned Amber Quarry

Natural habitats, including extreme ones, are potential sources of new antimicrobial compound producers, such as bacteriocins and enzymes, capable of degrading the matrix polysaccharides of bacterial biofilms. This study aimed to investigate biodiversity and evaluate the antibacterial potential of psychrophilic and psychrotrophic microbial communities of the flooded Walter amber quarry (Kaliningrad region, Russia). As a result of 16S rDNA high-throughput profiling, 127 genera of bacteria belonging to 12 phyla of bacteria were found in sediment samples: Acidobacteria sp., Actinobacteria sp., Armatimonadetes sp., Bacteroidetes sp., Chloroflexi sp., Cyanobacteria sp., Firmicutes sp., Gemmatimonadetes sp., Planctomycetes sp., Proteobacteria sp., Tenericutes sp., and Verrucomicrobia sp. The dominant bacteria groups were the families Ruminococcaceae and Lachnospiraceae, belonging to the order Clostridiales phylum Firmicutes. Analysis of enrichment cultures obtained from sediments showed the presence of antibacterial and cellulolytic activity. It seems likely that the bacteria of the studied communities are producers of antimicrobial compounds and have the potential for biotechnological use.

Exploitation of Potential Extremophiles for Bioremediation of Xenobiotics Compounds: A Biotechnological Approach

Microorganisms that are capable of live and adapt in hostile habitats of different environmental factors such as extremes temperature, salinity, nutrient availability and pressure are known as extremophiles. Exposure to xenobiotic compounds is global concern influencing the world population as a health hazard. Hence their removal is warranted using biological means that is very sustainable, potentially cost-effective and eco-friendly. Due to adaptation in extreme environments and unique defense mechanisms, they are receiving more attention for the bioremediation of the xenobiotic compounds. They possess robust enzymatic and biocatalytic systems that make them suitable for the effective removal of pollutants from the contaminated environment. Additionally, the extremophiles act as microfactories having specific genetic and biotechnological potential for the production of biomolecules. This mini review will provide an overview of microbial degradation metabolic pathways for bioremediation along with the molecular and physiological properties of diverse extremophiles from variety of habitats. Furthermore, the factors affecting the bioremediation process is also summarized.

Computational Analysis of the Primary and Secondary Structure of Amidases in Relation to their pH Adaptation

Background:

Amidases are ubiquitous enzymes and biological functions of these enzymes vary widely. They are considered to be synergistically involved in the synthesis of a wide variety of carboxylic acids, hydroxamic acids and hydrazides, which find applications in commodity chemicals synthesis, pharmaceuticals agrochemicals and wastewater treatments.

Methods:

They hydrolyse a wide variety of amides (short-chain aliphatic amides, mid-chain amides, arylamides, α-aminoamides and α-hydroxyamides) and can be grouped on the basis of their catalytic site and preferred substrate. Despite their economic importance, we lack knowledge as to how these amidases withstand elevated pH and temperature whereas others cannot.

Results:

The present study focuses on the statistical comparison between the acid-tolerant, alkali tolerant and neutrophilic organisms. In silico analysis of amidases of acid-tolerant, alkali tolerant and neutrophilic organisms revealed some striking trends as to how amino acid composition varies significantly. Statistical analysis of primary and secondary structure revealed amino acid trends in amidases of these three groups of bacteria. The abundance of isoleucine (Ile, I) in acid-tolerant and leucine (Leu, L) in alkali tolerant showed the aliphatic amino acid dominance in extreme conditions of pH in acidtolerant and alkali tolerant amidases.

Conclusion:

The present investigation insights physiochemical properties and dominance of some crucial amino acid residues in the primary and secondary structure of some amidases from acid-tolerant, alkali tolerant and neutrophilic microorganisms.

Stability/activity tradeoffs in Thermusthermophilus HB27 laccase

We report the temperature dependence of the formal potential of type 1 copper (Cu_T1) in Thermusthermophilus HB27 laccase. Employing [Ru(NH₃)₄(bpy)](PF₆)₂ (0.505 vs. NHE) as the redox titrant, we found that the Cu_T1^2+/+ potential decreased from approximately 480 to 420 mV (vs. NHE) as the temperature was raised from 20 to 65 °C. Of importance is that the ΔS_rc° of - 120 J mol^-1 K^-1 is substantially more negative than those for other blue copper proteins. We suggest that the highly unfavorable reduction entropy is attributable to Cu_T1 inaccessibility to the aqueous medium. Although the active site residues are buried, which is critical for maintaining thermostability, the flexibility around Cu_T1 is maintained, allowing enzyme activity at ambient temperature.

Identification of a novel protease from the thermophilic Anoxybacillus kamchatkensis M1V and its application as laundry detergent additive

A thermostable extracellular alkaline protease (called SAPA) was produced (4600 U/mL) by Anoxybacillus kamchatkensis M1V, purified to homogeneity, and biochemically characterized. SAPA is a monomer with a molecular mass of 28 kDa estimated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), Native-PAGE, casein-zymography, and size exclusion using high performance liquid chromatography (HPLC). The sequence of its NH₂-terminal amino-acid residues showed high homology with those of Bacillus proteases. The SAPA irreversible inhibition by diiodopropyl fluorophosphates (DFP) and phenylmethanesulfonyl fluoride (PMSF) confirmed its belonging to the serine proteases family. Optimal activity of SAPA was at pH 11 and 70 °C. The sapA gene was cloned and expressed in the extracellular fraction of E. coli. The highest sequence identity value (95%) of SAPA was obtained with peptidase S8 from Bacillus subtilis WT 168, but with 16 amino-acids of difference. The biochemical characteristics of the purified recombinant extracellular enzyme (called rSAPA) were analogous to those of native SAPA. Interestingly, rSAPA exhibit a degree of hydrolysis that were 1.24 and 2.6 than SAPB from Bacillus pumilus CBS and subtilisin A from Bacillus licheniformis, respectively. Furthermore, rSAPA showed a high detergent compatibility and an outstanding stain removal capacity compared to commercial enzymes: savinase™ 16L, type EX and alcalase™ Ultra 2.5 L.