Chilled in Translation: Adapting to Bacterial Climate Change

Promoting health and survival through lowered body temperature

Core body temperature (Tb) is a long-established determinant of longevity across species. In this Perspective, we first summarize evidence demonstrating that reducing Tb increases lifespan and that lowered Tb contributes to the antiaging effects of calorie restriction. Next, we discuss recent data that diverge from prior hypotheses on the mechanisms by which Tb affects longevity, suggesting these are limited neither to the thermodynamics of nonenzymatic chemical reactions, nor reduced formation of mitochondrial reactive oxygen species nor lowered metabolic rate. Instead, recent findings in invertebrates show that cold promotes longevity via specific pathways including nutrient sensing and proteostasis, as well as modulating the thermodynamics of proteins and nucleic acids by changing their structure and function, for example, affecting temperature-sensitive ion channels, long-lived temperature-sensitive dauer mutations, base-pair stability and stem-loop RNA structures. Temperature affects the epigenetic signature and inflammation, and lowering Tb can also induce RNA-binding cold shock proteins, activate cold-sensitive kinases and differential splicing to potentially reshape the cellular environment. Finally, we reflect on important future work and the translational potential of temperature management and temperature mimetics.

Intact Mass Proteomics Using a Proteoform Atlas

Top-down proteomics, the characterization of intact proteoforms by tandem mass spectrometry, is the principal method for proteoform characterization in complex samples. Top-down proteomics relies on precursor isolation and subsequent gas-phase fragmentation to make proteoform identifications. While this strategy can produce highly detailed molecular information, the reliance on time-intensive tandem MS limits the speed with which proteoforms can be identified. We suggest that once proteoforms have been identified by top-down analysis in a system of interest, and archived in a system-specific Proteoform Atlas, subsequent analyses in that system can utilize the Atlas information to enable simpler and faster MS1-only identifications. We explore this idea here, using the E. coli ribosome as a model system of limited complexity. We used deep top-down analysis to construct an E. coli ribosomal Proteoform Atlas containing 2099 proteoforms from 52 of the 54 proteins that make up the E. coli ribosome. We show that using the Atlas enables confident MS1-only identifications of E. coli ribosomal proteoforms from E. coli that were perturbed by exposure to cold. Furthermore, this Atlas strategy identifies proteoforms up to 77% more rapidly compared to top-down identifications that require acquisition of both MS1 and MS2 spectra.

Active microbiota persist in dry permafrost and active layer from Elephant Head, Antarctica

Dry permafrost is a challenging environment for microbial life due to cold, dry, and often oligotrophic conditions. In 2016, Elephant Head, Antarctica, was confirmed as the second site on Earth to contain dry permafrost. It is geographically distinct from the McMurdo Dry Valleys where dry permafrost has been studied previously. Here, we present the first study of the microbial activity, diversity, and functional potential of Elephant Head dry permafrost. Microbial activity was measured using radiorespiration assays with radiolabeled acetate as a carbon source at 5, 0, and -5°C. Low, but detectable, rates of microbial activity were measured in some samples at 0 and -5°C. This is distinct from previous studies of McMurdo Dry Valley dry permafrost which concluded that dry permafrost represents a cold-arid limit to life on the planet. The isolation of cold-adapted organisms from these soils, including one capable of subzero growth, further supports that the Elephant Head dry active layer and dry permafrost harbor viable microbial life, which may be active in situ. Metagenomic, 16S rRNA gene, and internal transcribed spacer and amplicon sequencing identified similar microbial communities to other Antarctic and cold environments. The Elephant Head microbial community appears to be adapted for survival in cold, dry, and oligotrophic conditions based on the presence of cold adaptation and stress response genes in the metagenomes. Together, our results show that dry permafrost environments do not exclude active microbial life at subzero temperatures, suggesting that the cold, dry soils of Mars may also not be as inhospitable as previously thought.

The ribosome assembly GTPase EngA is involved in redox signaling in cyanobacteria

Photosynthetic organisms must cope with environmental challenges, like those imposed by the succession of days and nights or by sudden changes in light intensities, that trigger global changes in gene expression and metabolism. The photosynthesis machinery is particularly susceptible to environmental changes and adaptation to them often involves redox-sensing proteins that are the targets of reactive oxygen species generated by photosynthesis activity. Here we show that EngA, an essential GTPase and ribosome-assembly protein involved in ribosome biogenesis in bacteria and chloroplasts, also plays a role in acclimatization to environmentally relevant stress in Synechococcus elongatus PCC7942 and that PipX, a promiscuous regulatory protein that binds to EngA, appears to fine-tune EngA activity. During growth in cold or high light conditions, the EngA levels rise, with a concomitant increase of the EngA/PipX ratio. However, a sudden increase in light intensity turns EngA into a growth inhibitor, a response involving residue Cys122 of EngA, which is part of the GD1-G4 motif NKCES of EngA proteins, with the cysteine conserved just in the cyanobacteria-chloroplast lineage. This work expands the repertoire of ribosome-related factors transmitting redox signals in photosynthetic organisms and provides additional insights into the complexity of the regulatory interactions mediated by EngA and PipX.

Targeting an essential Plasmodium cold shock protein to block growth and transmission of malaria parasite

Cold shock proteins are characterized by the presence of one or more cold shock domains that bestow them with nucleic acid binding ability. Although cold shock proteins are well characterized in bacteria, plants and humans, there is no information on their existence and role in malaria parasite. Here, we have identified and delineated the function of a cold shock protein of Plasmodium falciparum (Pf) 'PfCoSP'. We demonstrate that PfCoSP exhibits nucleic acid binding properties and regulates gene expression. PfCoSP promotes microtubule assembly by interacting with Pf α/β tubulin. We identified a human cold shock protein LIN28A inhibitor 'LI71' as a binding partner of PfCoSP which inhibited PfCoSP-DNA and α/β tubulin interactions and, also inhibited the development of asexual blood stages and gametocyte stage of malaria parasite. Because PfCoSP is essential for parasite survival, characterization of its interacting partners may form the basis for development of future anti-malarials.

Adaptation of anammox bacteria to low temperature via gradual acclimation and cold shocks: Distinctions in protein expression, membrane composition and activities

Anammox bacteria enable efficient removal of nitrogen from sewage in processes involving partial nitritation and anammox (PN/A) or nitrification, partial denitrification, and anammox (N-PdN/A). In mild climates, anammox bacteria must be adapted to ≤15 °C, typically by gradual temperature decrease; however, this takes months or years. To reduce the time necessary for the adaptation, an unconventional method of 'cold shocks' is promising, involving hours-long exposure of anammox biomass to extremely low temperatures. We compared the efficacies of gradual temperature decrease and cold shocks to increase the metabolic activity of anammox (fed batch reactor, planktonic "Ca. Kuenenia"). We assessed the cold shock mechanism on the level of protein expression (quantitative shot-gun proteomics, LCHRMS/MS) and the structure of membrane lipids (UPLCHRMS/MS). The shocked culture was more active (0.66±0.06 vs 0.48±0.06 kg-N/kg-VSS/d) and maintained the relative content of N-respiration proteins at levels consistent levels with the initial state, whereas the content of these proteins decreased in gradually acclimated culture. Cold shocks also induced a more efficient expression of potential cold shock proteins (e.g. ppiD, UspA, pqqC), while putative cold shock proteins CspB and TypA were upregulated in both cultures. Ladderane lipids characteristic for anammox evolved to a similar end-point in both cultures; this confirms their role in anammox bacteria adaptation to cold and indicates a three-pronged adaptation mechanism (ladderane alkyl length, introduction of shorter non-ladderane alkyls, polar headgroup). Overall, we show the outstanding potential of cold shocks for low-temperature adaptation of anammox bacteria and provide yet unreported detailed mechanisms of anammox adaptation to low temperatures.

Y-box Binding Protein 1: Looking Back to the Future

Y-box binding protein 1 is a member of the cold shock domain (CSD) protein family and one of the most studied proteins associated with a large number of human diseases. This review aims to critically reassess the growing number of pathological functions ascribed to YB-1 in the past decades. The focus is given on the important role of YB-1 and related CSD proteins in the physiology of normal cells. The functional significance of these proteins is highlighted by their high evolutionary conservation from bacteria to men, where they are ubiquitously expressed and involved in coordinating all steps of mRNA biogenesis, including transcription, translation, storage, and degradation. Their activities are especially important under conditions requiring rapid change in the gene expression programs, such as early embryonic development, differentiation, stress, and adaptation to new environments. Therefore, to define a precise role of YB-1 in tumorigenic transformation and in other pathological conditions, it is important to understand its basic properties and functions in normal cells, and how they are interrupted in complex diseases including cancer.

In vivo demonstration of a novel non-invasive model for inducing localized hypothermia to ameliorate hepatotoxicity

Moderate hypothermia (32 °C) has been previously shown to ameliorate drug-induced liver injuries in vitro. However, there are concerns regarding its clinical relevance as it remains a challenge to perform selective liver cooling in a non-invasive manner. To reconcile this dilemma, we propose the use of pulsed cooling for regional hypothermic conditioning in liver. This involves intermittent cooling applied in pulses of 15 min each, with a one-hour recovery interval between pulses. Cooling is achieved by applying ice packs to the cutaneous region overlying the liver. Through an in vivo C57BL/6NTac mouse study, we demonstrated the feasibility of attaining localized hypothermia close to the liver while maintaining core body temperature. This has successfully ameliorated acetaminophen-induced liver injury based on the liver function tests, liver histology and total weight change. Collectively, we provide a proof of concept for pulsed external localized cooling as being clinically actionable to perform induced selective hypothermia.

YBX1 mediates translation of oncogenic transcripts to control cell competition in AML

Persistence of malignant clones is a major determinant of adverse outcome in patients with hematologic malignancies. Despite the fact that the majority of patients with acute myeloid leukemia (AML) achieve complete remission after chemotherapy, a large proportion of them relapse as a result of residual malignant cells. These persistent clones have a competitive advantage and can re-establish disease. Therefore, targeting strategies that specifically diminish cell competition of malignant cells while leaving normal cells unaffected are clearly warranted. Recently, our group identified YBX1 as a mediator of disease persistence in JAK2-mutated myeloproliferative neoplasms. The role of YBX1 in AML, however, remained so far elusive. Here, inactivation of YBX1 confirms its role as an essential driver of leukemia development and maintenance. We identify its ability to amplify the translation of oncogenic transcripts, including MYC, by recruitment to polysomal chains. Genetic inactivation of YBX1 disrupts this regulatory circuit and displaces oncogenic drivers from polysomes, with subsequent depletion of protein levels. As a consequence, leukemia cells show reduced proliferation and are out-competed in vitro and in vivo, while normal cells remain largely unaffected. Collectively, these data establish YBX1 as a specific dependency and therapeutic target in AML that is essential for oncogenic protein expression.

Recent advances in understanding the effect of acid-adaptation on the cross-protection to food-related stress of common foodborne pathogens

Acid stress is one of the most common stresses that foodborne pathogens encounter. It could occur naturally in foods as a by-product of anaerobic respiration (fermentation), or with the addition of acids. However, foodborne pathogens have managed to survive to acid conditions and consequently develop cross-protection to subsequent stresses, challenging the efficacy of hurdle technologies. Here, we cover the studies describing the cross-protection response following acid-adaptation, and the possible molecular mechanisms for cross-protection. The current and future prospective of this research topic with the knowledge gaps in the literature are also discussed. Exposure to acid conditions (pH 3.5 - 5.5) could induce cross-protection for foodborne pathogens against subsequent stress or multiple stresses such as heat, cold, osmosis, antibiotic, disinfectant, and non-thermal technology. So far, the known molecular mechanisms that might be involved in cross-protection include sigma factors, glutamate decarboxylase (GAD) system, protection or repair of molecules, and alteration of cell membrane. Cross-protection could pose a serious threat to food safety, as many hurdle technologies are believed to be effective in controlling foodborne pathogens. Thus, the exact mechanisms underlying cross-protection in a diversity of bacterial species, stress conditions, and food matrixes should be further studied to reduce potential food safety risks. HighlightsFoodborne pathogens have managed to survive to acid stress, which may provide protection to subsequent stresses, known as cross-protection.Acid-stress may induce cross-protection to many stresses such as heat, cold, osmotic, antibiotic, disinfectant, and non-thermal technology stress.At the molecular level, foodborne pathogens use different cross-protection mechanisms, which may correlate with each other.

Pleiotropic roles of cold shock proteins with special emphasis on unexplored cold shock protein member of Plasmodium falciparum

The cold shock domain (CSD) forms the hallmark of the cold shock protein family that provides the characteristic feature of binding with nucleic acids. While much of the information is available on bacterial, plants and human cold shock proteins, their existence and functions in the malaria parasite remains undefined. In the present review, the available information on functions of well-characterized cold shock protein members in different organisms has been collected and an attempt was made to identify the presence and role of cold shock proteins in malaria parasite. A single Plasmodium falciparum cold shock protein (PfCoSP) was found in P. falciparum which is reported to be essential for parasite survival. Essentiality of PfCoSP underscores its importance in malaria parasite life cycle. In silico tools were used to predict the features of PfCoSP and to identify its homologues in bacteria, plants, humans, and other Plasmodium species. Modelled structures of PfCoSP and its homologues in Plasmodium species were compared with human cold shock protein 'YBOX-1' (Y-box binding protein 1) that provide important insights into their functioning. PfCoSP model was subjected to docking with B-form DNA and RNA to reveal a number of residues crucial for their interaction. Transcriptome analysis and motifs identified in PfCoSP implicate its role in controlling gene expression at gametocyte, ookinete and asexual blood stages of malaria parasite. Overall, this review emphasizes the functional diversity of the cold shock protein family by discussing their known roles in gene expression regulation, cold acclimation, developmental processes like flowering transition, and flower and seed development, and probable function in gametocytogenesis in case of malaria parasite. This enables readers to view the cold shock protein family comprehensively.

Cold shock proteins: from cellular mechanisms to pathophysiology and disease

Cold shock proteins are multifunctional RNA/DNA binding proteins, characterized by the presence of one or more cold shock domains. In humans, the best characterized members of this family are denoted Y-box binding proteins, such as Y-box binding protein-1 (YB-1). Biological activities range from the regulation of transcription, splicing and translation, to the orchestration of exosomal RNA content. Indeed, the secretion of YB-1 from cells via exosomes has opened the door to further potent activities. Evidence links a skewed cold shock protein expression pattern with cancer and inflammatory diseases. In this review the evidence for a causative involvement of cold shock proteins in disease development and progression is summarized. Furthermore, the potential application of cold shock proteins for diagnostics and as targets for therapy is elucidated.