A Mutant Chaperonin That Is Functional at Lower Temperatures Enables Hyperthermophilic Archaea To Grow under Cold-Stress Conditions

Genetic and structural insights into the functional importance of the conserved gly-met-rich C-terminal tails in bacterial chaperonins

E. coli chaperonin GroEL forms nano-cages for protein folding. Although the chaperonin-mediated protein folding mechanism is well understood, the role of the conserved glycine and methionine-rich carboxy-terminal residues remains unclear. Bacteria with multiple chaperonins always retain at least one paralogue having the gly-met-rich C-terminus, indicating an essential conserved function. Here, we observed a stronger selection pressure on the paralogues with gly-met-rich C-termini, consistent with their ancestral functional importance. E. coli GroEL variants having mutations in their C-termini failed to functionally replace GroEL, suggesting the functional significance of the gly-met-rich C-termini. Further, our structural modelling and normal mode analysis showed that the C-terminal region shuttles between two cavity-specific conformations that correlate with the client-protein-binding apical domains, supporting C-termini's role in client protein encapsulation. Therefore, employing phylogenetic, genetic, and structural tools, we demonstrate that the gly-met-rich C-termini are functionally significant in chaperonin-mediated protein folding function. Owing to the pathogenic roles of the chaperonins having non-canonical C-termini, future investigations on the client protein selectivity will enable understanding the disease-specific client protein folding pathways and treatment options.

Whitefly-Mediated Transmission and Subsequent Acquisition of Highly Similar and Naturally Occurring Tomato Yellow Leaf Curl Virus Variants

Begomoviruses are whitefly-transmitted viruses that infect many agricultural crops. Numerous reports exist on individual host plants harboring two or more begomoviruses. Mixed infection allows recombination events to occur among begomoviruses. However, very few studies have examined mixed infection of different isolates/variants/strains of a Begomovirus species in hosts. In this study, the frequency of mixed infection of tomato yellow leaf curl virus (TYLCV) variants in field-grown tomato was evaluated. At least 60% of symptomatic field samples were infected with more than one TYLCV variant. These variants differed by a few nucleotides and amino acids, resembling a quasispecies. Subsequently, in the greenhouse, single and mixed infection of two TYLCV variants (variant #2 and variant #4) that shared 99.5% nucleotide identity and differed by a few amino acids was examined. Plant-virus variant-whitefly interactions including transmission of one and/or two variants, variants' concentrations, competition between variants in inoculated tomato plants, and whitefly acquisition of one and/or two variants were assessed. Whiteflies transmitted both variants to tomato plants at similar frequencies; however, the accumulation of variant #4 was greater than that of variant #2 in tomato plants. Despite differences in variants' accumulation in inoculated tomato plants, whiteflies acquired variant #2 and variant #4 at similar frequencies. Also, whiteflies acquired greater amounts of TYLCV from singly infected plants than from mixed-infected plants. These results demonstrated that even highly similar TYLCV variants could differentially influence component (whitefly-variant-plant) interactions.

Cross-Stress Adaptation in a Piezophilic and Hyperthermophilic Archaeon From Deep Sea Hydrothermal Vent

Hyperthermophiles, living in environments above 80°C and usually coupling with multi-extreme environmental stresses, have drawn great attention due to their application potential in biotechnology and being the primitive extant forms of life. Studies on their survival and adaptation mechanisms have extended our understanding on how lives thrive under extreme conditions. During these studies, the "cross-stress" behavior in various organisms has been observed between the extreme high temperature and other environmental stresses. Despite the broad observation, the global view of the cross-stress behavior remains unclear in hyperthermophiles, leaving a knowledge gap in our understanding of extreme adaptation. In this study, we performed a global quantitative proteomic analysis under extreme temperatures, pH, hydrostatic pressure (HP), and salinity on an archaeal strain, Thermococcus eurythermalis A501, which has outstanding growth capability on a wide range of temperatures (50-100°C), pH (4-9), and HPs (0.1-70 MPa), but a narrow range of NaCl (1.0-5.0 %, w/v). The proteomic analysis (79.8% genome coverage) demonstrated that approximately 61.5% of the significant differentially expressed proteins (DEPs) responded to multiple stresses. The responses to most of the tested stresses were closely correlated, except the responses to high salinity and low temperature. The top three enriched universal responding processes include the biosynthesis and protection of macromolecules, biosynthesis and metabolism of amino acids, ion transport, and binding activities. In addition, this study also revealed that the specific dual-stress responding processes, such as the membrane lipids for both cold and HP stresses and the signal transduction for both hyperosmotic and heat stresses, as well as the sodium-dependent energetic processes might be the limiting factor of the growth range in salinity. The present study is the first to examine the global cross-stress responses in a piezophilic hyperthermophile at the proteomic level. Our findings provide direct evidences of the cross-stress adaptation strategy (33.5% of coding-genes) to multiple stresses and highlight the specific and unique responding processes (0.22-0.63% of coding genes for each) to extreme temperature, pH, salinity, and pressure, which are highly relevant to the fields of evolutionary biology as well as next generation industrial biotechnology (NGIB).

Microbe Profile: Thermococcus kodakarensis: the model hyperthermophilic archaeon

Thermococcus kodakarensis is a hyperthermophilic Euryarchaeon that grows well under laboratory conditions and, being naturally competent for genetic transformation, it has become a widely studied experimental model species. With the genome sequence available since 2004, combining genetic, enzymological and structural biochemical approaches has revealed previously unknown and unanticipated features of archaeal molecular biology and metabolism. T. kodakarensis DNA polymerase is already commercialized and with the details of metabolism and hydrogenase available, generating H2 from biopolymers solubilized at high temperatures, most notably chitin, now seems a very attractive possibility as a renewable energy bioprocess.

Heat shock response in archaea

An adequate response to a sudden temperature rise is crucial for cellular fitness and survival. While heat shock response (HSR) is well described in bacteria and eukaryotes, much less information is available for archaea, of which many characterized species are extremophiles thriving in habitats typified by large temperature gradients. Here, we describe known molecular aspects of archaeal heat shock proteins (HSPs) as key components of the protein homeostasis machinery and place this in a phylogenetic perspective with respect to bacterial and eukaryotic HSPs. Particular emphasis is placed on structure–function details of the archaeal thermosome, which is a major element of the HSR and of which subunit composition is altered in response to temperature changes. In contrast with the structural response, it is largely unclear how archaeal cells sense temperature fluctuations and which molecular mechanisms underlie the corresponding regulation. We frame this gap in knowledge by discussing emerging questions related to archaeal HSR and by proposing methodologies to address them. Additionally, as has been shown in bacteria and eukaryotes, HSR is expected to be relevant for the control of physiology and growth in various stress conditions beyond temperature stress. A better understanding of this essential cellular process in archaea will not only provide insights into the evolution of HSR and of its sensing and regulation, but also inspire the development of biotechnological applications, by enabling transfer of archaeal heat shock components to other biological systems and for the engineering of archaea as robust cell factories.

Function of a thermophilic archaeal chaperonin is enhanced by electrostatic interactions with its targets

Molecular chaperonin CpkB from Thermococcus kodakarensis possesses a unique negatively charged carboxy-terminal region that functions in target protein recognition. In the present study, green fluorescent protein (GFP), 4-oxalocrotonate tautomerase (4OTA) and glutamine:fructose-6-phosphate amidotransferase (GFAT) were fused with a positively charged tag, selected using docking simulation in silico, to enhance their electrostatic interactions with CpkB. Target proteins were heated at 75°C in the presence or absence of CpkB, and the remaining enzymatic activity was measured. The half-life (t_1/2) of the positively charged tagged targets was significantly longer than that of their tagless counterparts. Escherichia coli cell extracts containing heterologously expressed targets (GFP, 4OTA and GFAT and their tagged variants) were incubated at 75°C in the presence or absence of CpkB, and the proportion remaining in the soluble fraction was evaluated by SDS-PAGE. Only positively charged tagged targets remained predominantly in the soluble fraction in the presence of CpkB but not in the absence of CpkB. When tagless or negatively charged tagged targets were employed, the targets were barely detected in the soluble fraction, suggesting that CpkB protected positively charged tagged proteins more efficiently than tagless targets. Attachment of a positively charged tag may be a generally applicable method for enhancing target recognition by chaperonins carrying negatively charged carboxy-terminal regions, such as the archaeal chaperonin CpkB.

cDNA-AFLP analysis of transcripts induced in chickpea plants by TiO2 nanoparticles during cold stress

We evaluated the effect of TiO₂ nanoparticles (NPs) on cold tolerance (CT) development in two chickpea (Cicer arietinum L.) genotypes (Sel96Th11439, cold tolerant, and ILC533, cold susceptible) by using cDNA-amplified fragment length polymorphism (cDNA-AFLP) technique during the first and sixth days of cold stress (CS) at 4 °C. Selective amplification by primer combinations generated 4200 transcript-derived fragments (TDFs) while 100 of them (2.62%) were differentially expressed. During CS, 60 differentially expressed TDFs of TiO₂ NPs-treated plants were cloned and 10 of them produced successfully readable sequences. These data represented different groups of genes involved in metabolism pathways, cellular defense, cell connections and signaling, transcriptional regulation and chromatin architecture. Two out of 10 TDFs were unknown genes with uncharacterized functions or sequences without homology to known ones. The network-based analysis showed a gene-gene relationship in response to CS. Quantitative reverse-transcriptase polymerase chain reaction (qPCR) confirmed differential expression of identified genes (six out of 10 TDFs) with potential functions in CT and showed similar patterns with cDNA-AFLP results. An increase in transcription level of these TDFs, particularly on the first day of CS, was crucial for developing CT through decreasing electrolyte leakage index (ELI) content in tolerant plants compared to susceptible ones, as well as in TiO₂ NPs-treated plants compared to control ones. It could also indicate probable role of TiO₂ NPs against CS-induced oxidative stress. Therefore, a new application of TiO₂ NPs in CT development is suggested for preventing or controlling the damages in field conditions and increasing crop productivity.