Correlative Fluorescence and Raman Microscopy to Define Mitotic Stages at the Single-Cell Level: Opportunities and Limitations in the AI Era.

Nowadays, morphology and molecular analyses at the single-cell level have a fundamental role in understanding biology better. These methods are utilized for cell phenotyping and in-depth studies of cellular processes, such as mitosis. Fluorescence microscopy and optical spectroscopy techniques, including Raman micro-spectroscopy, allow researchers to examine biological samples at the single-cell level in a non-destructive manner. Fluorescence microscopy can give detailed morphological information about the localization of stained molecules, while Raman microscopy can produce label-free images at the subcellular level; thus, it can reveal the spatial distribution of molecular fingerprints, even in live samples. Accordingly, the combination of correlative fluorescence and Raman microscopy (CFRM) offers a unique approach for studying cellular stages at the single-cell level. However, subcellular spectral maps are complex and challenging to interpret. Artificial intelligence (AI) may serve as a valuable solution to characterize the molecular backgrounds of phenotypes and biological processes by finding the characteristic patterns in spectral maps. The major contributions of the manuscript are: (I) it gives a comprehensive review of the literature focusing on AI techniques in Raman-based cellular phenotyping; (II) via the presentation of a case study, a new neural network-based approach is described, and the opportunities and limitations of AI, specifically deep learning, are discussed regarding the analysis of Raman spectroscopy data to classify mitotic cellular stages based on their spectral maps.

Intensification of Ex Situ Bioremediation of Soils Polluted with Used Lubricant Oils: A Comparison of Biostimulation and Bioaugmentation with a Special Focus on the Type and Size of the Inoculum.

Used lubricant oils (ULOs) strongly bind to soil particles and cause persistent pollution. In this study, soil microcosm experiments were conducted to model the ex situ bioremediation of a long term ULO-polluted area. Biostimulation and various inoculation levels of bioaugmentation were applied to determine the efficacy of total petrol hydrocarbon (TPH) removal. ULO-contaminated soil microcosms were monitored for microbial respiration, colony-forming units (CFUs) and TPH bioconversion. Biostimulation with inorganic nutrients was responsible for 22% of ULO removal after 40 days. Bioaugmentation using two hydrocarbon-degrader strains: Rhodococcus quingshengii KAG C and Rhodococcus erythropolis PR4 at a small inoculum size (107 CFUs g-1 soil), reduced initial TPH concentration by 24% and 29%, respectively; the application of a higher inoculum size (109 CFUs g-1 soil) led to 41% and 32% bioconversion, respectively. After 20 days, all augmented CFUs decreased to the same level as measured in the biostimulated cases, substantiating the challenge for the newly introduced hydrocarbon-degrading strains to cope with environmental stressors. Our results not only highlight that an increased number of degrader cells does not always correlate with enhanced TPH bioconversion, but they also indicate that biostimulation might be an economical solution to promote ULO biodegradation in long term contaminated soils.

Photosystem I oligomerization affects lipid composition in Synechocystis sp. PCC 6803.

In cyanobacteria, increasing growth temperature decreases lipid unsaturation and the ratio of monomer/trimer photosystem I (PSI) complexes. In the present study we applied Fourier-transform infrared (FTIR) spectroscopy and lipidomic analysis to study the effects of PSI monomer/oligomer ratio on the physical properties and lipid composition of thylakoids. To enhance the presence of monomeric PSI, a Synechocystis sp. PCC6803/ΔpsaL mutant strain (PsaL) was used which, unlike both trimeric and monomeric PSI-containing wild type (WT) cells, contain only the monomeric form. The protein-to-lipid ratio remained unchanged in the mutant but, due to an increase in the lipid disorder in its thylakoids, the gel to liquid-crystalline phase transition temperature (Tm) is lower than in the WT. In thylakoid membranes of the mutant, digalactosyldiacylglycerol (DGDG), the most abundant bilayer-forming lipid is accumulated, whereas those in the WT contain more monogalactosyldiacylglycerol (MGDG), the only non-bilayer-forming lipid in cyanobacteria. In PsaL cells, the unsaturation level of sulphoquinovosyldiacylglycerol (SQDG), a regulatory anionic lipid, has increased. It seems that merely a change in the oligomerization level of a membrane protein complex (PSI), and thus the altered protein-lipid interface, can affect the lipid composition and, in addition, the whole dynamics of the membrane. Singular value decomposition (SVD) analysis has shown that in PsaL thylakoidal protein-lipid interactions are less stable than in the WT, and proteins start losing their native secondary structure at much milder lipid packing perturbations. Conclusions drawn from this system should be generally applicable for protein-lipid interactions in biological membranes.

Formulation of paracetamol-containing pastilles with in situ coating technology.

The focus of this research was to apply the in situ coating technology for producing paracetamol- (PCT-) containing pastilles for paediatric use from a eutectic of two sugar alcohols (sorbitol, xylitol) in one step. This type of melt-technology is more cost-efficient and simpler than other conventional tableting technologies, whereby the formation of the pastilles and their coating occur upon the same fabrication step. We managed to produce pastilles having a softer core and a harder, resistant shell in one cooling step. Adding polyethylene glycol (PEG) 2000 or 6000 to the PCT-containing eutectic, the dissolution rate of PCT could be considerably increased, especially when using PEG 2000, reaching equal dissolution characteristics both under mouth- and gastric-specific conditions. Distributions of the components within the pastilles have been determined by X-ray scattering and Raman spectroscopy. Physico-chemical parameters of the xylitol-sorbitol eutectic and their changes upon adding PCT and PEGs have been determined, and it has been revealed that xylitol and sorbitol form a new entity with a distinguished crystal structure. The significant changes in viscosity were explained and the interaction in the eutectic mixture was investigated using Fourier transform infrared spectroscopy (FT-IR). The uniformity of the physical parameters of the pastilles (including size, weight and drug content) also demonstrates the feasibility of using the cost-efficient and simple one-step eutectic-cooling technology for manufacturing pastilles.

Sprayed cells and polyelectrolyte films for biomaterial functionalization: the influence of physical PLL-PGA film treatments on dental pulp cell behavior.

Further development of biomaterials is expected as advanced therapeutic products must be compliant to good manufacturing practice regulations. A spraying method for building-up polyelectrolyte films followed by the deposition of dental pulp cells by spraying is presented. Physical treatments of UV irradiation and a drying/wetting process are applied to the system. Structural changes and elasticity modifications of the obtained coatings are revealed by atomic force microscopy and by Raman spectroscopy. This procedure results in thicker, rougher and stiffer film. The initially ordered structure composed of mainly α helices is transformed into random/ß-structures. The treatment enhanced dental pulp cell adhesion and proliferation, suggesting that this system is promising for medical applications.

Altered expression of genes for Kir ion channels in dilated cardiomyopathy.

Dilated cardiomyopathy (DCM) is a multifactorial disease characterized by left ventricular dilation that is associated with systolic dysfunction and increased action potential duration. The Kir2.x K⁺ channels (encoded by KCNJ genes) regulate the inward rectifier current (IK1) contributing to the final repolarization in cardiac muscle. Here, we describe the transitions in the gene expression profiles of 4 KCNJ genes from healthy or dilated cardiomyopathic human hearts. In the healthy adult ventricles, KCNJ2, KCNJ12, and KCNJ4 (Kir2.1-2.3, respectively) genes were expressed at high levels, while expression of the KCNJ14 (Kir2.4) gene was low. In DCM ventricles, the levels of Kir2.1 and Kir2.3 were upregulated, but those of Kir2.2 channels were downregulated. Additionally, the expression of the DLG1 gene coding for the synapse-associated protein 97 (SAP97) anchoring molecule exhibited a 2-fold decline with increasing age in normal hearts, and it was robustly downregulated in young DCM patients. These adaptations could offer a new aspect for the explanation of the generally observed physiological and molecular alterations found in DCM.

Hofmeister ions control protein dynamics.

BACKGROUND: Recently, we have elaborated a thermodynamic theory that could coherently interpret the diverse effects of Hofmeister ions on proteins, based on a single physical parameter, the protein-water interfacial tension (Dér et al., Journal of Physical Chemistry B. 2007, 111, 5344-5350). This theory, implying a "liquid drop model", predicts changes in protein conformational fluctuations upon addition of Hofmeister salts (containing either kosmotropic or chaotropic anions) to the medium. METHODS: Here, we report experimental tests of this prediction using a complex approach by applying methods especially suited for the detection of protein fluctuation changes (neutron scattering, micro-calorimetry, and Fourier-transform infrared spectroscopy). RESULTS: It is demonstrated that Hofmeister salts, via setting the hydrophobic/hydrophilic properties of the protein-water interface, control conformational fluctuations even in the interior of the typical membrane transport protein bacteriorhodopsin, around its temperature-induced, unusual α(II)→α(I) conformational transition between 60 and 90°C. We found that below this transition kosmotropic (COOCH3(-)), while above it chaotropic (ClO4(-)) anions increase structural fluctuations of bR. It was also shown that, in each case, an onset of enhanced equilibrium fluctuations presages this phase transition in the course of the thermotropic response of bR. CONCLUSIONS: These results are in full agreement with the theory, and demonstrate that predictions based on protein-water interfacial tension changes can describe Hofmeister effects and interpret protein dynamics phenomena even in unusual cases. GENERAL SIGNIFICANCE: This approach is expected to provide a useful guide to understand the principles governing the interplay between protein interfacial properties and conformational dynamics, in general.

κ-Casein terminates casein micelle build-up by its "soft" secondary structure.

In our previous paper (Nagy et al. in J Biol Chem 285:38811-38817, 2010) by using a multilayered model system, we showed that, from α-casein, aggregates (similar to natural casein micelles) can be built up step by step if Ca-phosphate nanocluster incorporation is ensured between the protein adsorption steps. It remained, however, an open question whether the growth of the aggregates can be terminated, similarly to in nature with casein micelles. Here, we show that, in the presence of Ca-phosphate nanoclusters, upon adsorbing onto earlier α-casein surfaces, the secondary structure of α-casein remains practically unaffected, but κ-casein exhibits considerable changes in its secondary structure as manifested by a shift toward having more ß-structures. In the absence of Ca-phosphate, only κ-casein can still adsorb onto the underlying casein surface; this κ-casein also expresses considerable shift toward ß-structures. In addition, this κ-casein cover terminates casein aggregation; no further adsorption of either α- or κ-casein can be achieved. These results, while obtained on a model system, may show that the Ca-insensitive κ-casein can, indeed, be the outer layer of the casein micelles, not only because of its "hairy" extrusion into the water phase, but because of its "softer" secondary structure, which can "occlude" the interacting motifs serving casein aggregation. We think that the revealed nature of the molecular interactions, and the growth mechanism found here, might be useful to understand the aggregation process of casein micelles also in vivo.

Casein aggregates built step-by-step on charged polyelectrolyte film surfaces are calcium phosphate-cemented.

The possible mechanism of casein aggregation and micelle buildup was studied in a new approach by letting α-casein adsorb from low concentration (0.1 mg·ml(-1)) solutions onto the charged surfaces of polyelectrolyte films. It was found that α-casein could adsorb onto both positively and negatively charged surfaces. However, only when its negative phosphoseryl clusters remained free, i.e. when it adsorbed onto a negative surface, could calcium phosphate (CaP) nanoclusters bind to the casein molecules. Once the CaP clusters were in place, step-by-step building of multilayered casein architectures became possible. The presence of CaP was essential; neither Ca(2+) nor phosphate could alone facilitate casein aggregation. Thus, it seems that CaP is the organizing motive in the casein micelle formation. Atomic force microscopy revealed that even a single adsorbed casein layer was composed of very small (in the range of tens of nanometers) spherical forms. The stiffness of the adsorbed casein layer largely increased in the presence of CaP. On this basis, we can imagine that casein micelles emerge according to the following scheme. The amphipathic casein monomers aggregate into oligomers via hydrophobic interactions even in the absence of CaP. Full scale, CaP-carrying micelles could materialize by interlocking these casein oligomers with CaP nanoclusters. Such a mechanism would not contradict former experimental results and could offer a synthesis between the submicelle and the block copolymer models of casein micelles.

Lipids, proteins, and their interplay in the dynamics of temperature-stressed membranes of a cyanobacterium, Synechocystis PCC 6803.

Proper responses to low- and high-temperature stresses are essential for the survival of many organisms. It has been established that at low-temperature stress the sufficient microviscosity of the lipids is decisive in this respect. In many organisms, adapting the level of lipid unsaturation to the low growth temperature regulates this feature. At high-temperature stresses, however, there are no unequivocal results concerning the role of the lipids. In these temperature ranges, the lipids are all disordered and fluid and their physical parameters change slowly with increasing temperatures, while biological organisms give characteristic stress responses in rather narrow temperature ranges. Therefore, one may speculate that other membrane parameters/components, which change sharply in the range of the high-temperature stress, may give a signal to initiate the general response of the cells. For such a role, proteins are the trivial candidates. To reveal the role of the lipids and the proteins in these processes, we used a genetically engineered system, based on a cyanobacterium, Synechocystis PCC 6803. In the wild-type cells of this bacterium, by altering the growth temperature, the polyunsaturated lipid content of the cell membranes can be varied considerably (as required by the homeoviscous adaptation principle). In the case of desA(-)/desD(-) mutant cells, which can contain only monounsaturated fatty acyl chains in their lipids, homeoviscous adaptation of the lipids is not possible. Since desA(-)/desD(-) mutation affects only the lipids, additional perturbations (e.g., altered protein content) should minimally disturb the comparison of the lipid behaviors in wild-type and mutant cells. Infrared spectra of thylakoid and cytoplasmic membranes isolated from wild-type and mutant cells were recorded in 3 degrees C steps between 8 and 92 degrees C. By analyzing the rates of protein structural changes, hydrogen-deuterium exchange, in-membrane lipid disorder, and water-membrane interfacial order/hydration as functions of the temperature, we conclude that (i) the gel-to-liquid crystalline phase transition of the lipids correlates with the growth temperature in the wild-type cells but not in the desA(-)/desD(-) mutants, (ii) over the physiological temperature range, both protein and lipid dynamics are regulating/regulated, providing remarkably constant dynamics for both the thylakoid and cytoplasmic membrane, (iii) in the high-temperature stress region, protein structure and dynamics are changing sharply without any correlation with growth temperature and/or mutation, i.e., membrane protein stability does not seem to depend on the lipid composition of the membrane (this finding points to the possible primacy of proteins as initiators/targets of heat-shock alarms), and (iv) there are substantial differences between the dynamics of the proteins of the thylakoid and cytoplasmic membranes, reflecting their different protein complexes and lipid-to-protein ratios.

Membrane protein dynamics: limited lipid control.

Correlation of lipid disorder with membrane protein dynamics has been studied with infrared spectroscopy, by combining data characterizing lipid phase, protein structure and, via hydrogen-deuterium (H/D) exchange, protein dynamics. The key element was a new measuring scheme, by which the combined effects of time and temperature on the H/D exchange could be separated. Cyanobacterial and plant thylakoid membranes, mammalian mitochondria membranes, and for comparison, lysozyme were investigated. In dissolved lysozyme, as a function of temperature, H/D exchange involved only reversible movements (the secondary structure did not change considerably); heat-denaturing was a separate event at much higher temperature. Around the low-temperature functioning limit of the biomembranes, lipids affected protein dynamics since changes in fatty acyl chain disorders and H/D exchange exhibited certain correlation. H/D exchange remained low in all membranes over physiological temperatures. Around the high-temperature functioning limit of the membranes, the exchange rates became higher. When temperature was further increased, H/D exchange rates went over a maximum and afterwards decreased (due to full H/D exchange and/or protein denaturing). Maximal H/D exchange rate temperatures correlated neither with the disorder nor with the unsaturation of lipids. In membrane proteins, in contrast to lysozyme, the onsets of sizable H/D exchange rates were the onsets of irreversible denaturing as well. Seemingly, at temperatures where protein self-dynamics allows large-scale H/D exchange, lipid-protein coupling is so weak that proteins prefer aggregating to limit the exposure of their hydrophobic surface regions to water. In all membranes studied, dynamics seemed to be governed by lipids around the low-temperature limit, and by proteins around the high-temperature limit of membrane functionality.PACS codes: 87.14.ep, 87.14.cc, 87.16.D.

Phospholipid bilayers as biomembrane-like barriers in layer-by-layer polyelectrolyte films.

Dipalmitoylphosphatidylcholine (DPPC) bilayer was created on the surface of an exponentially growing poly(glutamic acid)/poly(lysine) (PGA/PLL) layer-by-layer polyelectrolyte film. The lipid bilayer decreased the surface roughness of the polyelectrolyte film. The layer-by-layer construction of the polyelectrolyte film could be continued on the top of the DPPC layer. The lipid bilayer, however, formed a barrier in the interior of the polyelectrolyte film, which blocked the diffusion (a prerequisite for exponential growth) of the polyelectrolytes. Thus, a new growth regime started in the upper part of the polyelectrolyte film, which was added to embed the DPPC bilayer. The structure and the dynamics of the DPPC bilayer on the polyelectrolyte film surface remained similar to that of its hydrated multibilayers, except that the phase transition became wider. In the case of embedded DPPC bilayers, in addition, the phase-transition temperature also decreased. This is the result of interactions with the nonconcerted movements of the barrier-separated lower and higher parts of the polyelectrolyte film. Gramicidin A (GRA) as a model of lipid-soluble peptides and proteins was successfully incorporated into such DPPC films. The DPPC films, either with or without GRA, were remarkably stable; as many heating-cooling cycles to measure phase transition could be carried out without visible alterations as wanted.

Polyelectrolyte-mediated adsorption of amelogenin monomers and nanospheres forming mono- or multilayers.

We have applied optical waveguide lightmode spectroscopy combined with streaming potential measurements and Fourier-transformed infrared spectroscopy to investigate adsorption of amelogenin nanospheres onto polyelectrolytes. The long-term objective was to better understand the chemical nature of these assemblies and to gain further insight into the molecular mechanisms involved during self-assembly. It was found that monolayers of monomers and negatively charged nanospheres of a recombinant amelogenin (rM179) irreversibly adsorbed onto a positively charged polyelectrolyte multilayer films. On the basis of measurements performed at different temperatures, it was demonstrated that intermolecular interactions for the formation of nanospheres were not affected by their adsorption onto polyelectrolytes. Consecutive adsorption of nanospheres resulting in the formation of multilayer structures was possible by using cationic poly(l-lysine) as mediators. N-Acetyl-d-glucosamine (GlcNac) did not disturb the nanosphere-assembled protein's structure, and it only affected the adsorption of monomeric amelogenin. Infrared spectroscopy of adsorbed amelogenin revealed conformational differences between the monomeric and assembled forms of rM179. While there was a considerable amount of alpha-helices in the monomers, beta-turn and beta-sheet structures dominated the assembled proteins. Our work constitutes the first report on a structurally controlled in vitro buildup of an rM179 nanosphere monolayer-based matrix. Our data support the notion that amelogenin self-assembly is mostly driven by hydrophobic interactions and that amelogenin/PEM interactions are dominated by electrostatic forces. We suggest that similar forces can govern amelogenin interactions with non-amelogenins or the mineral phase during enamel biomineralization.

Partial poly(glutamic acid) <--> poly(aspartic acid) exchange in layer-by-layer polyelectrolyte films. Structural alterations in the three-component architectures.

Layer-by-layer (LBL) polyelectrolyte films were constructed from poly(L-glutamic acid) (PGA) and poly(L-aspartic acid) (PAA) as polyanions, and from poly(L-lysine) (PLL) as the polycation. The terminating layer of the films was always PLL. According to attenuated total reflection Fourier transform infrared measurements, the PGA/PLL and PAA/PLL films, despite their chemical similarity, had largely different secondary structures. Extended beta-sheets dominated the PGA/PLL films, while alpha-helices and intramolecular beta-sheets dominated the PAA/PLL films. The secondary structure of the polyelectrolyte film affected the adsorption of human serum albumin (HSA) as well. HSA preserved its native secondary structure on the PGA/PLL film, but it became largely deformed on PAA/PLL films. Both PGA and PAA were able to extrude to a certain extent the other polyanion from the films, but the structural consequences were different. Adding PAA to a (PGA/PLL)5-PGA film resulted in a simple exchange and incorporation: PGA/PLL and PAA/PLL complexes coexisted with their unaltered secondary structures in the mixed film. The incorporation of PGA into a (PAA/PLL)5-PAA film was up to 50% and caused additional beta-structure increase in the secondary structure of the film. The proportions of the two polyanions were roughly the same on the surfaces and in the interiors of the films, indicating practically free diffusion for both polyanions. The abundance of PAA/PLL and PGA/PLL domains on the film surfaces was monitored by the analysis of the amide I region of the infrared spectrum of a reporter molecule, HSA, adsorbed onto the three-component polyelectrolyte films.

Streptococcal antigen I/II binds to extracellular proteins through intermolecular beta-sheets.

One of the functions associated with the oral streptococcal surface protein I/II is to bind to human extracellular matrix molecules or blood components, which could act as opportunistic ligands in pathological circumstances. In order to understand the relative specificity of the binding repertoire of this bacterial adhesin, we examined by infrared measurements the mode of binding of the protein I/II from Streptococcus mutans OMZ175 (I/IIf) to fibronectin and fibrinogen. This approach revealed the beta-structure forming capacity of I/IIf upon interaction with both proteins. The forming of intermolecular beta-structures may provide a non-selective way of interaction between I/IIf and its possible targets.

Human serum albumin self-assembly on weak polyelectrolyte multilayer films structurally modified by pH changes.

Adsorption of proteins onto film surfaces built up layer by layer from oppositely charged polyelectrolytes is a complex phenomenon, governed by electrostatic forces, hydrogen bonds, and hydrophobic interactions. The amounts of the interacting charges, however, both in polyelectrolytes and in proteins adsorbed on such films are a function of the pH of the solution. In addition, the number and the accessibility of free charges in proteins depend on the secondary structure of the protein. The subtle interplay of all these factors determines the adsorption of the proteins onto the polyelectrolyte film surfaces. We investigated the effect of these parameters for polyelectrolyte films built up from weak "protein-like" polyelectrolytes (i.e., polypeptides), poly(L-lysine) (PLL), and poly(glutamic acid) (PGA) and for the adsorption of human serum albumin (HSA) onto these films in the pH range 3.0-10.5. It was found that the buildup of the polyelectrolyte films is not a simple function of the pure charges of the individual polyelectrolytes, as estimated from their respective pKa values. The adsorption of HSA onto (PLL/PGA)n films depended strongly on the polyelectrolyte terminating the film. For PLL-terminated polyelectrolyte films, at low pH, repulsion, as expected, is limiting the adsorption of HSA (having net positive charge below pH 4.6) since PLL is also positively charged here. At high pH values, an unexpected HSA uptake was found on the PGA-ending films, even when both PGA and HSA were negatively charged. It is suggested that the higher surface rugosity and the decrease of the alpha-helix content at basic pH values (making accessible certain charged groups of the protein for interactions with the polyelectrolyte film) could explain this behavior.

Structural consequences of genetically engineered saturation of the fatty acids of phosphatidylglycerol in tobacco thylakoid membranes. An FTIR study.

The role of phosphatidylglycerol (PG) in protein-lipid interactions and membrane dynamics has been studied in the thylakoids of wild type and manipulated tobacco plants transformed with complementary DNAs for glycerol-3-phosphate acyltransferases (GPATs) from squash and Arabidopsis. The expression of the foreign enzymes resulted in the level of saturation of the PG molecules being higher in the squash and lower in the Arabidopsis transformants, as compared with the level in wild-type tobacco. For the analysis of fatty acyl chain dynamics in the thylakoid membranes, the nu(sym)CH(2) vibration bands of the infrared specta were decomposed into two components, corresponding to ordered and disordered fatty acyl chain segments. With this approach, it was shown that in squash GPAT-transformed tobacco thylakoids a rigid lipid domain exists below 25 degrees C. Above 25 degrees C, the dynamics of all thylakoid membranes were very similar, regardless of the manipulations. PG seems to tune the dynamics at the protein-lipid interface rather than to affect the structure of the proteins directly. Above 50 degrees C, the frequencies of the disordered nu(sym)CH(2) component bands were decreased. This lipid-related phenomenon correlated with protein denaturing. It is demonstrated that the protein aggregation appearing upon heat denaturing changes the conformational distribution of the disordered lipid population. The data also reveal that the protein stability does not depend on the fatty acid composition of the PG molecules; other lipids should provide the environment governing the protein stability in the thylakoid membrane. This is the first such detailed analysis of the infrared spectra of biological membranes that permits a differentiation between structurally different lipid populations within a membrane.

Gene-engineered rigidification of membrane lipids enhances the cold inducibility of gene expression in synechocystis.

A sudden decrease in ambient temperature induces the expression of a number of genes in poikilothermic organisms. We report here that the cold inducibility of gene expression in Synechocystis sp. PCC 6803 was enhanced by the rigidification of membrane lipids that was engineered by disruption of genes for fatty acid desaturases. DNA microarray analysis revealed that cold-inducible genes could be divided into three groups according to the effects of the rigidification of membrane lipids. The first group included genes whose expression was not induced by cold in wild-type cells but became strongly cold-inducible upon rigidification of membrane lipids. This group included certain heat-shock genes, genes for subunits of the sulfate transport system, and the hik34 gene for a histidine kinase. The second group consisted of genes whose cold inducibility was moderately enhanced by the rigidification of membrane lipids. Most genes in this group encoded proteins of as yet unknown function. The third group consisted of genes whose cold inducibility was unaffected by the rigidification of membrane lipids. This group included genes for an RNA helicase and an RNA-binding protein. DNA microarray analysis also indicated that the rigidification of membrane lipids had no effect on the heat inducibility of gene expression. Hik33, a cold-sensing histidine kinase, regulated the expression of most genes in the second and third groups but of only a small number of genes in the first group, an observation that suggests that the cold-inducible expression of genes in the first group might be regulated by a cold sensor that remains to be identified.