Conserved structural features and sequence patterns in the GroES fold family

Computational analysis of human medium-chain dehydrogenases/reductases revealing substrate- and coenzyme-binding characteristics

The medium-chain dehydrogenase/reductase (MDR) superfamily has more than 600,000 members in UniProt as of March 2023. As the family has been growing, the proportion of functionally characterized proteins has been falling behind. The aim of this project was to investigate the binding pockets of nine different MDR protein families based on sequence conservation patterns and three-dimensional structures of members within the respective families. A search and analysis methodology was developed. Using this, a total of 2000 eukaryotic MDR sequences belonging to nine different families were identified. The pairwise sequence identities within each of the families were 80-90 % for the mammalian sequences, like the levels observed for alcohol dehydrogenase, another MDR family. Twenty conserved residues were identified in the coenzyme part of the binding site by matching structural and conservation data of all nine protein families. The conserved residues in the substrate part of the binding pocket varied between the nine MDR families, implying divergent functions for the different families. Studying each family separately made it possible to identify multiple conserved residues that are expected to be important for substrate binding or catalysis of the enzymatic reaction. By combining structural data with the conservation of the amino acid residues in each protein, important residues in the binding pocket were identified for each of the nine MDRs. The obtained results add new positions of interest for the binding and activity of the enzyme family as well as fit well to earlier published data. Three distinct types of binding pockets were identified, containing no, one, or two tyrosine residues.

Mitochondrial matrix RTN4IP1/OPA10 is an oxidoreductase for coenzyme Q synthesis

Targeting proximity-labeling enzymes to specific cellular locations is a viable strategy for profiling subcellular proteomes. Here, we generated transgenic mice (MAX-Tg) expressing a mitochondrial matrix-targeted ascorbate peroxidase. Comparative analysis of matrix proteomes from the muscle tissues showed differential enrichment of mitochondrial proteins. We found that reticulon 4-interacting protein 1 (RTN4IP1), also known as optic atrophy-10, is enriched in the mitochondrial matrix of muscle tissues and is an NADPH oxidoreductase. Interactome analysis and in vitro enzymatic assays revealed an essential role for RTN4IP1 in coenzyme Q (CoQ) biosynthesis by regulating the O-methylation activity of COQ3. Rtn4ip1-knockout myoblasts had markedly decreased CoQ9 levels and impaired cellular respiration. Furthermore, muscle-specific knockdown of dRtn4ip1 in flies resulted in impaired muscle function, which was reversed by dietary supplementation with soluble CoQ. Collectively, these results demonstrate that RTN4IP1 is a mitochondrial NAD(P)H oxidoreductase essential for supporting mitochondrial respiration activity in the muscle tissue.

Genome-Wide Identification and Characterization of the Medium-Chain Dehydrogenase/Reductase Superfamily of Trichosporon asahii and Its Involvement in the Regulation of Fluconazole Resistance

The medium-chain dehydrogenase/reductase (MDR) superfamily contains many members that are widely present in organisms and play important roles in growth, metabolism, and stress resistance but have not been studied in Trichosporon asahii. In this study, bioinformatics and RNA sequencing methods were used to analyze the MDR superfamily of T. asahii and its regulatory effect on fluconazole resistance. A phylogenetic tree was constructed using Saccharomyces cerevisiae, Candida albicans, Cryptococcus neoformans, and T. asahii, and 73 MDRs were identified, all of which contained NADPH-binding motifs. T. asahii contained 20 MDRs that were unevenly distributed across six chromosomes. T. asahii MDRs (TaMDRs) had similar 3D structures but varied greatly in their genetic evolution at different phylum levels. RNA-seq and gene expression analyses revealed that the fluconazole-resistant T. asahii strain upregulates xylitol dehydrogenase, and downregulated alcohol dehydrogenase and sorbitol dehydrogenase concluded that the fluconazole-resistant T. asahii strain was less selective toward carbon sources and had higher adaptability to the environment. Overall, our study contributes to our understanding of TaMDRs, providing a basis for further analysis of the genes associated with drug resistance in T. asahii.

Genome-wide identification and characterization of ADH gene family and the expression under different abiotic stresses in tomato (Solanum lycopersicum L.)

The SlADH gene plays a key role in environmental stress response. However, limited studies exist regarding the tomato SlADH gene. In this study, we identified 35 SlADH genes in tomato by genome-wide identification. Among the 12 chromosomes of tomato, SlADH gene is distributed on 10 chromosomes, among which the 7th and 10th chromosomes have no family members, while the 11th chromosome has the most members with 8 family members. Members of this gene family are characterized by long coding sequences, few amino acids, and introns that make up a large proportion of the genetic structure of most members of this family. Moreover, the molecular weight of the proteins of the family members was similar, and the basic proteins were mostly, and the overall distribution was relatively close to neutral (pI = 7). This may indicate that proteins in this family have a more conserved function. In addition, a total of four classes of cis-acting elements were detected in all 35 SlADH promoter regions, most of which were associated with biotic and abiotic stresses. The results indicate that SlADH gene had a certain response to cold stress, salt stress, ABA treatment and PEG stress. This study provides a new candidate gene for improving tomato stress resistance.

Effects of Kiwifruit Rootstocks with Opposite Tolerance on Physiological Responses of Grafting Combinations under Waterlogging Stress

Kiwifruit is commonly sensitive to waterlogging stress, and grafting onto a waterlogging-tolerant rootstock is an efficient strategy for enhancing the waterlogging tolerance of kiwifruit plants. KR5 (Actinidia valvata) is more tolerant to waterlogging than ‘Hayward’ (A. deliciosa) and is a potential resistant rootstock for kiwifruit production. Here, we focused on evaluating the performance of the waterlogging-sensitive kiwifruit scion cultivar ‘Zhongmi 2′ when grafted onto KR5 (referred to as ZM2/KR5) and Hayward (referred to as ZM2/HWD) rootstocks, respectively, under waterlogging stress. The results showed ‘Zhongmi 2′ performed much better when grafted onto KR5 than when grafted onto ‘Hayward’, exhibiting higher photosynthetic efficiency and reduced reactive oxygen species (ROS) damage. Furthermore, the roots of ZM2/KR5 plants showed greater root activity and energy supply, lower ROS damage, and more stable osmotic adjustment ability than the roots of ZM2/HWD plants under waterlogging stress. In addition, we detected the expression of six key genes involved in the kiwifruit waterlogging response mechanism, and these genes were remarkably induced in the ZM2/KR5 roots but not in the ZM2/HWD roots under waterlogging stress. Moreover, principal component analysis (PCA) further demonstrated the differences in the physiological responses of the ZM2/KR5 and ZM2/HWD plants under waterlogging stress. These results demonstrated that the KR5 rootstock can improve the waterlogging tolerance of grafted kiwi plants by regulating physiological and biochemical metabolism and molecular responses.

The pathogenic biomarker alcohol dehydrogenase protein is involved in Bacillus cereus virulence and survival against host innate defence

Bacillus cereus is a spore forming bacteria recognized among the leading agents responsible for foodborne outbreaks in Europe. B. cereus is also gaining notoriety as an opportunistic human pathogen inducing local and systemic infections. The real incidence of such infection is likely underestimated and information on genetic and phenotypic characteristics of the incriminated strains is generally scarce. We have recently analyzed a large strain collection of varying pathogenic potential. Screening for biomarkers to differentiate among clinical and non-clinical strains, a gene encoding an alcohol dehydrogenase-like protein was identified among the leading candidates. This family of proteins has been demonstrated to be involved in the virulence of several bacterial species. The relevant gene was knocked out to elucidate its function with regards to resistance to host innate immune response, both in vitro and in vivo. Our results demonstrate that the adhB gene plays a significant role in resistance to nitric oxide and oxidative stress in vitro, as well as its pathogenic ability with regards to in vivo toxicity. These properties may explain the pathogenic potential of strains carrying this newly identified virulence factor.

Improved high-temperature ethanol production from sweet sorghum juice using Zymomonas mobilis overexpressing groESL genes

Zymomonas mobilis may encounter various types of stress during ethanol fermentation, which reduces ethanol production efficiency. This situation may be mitigated by molecular chaperones, including the chaperonin GroESL, which confers enhanced protection against various stresses. In this study, we successfully developed a Z. mobilis strain R301 that harbors groESL genes and can be used for high-temperature ethanol production from sweet sorghum juice. Sequence analyses of GroES and GroEL from Z. mobilis TISTR548 demonstrated conserved residues at specific positions within GroES and conserved glycine-glycine-methionine (GGM) repeats at the C-terminus of GroEL. The Z. mobilis wild-type and R301 strains were then evaluated for their tolerance to stresses, including high temperatures, high sugar concentrations, and high ethanol concentrations up to 40°C, 300 g/L, and 13% (v/v), respectively. Z. mobilis R301 exhibited better growth performance than the wild-type strain under all stress conditions. This is the first report on ethanol production at 40°C by recombinant Z. mobilis using sweet sorghum juice; this strain produced an ethanol concentration of 41.66 g/L, with a productivity of 0.87 g/L/h and a theoretical ethanol yield of 88.9%. Overexpression of groESL resulted in increased ethanol production, with values approximately 11% higher than those of the wild type at 40°C. Additionally, at 37°C, Z. mobilis R301 gave a higher theoretical ethanol yield (92.6%) than that shown in previous research. This work illustrates the potential for future enhancement of industrial-scale ethanol production at high temperatures utilizing Z. mobilis R301 in the bioconversion of sweet sorghum juice, a promising energy crop. KEY POINTS: • The groESL-overexpressing Z. mobilis strain was successfully constructed. • The recombinant Z. mobilis exhibited higher stress tolerance than the wild-type strain. • Overexpression of groESL genes improved ethanol production efficiency at high temperatures.

Proteomic and Biological Analyses Reveal the Effect on Growth under Flooding Stress of Chickpea Irradiated with Millimeter Waves

Chickpea cultivated on marginal lands in arid and semiarid tropics is one of the food legumes, and its growth is reduced by flooding stress. Millimeter-wave irradiation has influences on organisms, and it improves the growth of plants such as soybean. To reveal the dynamic effects of millimeter-wave irradiation on chickpea under flooding, gel- and label-free proteomic analysis was conducted. Millimeter-wave irradiation improved chickpea growth and its tolerance to flooding stress. According to functional categorization, oppositely changed proteins were correlated with photosynthesis, fermentation, and protein degradation. Immunoblot analysis confirmed that RuBisCO activase and large subunits decreased in leaves under flooding; however, they are recovered in irradiated chickpea even if it was in this condition. The activity and accumulation of alcohol dehydrogenase increased in roots under flooding; however, this followed the same pattern. Cell death was significantly increased and decreased by flooding on unirradiated and irradiated chickpeas, respectively. These findings suggest that irradiation with millimeter waves on chickpea seeds improves the recovery of plant growth through regulation of photosynthesis in leaves and fermentation in roots. Furthermore, millimeter-wave irradiation might promote chickpea tolerance under flooding via the regulation of cell death.

Genome-wide identification of alcohol dehydrogenase (ADH) gene family under waterlogging stress in wheat (Triticum aestivum)

Background

Alcohol dehydrogenase (ADH) plays an important role in plant survival under anaerobic conditions. Although some research about ADH in many plants have been carried out, the bioinformatics analysis of the ADH gene family from Triticum aestivum and their response to abiotic stress is unclear.

Methods

A total of 22 ADH genes were identified from the wheat genome, and these genes could be divided into two subfamilies (subfamily I and subfamily II). All TaADH genes belonged to the Medium-chain ADH subfamily. Sequence alignment analysis showed that all TaADH proteins contained a conservative GroES-like domain and Zinc-binding domain. A total of 64 duplicated gene pairs were found, and the Ka/Ks value of these gene pairs was less than 1, which indicated that these genes were relatively conservative and did not change greatly in the process of duplication.

Results

The organizational analysis showed that nine TaADH genes were highly expressed in all organs, and the rest of TaADH genes had tissue specificity. Cis-acting element analysis showed that almost all of the TaADH genes contained an anaerobic response element. The expression levels of ADH gene in waterlogging tolerant and waterlogging sensitive wheat seeds were analyzed by quantitative real-time PCR (qRT-PCR). This showed that some key ADH genes were significantly responsive to waterlogging stress at the seed germination stage, and the response of waterlogging tolerant and waterlogging sensitive wheat seeds to waterlogging stress was regulated by different ADH genes. The results may be helpful to further study the function of TaADH genes and to determine the candidate gene for wheat stress resistance breeding.

Identification and Functional Analysis of ThADH1 and ThADH4 Genes Involved in Tolerance to Waterlogging Stress in Taxodium hybrid 'Zhongshanshan 406'

The Taxodium hybrid 'Zhongshanshan 406' (T. hybrid 'Zhongshanshan 406') [Taxodium mucronatum Tenore × Taxodium distichum (L.). Rich] has an outstanding advantage in flooding tolerance and thus has been widely used in wetland afforestation in China. Alcohol dehydrogenase genes (ADHs) played key roles in ethanol metabolism to maintain energy supply for plants in low-oxygen conditions. Two ADH genes were isolated and characterized-ThADH1 and ThADH4 (GenBank ID: AWL83216 and AWL83217-basing on the transcriptome data of T. hybrid 'Zhongshanshan 406' grown under waterlogging stress. Then the functions of these two genes were investigated through transient expression and overexpression. The results showed that the ThADH1 and ThADH4 proteins both fall under ADH III subfamily. ThADH1 was localized in the cytoplasm and nucleus, whereas ThADH4 was only localized in the cytoplasm. The expression of the two genes was stimulated by waterlogging and the expression level in roots was significantly higher than those in stems and leaves. The respective overexpression of ThADH1 and ThADH4 in Populus caused the opposite phenotype, while waterlogging tolerance of the two transgenic Populus significantly improved. Collectively, these results indicated that genes ThADH1 and ThADH4 were involved in the tolerance and adaptation to anaerobic conditions in T. hybrid 'Zhongshanshan 406'.

Genome-wide identification and comparative analysis of the ADH gene family in Chinese white pear (Pyrus bretschneideri) and other Rosaceae species

Alcohol dehydrogenase (ADH) is essential to the formation of aromatic compounds in fruits. However, the evolutionary history and characteristics of ADH gene expression remain largely unclear in Rosaceae fruit species. In this study, 464 ADH genes were identified in eight Rosaceae fruit species, 68 of the genes were from pear and which were classified into four subgroups. Frequent single gene duplication events were found to have contributed to the formation of ADH gene clusters and the expansion of the ADH gene family in these eight Rosaceae species. Purifying selection was the major force in ADH gene evolution. The younger genes derived from tandem and proximal duplications had evolved faster than those derived from other types of duplication. RNA-Seq and qRT-PCR analysis revealed that the expression levels of three ADH genes were closely correlated with the content of aromatic compounds detected during fruit development.

Insight into the relationship between S-lignin and fiber quality based on multiple research methods

Cotton (Gossypium hirsutum) is an important cash crop, providing people with high quality natural fiber. Lignin is the main component of cotton fiber, second only to cellulose. As a main substance filled in the cellulose framework during the secondary wall thickening process, lignin plays a key role in the formation of cotton fiber quality. However, the mechanism behind it is still unclear. In this research, we screened candidate genes involved in lignin biosynthesis based on analysis of cotton genome and transcriptome sequence data. The authenticity of the transcriptome data was verified by qRT-PCR assay. Total 62 genes were identified from nine gene families. In the process, we found the key gene GhCAD7 that affects the biosynthesis of S-lignin and the ratio of syringyl/guaiacyl (S/G). In addition, in combination with the metabolites and transcriptome profiles of the line 0-153 with high fiber quality and the line sGK9708 with low fiber quality during cotton fiber development, we speculate that the ratio of syringyl/guaiacyl (S/G) is inseparable from the quality of cotton fiber. Finally, the S-type lignin synthesis branch may play a more important role in the formation of high-quality fiber. This work provides insights into the synthesis of lignin in cotton and lays the foundation for future research into improving fiber quality.

A polyextremophilic alcohol dehydrogenase from the Atlantis II Deep Red Sea brine pool

Enzymes originating from hostile environments offer exceptional stability under industrial conditions and are therefore highly in demand. Using single-cell genome data, we identified the alcohol dehydrogenase (ADH) gene, adh/a1a, from the Atlantis II Deep Red Sea brine pool. ADH/A1a is highly active at elevated temperatures and high salt concentrations (optima at 70 °C and 4 m KCl) and withstands organic solvents. The polyextremophilic ADH/A1a exhibits a broad substrate scope including aliphatic and aromatic alcohols and is able to reduce cinnamyl-methyl-ketone and raspberry ketone in the reverse reaction, making it a possible candidate for the production of chiral compounds. Here, we report the affiliation of ADH/A1a to a rare enzyme family of microbial cinnamyl alcohol dehydrogenases and explain unique structural features for halo- and thermoadaptation.

Alcohol dehydrogenase gene ADH3 activates glucose alcoholic fermentation in genetically engineered Dekkera bruxellensis yeast

Dekkera bruxellensis is a non-conventional Crabtree-positive yeast with a good ethanol production capability. Compared to Saccharomyces cerevisiae, its tolerance to acidic pH and its utilization of alternative carbon sources make it a promising organism for producing biofuel. In this study, we developed an auxotrophic transformation system and an expression vector, which enabled the manipulation of D. bruxellensis, thereby improving its fermentative performance. Its gene ADH3, coding for alcohol dehydrogenase, was cloned and overexpressed under the control of the strong and constitutive promoter TEF1. Our recombinant D. bruxellensis strain displayed 1.4 and 1.7 times faster specific glucose consumption rate during aerobic and anaerobic glucose fermentations, respectively; it yielded 1.2 times and 1.5 times more ethanol than did the parental strain under aerobic and anaerobic conditions, respectively. The overexpression of ADH3 in D. bruxellensis also reduced the inhibition of fermentation by anaerobiosis, the “Custer effect”. Thus, the fermentative capacity of D. bruxellensis could be further improved by metabolic engineering.

The differentially regulated genes TvQR1 and TvPirin of the parasitic plant Triphysaria exhibit distinctive natural allelic diversity

BACKGROUND

Plant parasitism represents an extraordinary interaction among flowering plants: parasitic plants use a specialized organ, the haustorium, to invade the host vascular system to deprive host plants of water and nutrients. Various compounds present in exudates of host plants trigger haustorium development. The two most effective haustorium inducing factors (HIFs) known for the parasitic plant Triphysaria versicolor (T. versicolor) are peonidin, an antioxidant flavonoid, and 2,6-dimethoxybenzoquinone (DMBQ), an oxidative stress agent. To date, two genes involved in haustorium initiation in T. versicolor have been identified: TvQR1, a quinone oxidoreductase that generates the active HIF from DMBQ, and TvPirin, a transcription co-factor that regulates several other DMBQ- responsive and -non-responsive genes. While the expression of these genes in response to DMBQ is well characterized, their expression in response to peonidin is not. In addition, the pattern of polymorphisms in these genes is unknown, even though nucleotide changes in TvQR1 and TvPirin may have contributed to the ability of T. versicolor to develop haustoria. To gain insights into these aspects, we investigated their transcriptional responses to HIFs and non-HIF and their natural nucleotide diversity.

RESULTS

Here we show that TvQR1 and TvPirin are transcriptionally upregulated by both DMBQ and peonidin in T. versicolor roots. Yet, while TvQR1 also responded to juglone, a non-HIF quinone with toxicity comparable to that of DMBQ, TvPirin did not. We further demonstrate that TvPirin encodes a protein shorter than the one previously reported. In the T. versicolor natural population of Northern California, TvQR1 exhibited remarkably higher molecular diversity and more recombination events than TvPirin, with the highest non-synonymous substitution rate in the substrate recognition and catalytic domain of the TvQR1 protein.

CONCLUSION

Our results suggest that TvQR1 and TvPirin have most likely evolved highly distinct roles for haustorium formation. Unlike TvPirin, TvQR1 might have been under diversifying selection to maintain a diverse collection of polymorphisms, which might be related to the recognition of an assortment of HIF and non-HIF quinones as substrates for successful haustorial establishment in a wide range of host plants.

Crystallization and preliminary X-ray crystallographic analysis of the putative NADP(H)-dependent oxidoreductase YncB from Vibrio vulnificus

The yncB gene product from Vibrio vulnificus, which belongs to the medium-chain dehydrogenase/reductase (MDR) superfamily, was crystallized using the microbatch crystallization method at 295 K. Diffraction data sets were collected using synchrotron radiation. Crystals of selenomethionine-substituted YncB protein belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 90.52, b = 91.56, c = 104.79 Å. Assuming the presence of two molecules in the asymmetric unit, the solvent content was estimated to be about 57%. Crystals of the YncB-NADP(H) complex belonged to space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell parameters a = b = 90.14, c = 105.61 Å. Assuming the presence of one molecule in the asymmetric unit, the solvent content was estimated to be about 56.42%.

Characterization of a novel flooding stress-responsive alcohol dehydrogenase expressed in soybean roots

Alcohol dehydrogenase (Adh) is the key enzyme in alcohol fermentation. We analyzed Adh expression in order to clarify the role of Adh of soybeans (Glycine max) to flooding stress. Proteome analysis confirmed that expression of Adh is significantly upregulated in 4-day-old soybean seedlings subjected to 2 days of flooding. Southern hybridization analysis and soybean genome database search revealed that soybean has at least 6 Adh genes. The GmAdh2 gene that responded to flooding was isolated from soybean cultivar Enrei. Adh2 expression was markedly increased 6 h after flooding and decreased 24 h after floodwater drainage. In situ hybridization and Western blot indicated that flooding strongly induces Adh2 expression in RNA and protein levels in the root apical meristem. Osmotic, cold, or drought stress did not induce expression of Adh2. These results indicate that Adh2 is a flooding-response specific soybean gene expressed in root tissue.

The plant ADH gene family

The structures, evolution and functions of alcohol dehydrogenase gene families and their products have been scrutinized for half a century. Our understanding of the enzyme structure and catalytic activity of plant alcohol dehydrogenase (ADH-P) is based on the vast amount of information available for its animal counterpart. The probable origins of the enzyme from a simple β-coil and eventual emergence from a glutathione-dependent formaldehyde dehydrogenase have been well described. There is compelling evidence that the small ADH gene families found in plants today are the survivors of multiple rounds of gene expansion and contraction. To the probable original function of their products in the terminal reaction of anaerobic fermentation have been added roles in yeast-like aerobic fermentation and the production of characteristic scents that act to attract animals that serve as pollinators or agents of seed dispersal and to protect against herbivores.

Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement

Background

The Medium-chain Dehydrogenases/Reductases (MDR) form a protein superfamily whose size and complexity defeats traditional means of subclassification; it currently has over 15000 members in the databases, the pairwise sequence identity is typically around 25%, there are members from all kingdoms of life, the chain-lengths vary as does the oligomericity, and the members are partaking in a multitude of biological processes. There are profile hidden Markov models (HMMs) available for detecting MDR superfamily members, but none for determining which MDR family each protein belongs to. The current torrential influx of new sequence data enables elucidation of more and more protein families, and at an increasingly fine granularity. However, gathering good quality training data usually requires manual attention by experts and has therefore been the rate limiting step for expanding the number of available models.

Results

We have developed an automated algorithm for HMM refinement that produces stable and reliable models for protein families. This algorithm uses relationships found in data to generate confident seed sets. Using this algorithm we have produced HMMs for 86 distinct MDR families and 34 of their subfamilies which can be used in automated annotation of new sequences. We find that MDR forms with 2 Zn²⁺ ions in general are dehydrogenases, while MDR forms with no Zn²⁺ in general are reductases. Furthermore, in Bacteria MDRs without Zn²⁺ are more frequent than those with Zn²⁺, while the opposite is true for eukaryotic MDRs, indicating that Zn²⁺ has been recruited into the MDR superfamily after the initial life kingdom separations. We have also developed a web site http://mdr-enzymes.org that provides textual and numeric search against various characterised MDR family properties, as well as sequence scan functions for reliable classification of novel MDR sequences.

Conclusions

Our method of refinement can be readily applied to create stable and reliable HMMs for both MDR and other protein families, and to confidently subdivide large and complex protein superfamilies. HMMs created using this algorithm correspond to evolutionary entities, making resolution of overlapping models straightforward. The implementation and support scripts for running the algorithm on computer clusters are available as open source software, and the database files underlying the web site are freely downloadable. The web site also makes our findings directly useful also for non-bioinformaticians.

Properties and evolution of an alcohol dehydrogenase from the Crenarchaeota Pyrobaculum aerophilum

The gene encoding a novel alcohol dehydrogenase (ADH) that belongs to the medium chain dehydrogenase/reductase (MDR) superfamily was identified in the hyperthermophilic archaeon, Pyrobaculum aerophilum. The P. aerophilum ADH gene (Pae2687) was over-expressed in Escherichia coli, and the protein (PyAeADHII) was purified to homogeneity and characterized. The PyAeADHII belongs to a medium chain class because its monomer size is 330 residues and even if it is structurally similar to other enzymes belonging to MDR superfamily, it lacks key residues involved in the coordination of the catalytic Zn ion and in the binding of alcoholic substrates typical of other ADHs. Consistently, PyAeADHII does not show activity on a large number of alcohols, aldheydes or ketones. It is active only when alpha-tetralone is used as a substrate. The enzyme has a strict requirement for NADP(H) as the coenzyme and has remarkable thermophilicity, displaying activity at temperatures up to 95 degrees C. The study of the metabolic pathways of P. aerophilum can provide information on the evolution of genes and enzymes and may be crucial for understanding the evolution of eukaryotic cells.

Medium- and short-chain dehydrogenase/reductase gene and protein families : the MDR superfamily

The MDR superfamily with ~350-residue subunits contains the classical liver alcohol dehydrogenase (ADH), quinone reductase, leukotriene B4 dehydrogenase and many more forms. ADH is a dimeric zinc metalloprotein and occurs as five different classes in humans, resulting from gene duplications during vertebrate evolution, the first one traced to ~500 MYA (million years ago) from an ancestral formaldehyde dehydrogenase line. Like many duplications at that time, it correlates with enzymogenesis of new activities, contributing to conditions for emergence of vertebrate land life from osseous fish. The speed of changes correlates with function, as do differential evolutionary patterns in separate segments. Subsequent recognitions now define at least 40 human MDR members in the Uniprot database (corresponding to 25 genes when excluding close homologues), and in all species at least 10888 entries. Overall, variability is large, but like for many dehydrogenases, subdivided into constant and variable forms, corresponding to household and emerging enzyme activities, respectively. This review covers basic facts and describes eight large MDR families and nine smaller families. Combined, they have specific substrates in metabolic pathways, some with wide substrate specificity, and several with little known functions.

Folding behavior of a backbone-reversed protein: reversible polyproline type II to beta-sheet thermal transitions in retro-GroES multimers with GroES-like features

The structural consequences of the reversal of polypeptide backbone direction (retro modification) remain insufficiently explored. Here, we describe the behavior of an engineered, backbone-reversed form of the 97 residues-long GroES co-chaperonin of Escherichia coli. FTIR and far-UV CD spectroscopy suggest that retro-GroES adopts a mixed polyproline type II (PPII)-beta-strand structure with a beta(II) type CD spectrum similar to that of GroES. Gel-filtration chromatography reveals that the protein adopts trimeric and/or pentameric quaternary structures, with solubility retained up to concentrations of 5.0-5.5 mg/ml in aqueous solutions. Mutations inserting a single tryptophan residue as a spectroscopic probe at three different sites cause no perturbation in the protein's CD spectral characteristics, or in its quaternary structural status. The protein is cooperatively dissociated, and non-cooperatively unfolded, by both guanidine hydrochloride and urea. Intriguingly, unlike with GroES, retro-GroES is not unfolded by heat. Instead, there is a reversible structural transition involving conversion of PPII structure to beta sheet structure, upon heating, with no attendant aggregation even at 90 degrees C. Retro-GroES does not bind GroEL. In summary, some structure-forming characteristics of GroES appear to be conserved through the backbone reversal process, although the differential conformational behavior upon heating also indicates differences.

Proteome map of Aspergillus nidulans during osmoadaptation

The model filamentous fungus Aspergillus nidulans, when grown in a moderate level of osmolyte (+0.6M KCl), was previously found to have a significantly reduced cell wall elasticity (Biotech Prog, 21:292, 2005). In this study, comparative proteomic analysis via two-dimensional gel electrophoresis (2de) and matrix-assisted laser desorption ionization/time-of-flight (MALDI-TOF) mass spectrometry was used to assess molecular level events associated with this phenomenon. Thirty of 90 differentially expressed proteins were identified. Sequence homology and conserved domains were used to assign probable function to twenty-one proteins currently annotated as "hypothetical." In osmoadapted cells, there was an increased expression of glyceraldehyde-3-phosphate dehydrogenase and aldehyde dehydrogenase, as well as a decreased expression of enolase, suggesting an increased glycerol biosynthesis and decreased use of the TCA cycle. There also was an increased expression of heat shock proteins and Shp1-like protein degradation protein, implicating increased protein turnover. Five novel osmoadaptation proteins of unknown functions were also identified.

Energetics of aliphatic deletions in protein cores

Although core residues can sometimes be replaced by shorter ones without introducing significant changes in protein structure, the energetic consequences are typically large and destabilizing. Many efforts have been devoted to understand and predict changes in stability from analysis of the environment of mutated residues, but the relationships proposed for individual proteins have often failed to describe additional data. We report here 17 apoflavodoxin large-to-small mutations that cause overall protein destabilizations of 0.6-3.9 kcal.mol(-1). By comparing two-state urea and three-state thermal unfolding data, the overall destabilizations observed are partitioned into effects on the N-to-I and on the I-to-U equilibria. In all cases, the equilibrium intermediate exerts a "buffering" effect that reduces the impact of the overall destabilization on the N-to-I equilibrium. The performance of several structure-energetics relationships, proposed to explain the energetics of hydrophobic shortening mutations, has been evaluated by using an apoflavodoxin data set consisting of 14 mutations involving branching-conservative aliphatic side-chain shortenings and a larger data set, including similar mutations implemented in seven model proteins. Our analysis shows that the stability changes observed for any of the different types of mutations (LA, IA, IV, and VA) in either data set are best explained by a combination of differential hydrophobicity and of the calculated volume of the modeled cavity (as previously observed for LA and IA mutations in lysozyme T4). In contrast, sequence conservation within the flavodoxin family, which is a good predictor for charge-reversal stabilizing mutations, does not perform so well for aliphatic shortening ones.

Cation-mediated interplay of loops in chaperonin-10

The ubiquitously occurring chaperonins consist of a large tetradecameric Chaperonin-60, forming a cylindrical assembly, and a smaller heptameric Chaperonin-10. For a functional protein folding cycle, Chaperonin-10 caps the cylindrical Chaperonin-60 from one end forming an asymmetric complex. The oligomeric assembly of Chaperonin-10 is known to be highly plastic in nature. In Mycobacterium tuberculosis, the plasticity has been shown to be modulated by reversible binding of divalent cations. Binding of cations confers rigidity to the metal binding loop, and also promotes stability of the oligomeric structure. We have probed the conformational effects of cation binding on the Chaperonin-10 structure through fluorescence studies and molecular dynamics simulations. Fluorescence studies show that cation binding induces reduced exposure and flexibility of the dome loop. The simulations corroborate these results and further indicate a complex landscape of correlated motions between different parts of the molecule. They also show a fascinating interplay between two distantly spaced loops, the metal binding "dome loop" and the GroEL-binding "mobile loop", suggesting an important cation-mediated role in the recognition of Chaperonin-60. In the presence of cations the mobile loop appears poised to dock onto the Chaperonin-60 structure. The divalent metal ions may thus act as key elements in the protein folding cycle, and trigger a conformational switch for molecular recognition.

Characterization of chaperonin 10 (Cpn10) from the intestinal human pathogen Entamoeba histolytica

Entamoeba histolytica is the causative agent of amoebiasis, a poverty-related disease that kills an estimated 100 000 people each year. E. histolytica does not contain "standard mitochondria", but harbours mitochondrial remnant organelles called mitosomes. These organelles are characterized by the presence of mitochondrial chaperonin Cpn60, but little else is known about the functions and molecular composition of mitosomes. In this study, a gene encoding molecular chaperonin Cpn10--the functional partner of Cpn60--was cloned, and its structure and expression were characterized, as well as the cellular localization of its encoded protein. The 5' untranslated region of the gene contains all of the structural promoter elements required for transcription in this organism. The amoebic Cpn10, like Cpn60, is not significantly upregulated upon heat-shock treatment. Computer-assisted protein modelling, and specific antibodies against Cpn10 and Cpn60, suggest that both proteins interact with each other, and that they function in the same intracellular compartment. Thus, E. histolytica appears to have retained at least two of the key molecular components required for the refolding of imported mitosomal proteins.

The Mycobacterium tuberculosis chaperonin 10 monomer exhibits structural plasticity

The conditions which favor dissociation of oligomeric Mycobacterium tuberculosis chaperonin 10 and the solution structure of the monomer were studied by analytical ultracentrifugation, size exclusion chromatography, fluorescence, and circular dichroism spectroscopies. At neutral pH and in the absence of divalent cations, the protein is fully monomeric below approximately a 4.7 microM concentration. Under these conditions the monomer forms completely unfolded and partially folded conformers which are in equilibrium with each other. One conformer accumulates over the others which is stable within a very narrow range of temperatures. It contains a beta-sheet-structured C-terminal half and a mostly disordered N-terminal half. Other components of the equilibrium include partially helical structures which do not completely unfold at high temperature or under strong acidic conditions. Complete unfolding of the monomer occurs in the presence of denaturants or below 14 degrees C. Cold-denaturation is detected at an unusually high temperature and this may be due to the concentration of hydrophobic residues, which is larger in chaperonins than in other globular proteins. Finally, the monomer self-associates in the pH range 5.8-2.9, where it forms small oligomers. A structure-activity relationship was investigated with the sequences known to be involved in the various biological activities of the monomer.

The TB structural genomics consortium: a resource for Mycobacterium tuberculosis biology

The TB Structural Genomics Consortium is an organization devoted to encouraging, coordinating, and facilitating the determination and analysis of structures of proteins from Mycobacterium tuberculosis. The Consortium members hope to work together with other M. tuberculosis researchers to identify M. tuberculosis proteins for which structural information could provide important biological information, to analyze and interpret structures of M. tuberculosis proteins, and to work collaboratively to test ideas about M. tuberculosis protein function that are suggested by structure or related to structural information. This review describes the TB Structural Genomics Consortium and some of the proteins for which the Consortium is in the progress of determining three-dimensional structures.

The relationship between conservation, thermodynamic stability, and function in the SH3 domain hydrophobic core

To investigate the relationships between sequence conservation, protein stability, and protein function, we have measured the thermodynamic stability, folding kinetics, and in vitro peptide-binding activity of a large number of single-site substitutions in the hydrophobic core of the Fyn SH3 domain. Comparison of these data to that derived from an analysis of a large alignment of SH3 domain sequences revealed a very good correlation between the distinct pattern of conservation observed at each core position and the thermodynamic stability of mutants. Conservation was also found to correlate well with the unfolding rates of mutants, but not to the folding rates, suggesting that evolution selects more strongly for optimal native state packing interactions than for maximal folding rates. Structural analysis suggests that residue-residue core packing interactions are very similar in all SH3 domains, which provides an explanation for the correlation between conservation and mutant stability effects studied in a single SH3 domain. We also demonstrate a correlation between stability and the in vivo activity of mutants, and between conservation and activity. However, the relationship between conservation and activity was very strong only for the three most conserved hydrophobic core positions. The weaker correlation between activity and conservation seen at the other seven core positions indicates that maintenance of protein stability is the dominant selective pressure at these positions. In general, the pattern of conservation at hydrophobic core positions appears to arise from conserved packing constraints, and can be effectively utilized to predict the destabilizing effects of amino acid substitutions.

Identification of conserved residue patterns in small beta-barrel proteins

Our abilities to predict three-dimensional conformation of a polypeptide, given its amino acid sequence, remain limited despite advances in structure analysis. Analysis of structures and sequences of protein families with similar secondary structural elements, but varying topologies, might help in addressing this problem. We have studied the small beta-barrel class of proteins characterized by four strands (n = 4) and a shear number of 8 (S = 8) to understand the principles of barrel formation. Multiple alignments of the various protein sequences were generated for the analysis. Positional entropy, as a measure of residue conservation, indicated conservation of non-polar residues at the core positions. The presence of a type II beta-turn among the various barrel proteins considered was another strikingly invariant feature. A conserved glycyl-aspartyl dipeptide at the beta-turn appeared to be important in guiding the protein sequence into the barrel fold. Molecular dynamics simulations of the type II beta-turn peptide suggested that aspartate is a key residue in the folding of the protein sequence into the barrel. Our study suggests that the conserved type II beta-turn and the non-polar residues in the barrel core are crucial for the folding of the protein's primary sequence into the beta-barrel conformation.

Sequence and structural differences between enzyme and nonenzyme homologs

To improve our understanding of the evolution of novel functions, we performed a sequence, structural, and functional analysis of homologous enzymes and nonenzymes of known three-dimensional structure. In most examples identified, the nonenzyme is derived from an ancestral catalytic precursor (as opposed to the reverse evolutionary scenario, nonenzyme to enzyme), and the active site pocket has been disrupted in some way, owing to the substitution of critical catalytic residues and/or steric interactions that impede substrate binding and catalysis. Pairwise sequence identity is typically insignificant, and almost one-half of the enzyme and nonenzyme pairs do not share any similarity in function. Heterooligomeric enzymes comprising homologous subunits in which one chain is catalytically inactive and enzyme polypeptides that contain internal catalytic and noncatalytic duplications of an ancient enzyme domain are also discussed.

"@-Tides": the 1,2-dihydro-3(6H)-pyridinone unit as a beta-strand mimic

The cyclic amino acid surrogate 1 was designed to mimic the extended conformation of a peptide unit and to provide hydrogen bond donor and acceptor functions conducive to beta-sheet formation. A convenient synthesis of this unit and solution and solid-phase methods for its incorporation into an oligomer alternating with peptide units have been devised. The resulting "@-tides", as these oligomers have been designated, show a high propensity for self-association in comparison to oligopeptides; insights into the structure and dynamical properties of their antiparallel dimers have been obtained by NMR.

Metal ions modulate the plastic nature of Mycobacterium tuberculosis chaperonin-10

Chaperonin-10s possess a highly flexible segment of approximately 10 residues that covers their dome-like structure and closes the central cavity of the chaperonin assembly. The dome loop is believed to contribute to the plasticity of their oligomeric structure. We have exploited the presence of a single tryptophan residue occurring in the dome loop of Mycobacterium tuberculosis chaperonin-10 (cpn-10), and through intrinsic fluorescence measurements show that in the absence of metal ions, the tryptophan is almost fully solvent exposed at neutral pH. The dome loop, however, assumes a closed conformation in the presence of metal ions, or at low pH. These changes are fully reversed in the presence of chelating agents such as EDTA, confirming the role of cations in modulating the metastable states of cpn-10.