On the origin of synonymous codon usage divergence between thermophilic and mesophilic prokaryotes

Synonymous codon usage analysis between thermophilic and mesophilic prokaryotes has gained wide attention in recent years. Although it is known that thermophilic and mesophilic prokaryotes use different subset of synonymous codons, no reason for this difference is known so far. In the present communication, by analyzing a large number of thermophilic and mesophilic prokaryotes, we provide evidence that bias in the selection of synonymous codons between thermophilic and mesophilic prokaryotes is related to differential folding pattern of mRNA secondary structures. Moreover, we observe that error-minimizing property has significant influence in differentiating the synonymous codon usage between thermophilic and mesophilic prokaryotes. Biological implications of these results are discussed.     

Nonadditive Interactions in Protein Folding: The Zipper Model of Cytochrome <Emphasis Type="Italic">c</Emphasis>

Hydrogen exchange experiments (Krishna et al. in J. Mol. Biol. 359:1410, 2006) reveal that folding–unfolding of cytochrome c occurs along a defined pathway in a sequential, stepwise manner. The simplified zipper-like model involving nonadditive coupling is proposed to describe the classical “on pathway” folding–unfolding behavior of cytochrome c. Using free energy factors extracted from HX experiments, the model can predict and explain cytochrome c behavior in spectroscopy studies looking at folding equilibria and kinetics. The implications of the proposed model are discussed for such problems as classical pathway vs. energy landscape conceptions, structure and function of a native fold, and interplay of secondary and tertiary interactions.     

Consequences of Domain Insertion on the Stability and Folding Mechanism of a Protein

SlyD, the sensitive-to-lysis protein from Escherichia coli, consists of two domains. They are not arranged successively along the protein chain, but one domain, the “insert-in-flap” (IF) domain, is inserted internally as a guest into a surface loop of the host domain, which is a prolyl isomerase of the FK506 binding protein (FKBP) type. We used SlyD as a model to elucidate how such a domain insertion affects the stability and folding mechanism of the host and the guest domain. For these studies, the two-domain protein was compared with a single-domain variant SlyDΔIF, SlyD* without the chaperone domain (residues 1-69 and 130-165) in which the IF domain was removed and replaced by a short loop, as present in human FKBP12. Equilibrium unfolding and folding kinetics followed an apparent two-state mechanism in the absence and in the presence of the IF domain. The inserted domain decreased, however, the stability of the host domain in the transition region and decelerated its refolding reaction by about 10-fold. This originates from the interruption of the chain connectivity by the IF domain and its inherent instability. To monitor folding processes in this domain selectively, a Trp residue was introduced as fluorescent probe. Kinetic double-mixing experiments revealed that, in intact SlyD, the IF domain folds and unfolds about 1000-fold more rapidly than the FKBP domain, and that it is strongly stabilized when linked with the folded FKBP domain. The unfolding limbs of the kinetic chevrons of SlyD show a strong downward curvature. This deviation from linearity is not caused by a transition-state movement, as often assumed, but by the accumulation of a silent unfolding intermediate at high denaturant concentrations. In this kinetic intermediate, the FKBP domain is still folded, whereas the IF domain is already unfolded.     

Protein processing as a regulatory mechanism in the synthesis of the photosynthetic antenna in Chloroflexus

Chloroflexus aurantiacus can be induced to shift from respiratory to photosynthetic energy production by introducing light and/or lowering the oxygen concentration of a culture. After induction, cells synthesize bacteriochlorophyll and proteins for the formation of a functional photosynthetic apparatus. Bacteriochlorophyll is detectable within 2 h after induction. Chlorosome polypeptides are detected after 8–12 h. Two proteins, M_r 60,000 and M_r 47,000, are present in both induced and noninduced cells and react specifically with antibodies against chlorosome polypeptides. Immunological data suggest that these proteins (M_r 60,000 and 47,000) are polyproteins which are transcribed and translated in the dark. When cells are exposed to light or low oxygen tension these proteins are processed into functional polypeptides required in the assembly of the chlorosome. The reaction center polypeptide (M_r 26,000) appears to be part of a separate genetic control system.Dedicated to Prof. G. Drews on occasion of his 60th birthday     

Development of PLEX, a plasmid-based expression system for production of heterologous gene products by the gram-positive bacteria Streptococcus gordonii

While Escherichia coli expression systems have been widely utilized for the production of heterologous proteins, these systems have limitations with regard to the production of particular protein products, including poor expression, expression of insoluble proteins into inclusion bodies, and/or expression of a truncated product. Using the surface protein expression (SPEX) system, chromosomally integrated heterologous genes are expressed and secreted into media by the naturally competent gram-positive organism Streptococcus gordonii. After E. coli turned out to be an inappropriate expression system to produce sufficient quantities of intact product, we successfully utilized SPEX to produce the heterologous antigen BH4XCRR that is designed from sequences homologous to the S. pyogenes M-protein C-repeat region. To further enhance production of this product by S. gordonii, we sought to develop a novel system for the production and secretion of heterologous proteins. We observed that under various growth conditions, S. gordonii secreted high levels of a 172 kDa protein, which was identified by N-terminal sequence analysis as the glucosyltransferase GTF. Here we report on the development of a plasmid-based expression system, designated as PLEX, which we used to enhance production of BH4XCRR by S. gordonii. A region from the S. gordonii chromosome that contains the positive regulatory gene rgg, putative gtfG promoter, and gtfG secretion-signal sequence was cloned into the E. coli/Streptococcus shuttle plasmid pVA838. Additionally, the bh4xcrr structural gene was cloned into the same plasmid downstream and in-frame with rgg and gtfG. This plasmid construct was transformed into S. gordonii and BH4XCRR was detected in culture supernatants from transformants at greater concentrations than in supernatants from a SPEX strain expressing the same product. BH4XCRR was easily purified from culture supernatant using a scalable two-step purification process involving hydrophobic-interaction and gel-filtration chromatography.     

Expression of a Highly Toxic Protein, Bax, in Escherichia coli by Attachment of a Leader Peptide Derived from the GroES Cochaperone

Expression of the human apoptosis modulator protein Bax in Escherichia coli is highly toxic, resulting in cell lysis at very low concentrations (Asoh, S., et al., J. Biol. Chem. 273, 11384–11391, 1998). Attempts to express a truncated form of murine Bax in the periplasm by using an expression vector that attached the OmpA signal sequence to the protein failed to alleviate this toxicity. In contrast, attachment of a peptide based on a portion of the E. coli cochaperone GroES reduced Bax's toxicity significantly and allowed good expression. The peptide, which was attached to the N-terminus, included the amino acid sequence of the mobile loop of GroES that has been demonstrated to interact with the chaperonin, GroEL. Under normal growth conditions, expression of this construct was still toxic, but generated a small amount of detectable recombinant Bax. However, when cells were grown in the presence of 2% ethanol, which stimulated overproduction of the molecular chaperones GroEL and DnaK, toxicity was reduced and good overexpression occurred. Two-dimensional gel electrophoresis analysis showed that approximately 15-fold more GroES-loop-Bax was produced under these conditions than under standard conditions and that GroEL and DnaK were elevated approximately 3-fold.     

A Study on the Synthetic Characteristics of the Extracellular Polysaccharide (EPS) of Ganoderma lucidum Cultured in Batch Fermentation Using a Kinetic Model

The synthetic characteristics of the extracellular polysaccharide (EPS) of Ganoderma lucidum in batch fermentation were studied. The result showed that the production of EPS was partially growth-associated. The cell dry weight (CDW) and EPS reached 15.56 g·L⁻¹ and 3.02 g·L⁻¹, respectively. The yield of EPS to cell dry weight (Y_p/x) was 0.19. On the basis of the test results of batch fermentation, a kinetic model was proposed by using the Logistic equation for cell growth, the Luedeking–Piret equation for EPS production, and the Luedeking-piret-like equation for the consumption of glucose as substrate. The calculated results using these models were satisfactorily compared with the experimental data under various concentrations of glucose, and the average of relative errors was found to be not more than 5%. The kinetic model had practical guidance interesting in producing PES by Ganoderma lucidum.     

Evolution of a Protein-Folding Machine: Genomic and Evolutionary Analyses Reveal Three Lineages of the Archaeal hsp70(dnaK) Gene

The stress chaperone protein Hsp70 (DnaK) (abbreviated DnaK) and its co-chaperones Hsp40(DnaJ) (or DnaJ) and GrpE are universal in bacteria and eukaryotes but occur only in some archaea clustered in the order 5′-grpE-dnaK-dnaJ-3′ in a locus termed Locus I. Three structural varieties of Locus I, termed Types I, II, and III, were identified, respectively, in Methanosarcinales, in Thermoplasmatales and Methanothermobacter thermoautotrophicus, and in Halobacteriales. These Locus I types corresponded to three groups identified by phylogenetic trees of archaeal DnaK proteins including the same archaeal subdivisions. These archaeal DnaK groups were not significantly interrelated, clustering instead with DnaKs from three bacterial lineages, Methanosarcinales with Firmicutes, Thermoplasmatales and M. thermoautotrophicus with Thermotoga, and Halobacteriales with Actinobacteria, suggesting that the three archaeal types of Locus I were acquired by independent events of lateral gene transfer. These associations, however, lacked strong bootstrap support and were sensitive to dataset choice and tree-reconstruction method. Structural features of dnaK loci in bacteria revealed that Methanosarcinales and Firmicutes shared a similar structure, also common to most other bacterial groups. Structural differences were observed instead in Thermotoga compared to Thermoplasmatales and M. thermoautotrophicus, and in Actinobacteria compared to Halobacteriales. It was also found that the association between the DnaK sequences from Halobacteriales and Actinobacteria likely reflects common biases in their amino acid compositions. Although the loci structural features and the DnaK trees suggested the possibility of lateral gene transfer between Firmicutes and Methanosarcinales, the similarity between the archaeal and the ancestral bacterial loci favors the more parsimonious hypothesis that all archaeal sequences originated from a unique prokaryotic ancestor. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Stephen Freeland]     

Energy allocation for reproduction in a marsupial arboreal folivore,the common ringtail possum (Pseudocheirus peregrinus)

This study examines the annual energetics of a small folivorous marsupial, Pseudocheirus peregrinus. Particular attention was given to the energy and time allocated to reproduction by the females. Daily energy expenditure was measured directly using the doubly labelled water technique. Energy transferred to the young via the milk was estimated from information on milk composition and production. There was no significant seasonal variation in the energy expenditure or water influx of males or females. The mean daily energy expenditure of a 1-kg non-lactating adult ringtail possum was 615 kJ day^–1 or 2.2 times standard metabolic rate. Females showed significant changes in daily energy expenditure according to their reproductive status. Without the burden of lactation the total annual energy expenditure of an adult female was estimated as 212.4 MJ kg^–1 year^–1. The total annual energy expenditure of a female rearing two young was 247.5 MJ kg^–1 year^–1, with the late stage of lactation constituting the most energetically expensive period accounting for 30% of the total yearly energy expenditure during 24% of the time. Total metabolisable energy allocation during reproduction (22 MJ kg) was similar to estimates available for other herbivores, although, the peak metabolisable energy allocation during lactation (759 kJ day^–1) was lower than values available for other herbivores. The total energy requirement for reproduction (metabolisable energy plus potential energy exported to young via milk) suggests that the ringtail possum also has a relatively low overall energy investment in reproduction. It is suggested that the lactational strategy of the ringtail possum has been selected in order to spread the energy demands of reproduction over time due to constraints on the rate of energy intake imposed by a leaf diet and/or to prolong the mother-young bond. The strategies a female ringtail possum may employ to achieve energy balance when faced with the energy demands of reproduction are discussed.     

Characterization of the Micromonospora rosaria pMR2 plasmid and development of a high G+C codon optimized integrase for site-specific integration

pMR2, an 11.1 kb plasmid was isolated from Micromonospora rosaria SCC2095, NRRL3718, and its complete nucleotide sequence determined. Analysis revealed 13 ORFs including homologs of a KorSA regulatory protein and TraB plasmid transfer protein found on other actinomycete plasmids. pMR2 contains att/int functions consisting of an integrase, an excisionase, and a putative plasmid attachment site (attP). The integrase gene contained a high frequency of codons rarely used in high G+C actinomycete coding regions. The gene was codon optimized for actinomycete codon usage to create the synthetic gene int-OPT. pSPRX740, containing an rpsL promoter and the att/int-OPT region, was introduced into Micromonospora halophytica var. nigra ATCC33088. Analysis of DNA flanking the pSPRX740 integration site confirmed site-specific integration into a tRNA(Phe) gene in the M. halopytica var. nigra chromosome. The pMR2 attP element and chromosomal attachment (attB) site contain a 63 bp region of sequence identity overlapping the 3' end of the tRNA(Phe) gene. Plasmids comprising the site-specific att/int-OPT functions of pMR2 can be used to integrate genes into the chromosome of actinomycetes with an appropriate tRNA gene. The development of an integrative system for Micromonospora will expand our ability to study antibiotic biosynthesis in this important actinomycete genus.     

A Simple Alternative Approach to Assessing the Fate of Absorbed Light Energy Using Chlorophyll Fluorescence

We propose a simplified alternative method for quantifying the partitioning of excitation energy between photochemistry, fluorescence and thermal dissipation. This alternative technique uses existing well-defined quantum efficiencies such as Phi(PS II), leaving no 'excess' efficiency unaccounted for, effectively separates regulated and constitutive thermal dissipation processes, does not require the use of F(o) and F'(o) measurements and gives very similar results to the method proposed by Kramer et al. [(2004) Photosynth Res 79: 209-218]. We demonstrate the use of the technique using chlorophyll fluorescence measurements in grapevine leaves and observe a high dependence on thermal dissipation processes (up to 75%) at both high light and low temperature.     

High Temperature Stress Resistance of Escherichia coli Induced by a Tobacco Class I Low Molecular Weight Heat-Shock Protein

TLHS1 is a class I low molecular weight heat-shock protein (LMW HSP) of tobacco (Nicotiana tabacum). For a functional study of TLHS1, a recombinant DNA coding for TLHS1 with a hexahistidine tag at the aminoterminus was constructed and expressed in Escherichia coli. An expressed fusion protein, H₆TLHS1, was purified using a Ni²⁺ affinity column and a Sephacryl S400 HR column. A polyclonal antibody against H₆TLHS1 was produced to follow the fate of H₆TLHS1 in E. coli. The fusion protein in E. coli maintained its solubility at a temperature of up to 90°C and most of the proteins in the E. coli cell lysate with H₆TLHS1 were prevented from thermally induced aggregation at up to 90°C. We compared the viability of E. coli cells expressing H₆TLHS1 to the E. coli cells without H₆TLHS1 at a temperature of 50°C. After 8 h of high temperature treatment, E. coli cells with H₆TLHS1 survived about three thousand times more than the bacterial cells without H₆TLHS1. These results showed that a plant class I LMW HSP, TLHS1, can protect proteins of E. coli from heat denaturation, which could lead to a higher survival rate of the bacterial cells at high temperature.     

Protein requirement of the prawn Marsupenaeus japonicus estimated by a factorial method

The protein requirement to give maximum body protein retention in the prawn Marsupenaeus japonicus was assessed by determining both daily protein needed for maintenance (M) and daily body protein increment (G) when the juvenile prawn was maintained on a diet containing high quality protein. The body protein increment was obtained by determining carcass nitrogen increment when the prawn was fed on casein-based diets. The protein required for maintenance was estimated by regressing weight gains of the prawn on the diets containing graded levels of casein. True daily increase or retention of body protein in the prawn corresponded to the sum of G and M, and it was 3.2 g protein per kg body weight per day. The dietary protein requirement of juvenile M. japonicus for maximum body protein retention was suggested to be about 10 g per kg body weight per day providing that the prawn was fed the casein-based diet containing 50% crude protein (net protein utilization = 32) at the feeding level of 2%.     

Analysis of the flt-1 Gene Encoding a ECM Protein, Flectin, in Caenorhabditis elegans

Flectin is a new type of extracellular matrix protein and its function was suggested to provide a micro-environment of great elasticity. The C. elegans genome database revealed the presence of a flectin homologue, flt-1, which shows approximately 40% similarity (20% identity) to chick flectin. Here we propose a new gene structure for the flt-1 based on our experiments and the partial cDNA clones obtained from Y. Kohara and further suggest that the previous gene prediction is incorrect. FLT-1 is shown to be expressed in various neurons, hypodermal cells, distal tip cells and vulva epithelial cells. Immunostaining results with anti-FLT-1 antibody, further confirm the FLT-1 expression in vulva epithelial cells. The lipophilic dye, DiI, was used to identify the head neurons expressing GFP and results indicated that none of the head neurons expressing GFP are the 6 chemosensory neurons. In order to determine the function of flt-1 gene, RNA-mediated interference (RNAi) experiments were conducted.     

Evidence for the production of a novel proteinaceous hemolytic exotoxin by dinoflagellate Alexandrium taylori

We found that a whole cell suspension of Alexandrium taylori, which is toxic to Artemia, causes species-specific hemolysis against mammalian erythrocytes. Among the erythrocytes tested, rabbit and guinea-pig erythrocytes were highly sensitive, but human, sheep, and cattle erythrocytes were insensitive. The cell-free culture supernatant also showed potent hemolytic activity toward rabbit erythrocytes as seen in whole cell suspension. The hemolytic activity in the culture medium gradually increased with increase in cell number during exponential growth phase, and relatively high activity was maintained even after reaching the death phase. These results suggest that the hemolytic substance is actively released into the medium from A. taylori cells rather than simple leakage from ruptured or dead cells, and a part of them are steadily accumulated in the medium during the algal growth. Chemical characterization with ultrafiltration and trypsin-treatment suggested that the hemolytic substance released into the medium is protein-like compound with molecular weight more than 10,000 Da. The ammonium sulfate precipitated fraction obtained from the cell-free supernatant of A. taylori showed cytotoxic effect on HeLa cells as well as the hemolytic activity in a similar concentration range on a protein content basis. Our results suggest that A. taylori produces a novel proteinaceous hemolytic exotoxin.     

Requirement of the SecB chaperone for export of a non-secretory polypeptide in Escherichia coli

Summary The SecB protein of Escherichia coli is a cytosolic component of the export machinery which can prevent some precursors from prematurely folding into export-incompatible conformations by binding to the newly synthesised polypeptide. The feature(s) of target proteins recognised by SecB, however, are unclear and have been a matter of controversy. Also, it has not been asked if binding of SecB is specific for secretory proteins. We demonstrate here that a non-secretory polypeptide, a fragment of a tail fiber protein of phage T4, fused to the signal peptide of the outer membrane protein OmpA has a very strong SecB requirement for export and that the signal peptide itself cannot, at least not alone, be responsible for this action of SecB. The data reported, together with those of the literature, suggest that SecB recognizes the polypeptide backbone of the target protein.     

Suppression of the Escherichia coli dnaA46 mutation by a mutation in trxA, the gene for thioredoxin

Summary The dasC mutation, an extragenic suppressor of dnaA46, was mapped by P1 transduction near the rep, trxA, rho region of the Escherichia coli chromosome. The dasC mutation could not be separated from trxA by P1 transduction indicating that dasC and trxA are allelic. Multicopy plasmids containing an intact trxA gene were able to reverse the suppressive effect of the dasC mutation on the dnaA46 mutation. Introduction of a frameshift mutation into the cloned trxA coding region abolished the ability of these recombinant plasmids to reverse the suppressive effect. These results indicate that dasC is allelic with trxA, the gene encoding thioredoxin.