The Escherichia coli heat shock gene htpY: mutational analysis, cloning, sequencing, and transcriptional regulation

Sulfur Amino Acids: From Prebiotic Chemistry to Biology and Vice Versa

Two sulfur-containing amino acids are included in the list of the 20 classical protein amino acids. A methionine residue is introduced at the start of the synthesis of all current proteins. Cysteine, thanks to its thiol function, plays an essential role in a very large number of catalytic sites. Here we present what is known about the prebiotic synthesis of these two amino acids and homocysteine, and we discuss their introduction into primitive peptides and more elaborate proteins.

1 Introduction

2 Sulfur Sources

3 Prebiotic Synthesis of Cysteine

4 Prebiotic Synthesis of Methionine

5 Homocysteine and Its Thiolactone

6 Methionine and Cystine in Proteins

7 Prebiotic Scenarios Using Sulfur Amino Acids

8 Introduction of Cys and Met in the Genetic Code

9 Conclusion

Identification of a Cryptic Bacterial Promoter in Mouse (mdr1a) P-Glycoprotein cDNA

The efflux transporter P-glycoprotein (P-gp) is an important mediator of various pharmacokinetic parameters, being expressed at numerous physiological barriers and also in multidrug-resistant cancer cells. Molecular cloning of homologous cDNAs is an important tool for the characterization of functional differences in P-gp between species. However, plasmids containing mouse mdr1a cDNA display significant genetic instability during cloning in bacteria, indicating that mdr1a cDNA may be somehow toxic to bacteria, allowing only clones containing mutations that abrogate this toxicity to survive transformation. We demonstrate here the presence of a cryptic promoter in mouse mdr1a cDNA that causes mouse P-gp expression in bacteria. This expression may account for the observed toxicity of mdr1a DNA to bacteria. Sigma 70 binding site analysis and GFP reporter plasmids were used to identify sequences in the first 321 bps of mdr1a cDNA capable of initiating bacterial protein expression. An mdr1a M107L cDNA containing a single residue mutation at the proposed translational start site was shown to allow sub-cloning of mdr1a in E. coli while retaining transport properties similar to wild-type P-gp. This mutant mdr1a cDNA may prove useful for efficient cloning of mdr1a in E. coli.

Specificity and promiscuity at the branch point in gentamicin biosynthesis

Gentamicin C complex is a mixture of aminoglycoside antibiotics used to treat severe Gram-negative bacterial infections. We report here key features of the late-stage biosynthesis of gentamicins. We show that the intermediate gentamicin X2, a known substrate for C-methylation at C-6' to form G418 catalyzed by the radical SAM-dependent enzyme GenK, may instead undergo oxidation at C-6' to form an aldehyde, catalyzed by the flavin-linked dehydrogenase GenQ. Surprisingly, GenQ acts in both branches of the pathway, likewise oxidizing G418 to an analogous ketone. Amination of these intermediates, catalyzed mainly by aminotransferase GenB1, produces the known intermediates JI-20A and JI-20B, respectively. Other pyridoxal phosphate-dependent enzymes (GenB3 and GenB4) act in enigmatic dehydroxylation steps that convert JI-20A and JI-20B into the gentamicin C complex or (GenB2) catalyze the epimerization of gentamicin C2a into gentamicin C2.

Phenotype of htgA (mbiA), a recently evolved orphan gene of Escherichia coli and Shigella, completely overlapping in antisense to yaaW

Overlapping embedded genes, such as htgA/yaaW, are assumed to be rare in prokaryotes. In Escherichia coli O157:H7, gfp fusions of both promoter regions revealed activity and transcription start sites could be determined for both genes. Both htgA and yaaW were inactivated strand specifically by introducing a stop codon. Both mutants exhibited differential phenotypes in biofilm formation and metabolite levels in a nontargeted analysis, suggesting that both are functional despite YaaW but not HtgA could be expressed. While yaaW is distributed all over the Gammaproteobacteria, an overlapping htgA-like sequence is restricted to the Escherichia-Klebsiella clade. Full-length htgA is only present in Escherichia and Shigella, and htgA showed evidence for purifying selection. Thus, htgA is an interesting case of a lineage-specific, nonessential and young orphan gene.

CAMBer: an approach to support comparative analysis of multiple bacterial strains

BACKGROUND

There is a large amount of inconsistency in gene structure annotations of bacterial strains. This inconsistency is a frustrating impedance to effective comparative genomic analysis of bacterial strains in promising applications such as gaining insights into bacterial drug resistance.

RESULTS

Here, we propose CAMBer as an approach to support comparative analysis of multiple bacterial strains. CAMBer produces what we called multigene families. Each multigene family reveals genes that are in one-to-one correspondence in the bacterial strains, thereby permitting their annotations to be integrated. We present results of our method applied to three human pathogens: Escherichia coli, Mycobacterium tuberculosis and Staphylococcus aureus.

CONCLUSIONS

As a result, more accurate and more comprehensive annotations of the bacterial strains can be produced.

Late steps of ribosome assembly in E. coli are sensitive to a severe heat stress but are assisted by the HSP70 chaperone machine

The late stages of 30S and 50S ribosomal subunits biogenesis have been studied in a wild-type (wt) strain of Escherichia coli (MC4100) subjected to a severe heat stress (45–46°C). The 32S and 45S ribosomal particles (precursors to 50S subunits) and 21S ribosomal particles (precursors to 30S subunits) accumulate under these conditions. They are authentic precursors, not degraded or dead-end particles. The 21S particles are shown, by way of a modified 3′5′ RACE procedure, to contain 16S rRNA unprocessed, or processed at its 5′ end, and not at the 3′ end. This implies that maturation of 16S rRNA is ordered and starts at its 5′-terminus, and that the 3′-terminus is trimmed at a later step. This observation is not limited to heat stress conditions, but it also can be verified in bacteria growing at a normal temperature (30°C), supporting the idea that this is the general pathway. Assembly defects at very high temperature are partially compensated by plasmid-driven overexpression of the DnaK/DnaJ chaperones. The ribosome assembly pattern in wt bacteria under a severe heat stress is therefore reminiscent of that observed at lower temperatures in E. coli mutants lacking the chaperones DnaK or DnaJ.

Functional cyanobacterial beta-carboxysomes have an absolute requirement for both long and short forms of the CcmM protein

Carboxysomes are an essential part of the cyanobacterial CO2-concentrating mechanism, consisting of a protein shell and an interior of Rubisco. The beta-carboxysome shell protein CcmM forms two peptides via a proposed internal ribosomal entry site (IRES) within the ccmM transcript in Synechococcus PCC7942. The abundant short form (35 kD, M35) consists of Rubisco small subunit-like repeats and binds Rubisco. The lower abundance long form (58 kD, M58) also contains a gamma-carbonic anhydrase-like domain, which binds the carboxysomal carbonic anhydrase, CcaA. We examined whether these CcmM forms arise via an IRES or by other means. Mutations of a putative internal start codon (GTG) and Shine-Dalgarno sequence within ccmM, along with a gene coding for M35 alone, were examined in the high-CO2-requiring (HCR) carboxysomeless mutant, DeltaccmM. Expression of wild-type ccmM in DeltaccmM restored the wild-type phenotype, while mutation of putative start and Shine-Dalgarno sequences led to as much as 20-fold reduction in M35 content with no recovery from HCR phenotype. These cells also contained small electron-dense structures. Cells producing little or no M58, but sufficient M35, were found to contain large electron-dense structures, no CcaA, and had a HCR phenotype. Large subcellular aggregates can therefore form in the absence of M58, suggesting a role for M35 in internal carboxysome Rubisco packing. The results confirm that M35 is independently translated via an IRES within ccmM. Importantly, the data reveal that functional carboxysomes require both M35 and M58 in sufficient quantities and with a minimum stoichiometry of close to 1:1.

The origin of a novel gene through overprinting in Escherichia coli

BACKGROUND

Overlapped genes originate by a) loss of a stop codon among contiguous genes coded in different frames; b) shift to an upstream initiation codon of one of the contiguous genes; or c) by overprinting, whereby a novel open reading frame originates through point mutation inside an existing gene. Although overlapped genes are common in viruses, it is not clear whether overprinting has led to new genes in prokaryotes.

RESULTS

Here we report the origin of a new gene through overprinting in Escherichia coli K12. The htgA gene coding for a positive regulator of the sigma 32 heat shock promoter arose by point mutation in a 123/213 phase within an open reading frame (yaaW) of unknown function, most likely in the lineage leading to E. coli and Shigella sp. Further, we show that yaaW sequences coding for htgA genes have a slower evolutionary rate than those lacking an overlapped htgA gene.

CONCLUSION

While overprinting has been shown to be rather frequent in the evolution of new genes in viruses, our results suggest that this mechanism has also contributed to the origin of a novel gene in a prokaryote. We propose the term janolog (from Jano, the two-faced Roman god) to describe the homology relationship that holds between two genes when one originated through overprinting of the other. One cannot dismiss the possibility that at least a small fraction of the large number of novel ORPhan genes detected in pan-genome and metagenomic studies arose by overprinting.

Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress

The heat-shock response (HSR), a universal cellular response to heat, is crucial for cellular adaptation. In Escherichia coli, the HSR is mediated by the alternative sigma factor, sigma32. To determine its role, we used genome-wide expression analysis and promoter validation to identify genes directly regulated by sigma32 and screened ORF overexpression libraries to identify sigma32 inducers. We triple the number of genes validated to be transcribed by sigma32 and provide new insights into the cellular role of this response. Our work indicates that the response is propagated as the regulon encodes numerous global transcriptional regulators, reveals that sigma70 holoenzyme initiates from 12% of sigma32 promoters, which has important implications for global transcriptional wiring, and identifies a new role for the response in protein homeostasis, that of protecting complex proteins. Finally, this study suggests that the response protects the cell membrane and responds to its status: Fully 25% of sigma32 regulon members reside in the membrane and alter its functionality; moreover, a disproportionate fraction of overexpressed proteins that induce the response are membrane localized. The intimate connection of the response to the membrane rationalizes why a major regulator of the response resides in that cellular compartment.

Long stretches of sequential and identical serine or alanine codons are compatible with an efficient full-length protein expression in Escherichia coli

The Schistosoma japonicum glutathione S-transferase (GST) recombinant cDNAs, carrying blocks of sequential and identical triplets, consisting of 15-30-45 GCT (Ala) codons or 15-30 and also up to 75 AGC (Ser) codons, are expressed efficiently in an Escherichia coli system in the form of full-length protein chains, as detected by Coomassie-stained SDS-polyacrylamide gels, and soluble fusion proteins are purified by GSH-affinity chromatography. High expression levels and high yields of purified recombinant proteins are achieved. The efficient protein expression is independent of the molecular context and position of the polySer/polyAla string inserted into the GST carrier (near the part of the gene encoding the N- or the C-terminus). These findings suggest that E. coli is a powerful biological system to express foreign genes carrying long stretches coding for Ser- or Ala-rich domains, which are not uncommon in eukaryotic proteins. Moreover, data reported here show that the negative effect of sequential serine codons on protein expression in bacteria, previously reported in the literature, is not a general phenomenon.

The role of the DIF motif of the DnaJ (Hsp40) co-chaperone in the regulation of the DnaK (Hsp70) chaperone cycle

To perform effectively as a molecular chaperone, DnaK (Hsp70) necessitates the assistance of its DnaJ (Hsp40) co-chaperone partner, which efficiently stimulates its intrinsically weak ATPase activity and facilitates its interaction with polypeptide substrates. In this study, we address the function of the conserved glycine- and phenylalanine-rich (G/F-rich) region of the Escherichia coli DnaJ in the DnaK chaperone cycle. We show that the G/F-rich region is critical for DnaJ co-chaperone functions in vivo and that despite a significant degree of sequence conservation among the G/F-rich regions of Hsp40 homologs from bacteria, yeast, or humans, functional complementation in the context of the E. coli DnaJ is limited. Furthermore, we found that the deletion of the whole G/F-rich region is mirrored by mutations in the conserved Asp-Ile/Val-Phe (DIF) motif contained in this region. Further genetic and biochemical analyses revealed that this amino acid triplet plays a critical role in regulation of the DnaK chaperone cycle, possibly by modulating a crucial step subsequent to DnaK-mediated ATP hydrolysis.

Analysis of the Escherichia coli Alp phenotype: heat shock induction in ssrA mutants

The major phenotypes of lon mutations, UV sensitivity and overproduction of capsule, are due to the stabilization of two substrates, SulA and RcsA. Inactivation of transfer mRNA (tmRNA) (encoded by ssrA), coupled with a multicopy kanamycin resistance determinant, suppressed both lon phenotypes and restored the rapid degradation of SulA. This novel protease activity was named Alp but was never identified further. We report here the identification, mapping, and characterization of a chromosomal mutation, faa (for function affecting Alp), that leads to full suppression of a Deltalon ssrA::cat host and thus bypasses the requirement for multicopy Kan(r); faa and ssrA mutants are additive in their ability to suppress lon mutants. The faa mutation was mapped to the C terminus of dnaJ(G232); dnaJ null mutants have similar effects. The identification of a lon suppressor in dnaJ suggested the possible involvement of heat shock. We find that ssrA mutants alone significantly induce the heat shock response. The suppression of UV sensitivity, both in the original Alp strain and in faa mutants, is reversed by mutations in clpY, encoding a subunit of the heat shock-induced ClpYQ protease that is known to degrade SulA. However, capsule synthesis is not restored by clpY mutants, probably because less RcsA accumulates in the Alp strain and because the RcsA that does accumulate is inactive. Both ssrA effects are partially relieved by ssrA derivatives encoding protease-resistant tags, implicating ribosome stalling as the primary defect. Thus, ssrA and faa each suppress two lon mutant phenotypes but by somewhat different mechanisms, with heat shock induction playing a major role.

Changes in lipopolysaccharide structure induce the σE-dependent response of Escherichia coli

The envelope of Escherichia coli is composed of an asymmetric lipid bilayer containing lipopolysaccharide, phospholipid and outer membrane proteins (OMPs). Physical and chemical stresses impact on the integrity of the outer membrane envelope and trigger the sigma(E)-dependent response, whereby E. coli activates the expression of genes that increase its capacity for folding OMPs and synthesizing lipopolysaccharide (LPS). While it has already been appreciated that misfolded OMPs induce the sigma(E) response, a role for LPS in activating this pathway was hitherto unknown. Here we show that ammonium metavandate (NH4VO3) induces multiple changes in E. coli LPS structure and activates the sigma(E)-dependent response without altering OMP. One such NH4VO3-mediated LPS decoration, the CrcA/PagP-catalysed addition of palmitate to lipid A, appeared to be alone sufficient to activate transcription at sigma(E)-dependent promoters. Furthermore, reduced acylation of LPS, caused by htrB or msbB mutations, also resulted in a constitutive expression of the sigma(E) regulon above wild-type levels. Production of these aberrant outer membrane lipids did not noticeably affect the composition or the amount of OMPs. A model is proposed whereby structural intermediates of the LPS biosynthetic pathway or modified LPS molecules may function as signals that activate the sigma(E) response.

Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea

We have addressed the distribution and abundance of 75 transcription factor (TF) families in complete genomes from 90 different bacterial and archaeal species. We found that the proportion of TFs increases with genome size. The deficit of TFs in some genomes might be compensated by the presence of proteins organizing and compacting DNA, such as histone-like proteins. Nine families are represented in all the bacteria and archaea we analyzed, whereas 17 families are specific to bacteria, providing evidence for regulon specialization at an early stage of evolution between the bacterial and archeal lineages. Ten of the 17 families identified in bacteria belong exclusively to the proteobacteria defining a specific signature for this taxonomical group. In bacteria, 10 families are lost mostly in intracellular pathogens and endosymbionts, while 9 families seem to have been horizontally transferred to archaea. The winged helix-turn-helix (HTH) is by far the most abundant structure (motif) in prokaryotes, and might have been the earliest HTH motif to appear as shown by its distribution and abundance in both bacterial and archaeal cellular domains. Horizontal gene transfer and lineage-specific gene losses suggest a progressive elimination of TFs in the course of archaeal and bacterial evolution. This analysis provides a framework for discussing the selective forces directing the evolution of the transcriptional machinery in prokaryotes.

Chaperone properties of Escherichia coli thioredoxin and thioredoxin reductase

Thioredoxin, thioredoxin reductase and NADPH form the thioredoxin system and are the major cellular protein disulphide reductase. We report here that Escherichia coli thioredoxin and thioredoxin reductase interact with unfolded and denatured proteins, in a manner similar to that of molecular chaperones that are involved in protein folding and protein renaturation after stress. Thioredoxin and/or thioredoxin reductase promote the functional folding of citrate synthase and alpha-glucosidase after urea denaturation. They also promote the functional folding of the bacterial galactose receptor, a protein without any cysteines. Furthermore, redox cycling of thioredoxin/thioredoxin reductase in the presence of NADPH and cystine stimulates the renaturation of the galactose receptor, suggesting that the thioredoxin system functions like a redox-powered chaperone machine. Thioredoxin reductase prevents the aggregation of citrate synthase under heat-shock conditions. It forms complexes that are more stable than those formed by thioredoxin with several unfolded proteins such as reduced carboxymethyl alpha-lactalbumin and unfolded bovine pancreatic trypsin inhibitor. These results suggest that the thioredoxin system, in addition to its protein disulphide isomerase activity possesses chaperone-like properties, and that its thioredoxin reductase component plays a major role in this function.

Specificity of elongation factor EF-TU for hydrophobic peptides

The elongation factor EF-Tu carries aminoacyl-tRNAs to the A-site of the ribosome during the elongation process of protein biosynthesis. We, and others, have recently reported that the Escherichia coli EF-Tu interacts with unfolded and denatured proteins and behaves like a chaperone in protein folding and protection against protein thermal denaturation. In this study, we have identified EF-Tu binding sites in protein substrates by screening cellulose-bound peptides scanning the sequences of several proteins. The binding motifs recognized by EF-Tu in protein substrates are also recognized by the chaperone DnaK and mainly consist of hydrophobic clusters. EF-Tu interacts as efficiently as DnaK with the membrane spanning sequence of the membrane protein phospholemman and with the signal sequence of alkaline phosphatase. It interacts less efficiently with several other hydrophobic clusters of lysozyme and alkaline phosphatase, which are also DnaK substrates and fails to bind to several DnaK binding sites. Our results suggest that EF-Tu, like DnaK, interacts albeit more weakly with the hydrophobic regions of substrate protein and are consistent with the hypothesis that it possesses chaperone properties.

Interaction of the conserved region 4.2 of sigma(E) with the RseA anti-sigma factor

Esigma(E) RNA polymerase transcribes a regulon of folding factors for the bacterial envelope and is induced by physical and chemical stresses. The RseA anti-sigma factor inhibits the activity of Esigma(E) RNA polymerase. It is shown here that the N-terminal portion of sigma(E), residues 1-153, binds core RNA polymerase. RseA interacts with residues 154-191 of sigma(E), a site that is homologous to region 4, the sigma factor binding site for promoter DNA. Mutations that reduce transcription of Esigma(E) RNA polymerase map to sigma(E) residues 178, 181, and 183. Variant sigma(E) proteins with amino acid substitutions at residues 178, 181, or 183 do not associate with RseA. A regulatory mechanism is proposed whereby RseA binds to a C-terminal peptide of sigma(E) and inhibits the transcription of Esigma(E) RNA polymerase by blocking promoter recognition.

Proteome analysis in the study of the bacterial heat-shock response

In recent years, it has become clear that, in addition to the regulation of the expression of specific genes, there are global regulatory systems that control the simultaneous expression of a large number of genes in response to a variety of environmental stresses. The first of these global control systems, and of substantial importance, is the heat-shock response. The heat-shock response is characterized by the induction of a large set of proteins (heat-shock proteins-HSPs) upon shifts to higher temperature and upon exposure to conditions in which proteins are denatured (i.e., alcohols, heavy metals). The heat-shock response is universal and many of the heat-shock proteins are highly conserved among species. In bacteria, the heat-shock response has been studied extensively in several Gram-positive bacteria (Bacillus subtilis) and in the Gram-negative bacteria (i.e., Escherichia coli, Agrobacterium tumefaciens). The first recognition of the molecular abundance of the bacterial heat-shock proteins took place with the introduction of high-resolution two-dimensional polyacrylamide gels (2D gels) to analyze complex mixtures of cellular proteins. Two-dimensional gels, followed by mass spectrometry, were used to define the heat-shock stimulons in several bacteria, and to study the regulatory elements that control the heat-shock response. Here, we review the heat-shock response and its regulation in bacteria. The review will emphasize the use of proteome analysis in the study of this response, and will point out those open questions that can be investigated with proteomics, including mass spectrometry techniques.

Chaperone-like properties of lysophospholipids

Lysophospholipids are metabolic intermediates in phospholipid turnover, detergent molecules with membrane-modulating effects, and multifunctional cellular growth factors in eukaryotic cells. In bacterial cells, lysophospholipids are mostly found in the form of lysophosphatidylethanolamine. We show that a heat shock from 30 to 42 degrees C increases four-fold the Escherichia coli pool of lysophosphoethanolamine and that lysophospholipids display chaperone-like properties. Lysophosphatidylethanolamine, like molecular chaperones such as DnaK, promotes the functional folding of citrate synthase and alpha-glucosidase after urea denaturation. Like chaperones, lysophophatidylethanolamine, lysophosphatidylcholine, lysophosphatidylinositol and lysophosphatidic acid prevent the aggregation of citrate synthase at 42 degrees C. The renaturation and solubilisation of proteins by lysophospholipids occur at micromolar concentrations of these compounds, close to their critical micellar concentration. Furthermore, lysophosphatidylethanolamine is much more efficient than other detergents tested for the renaturation and solubilisation of citrate synthase. In contrast with lysophospholipids, phosphatidylethanolamine and phosphatidylcholine are not able to promote citrate synthase folding nor to prevent its aggregation at 42 degrees C. The chaperone-like properties of lysophospholipids suggest that, in addition to their known functions, they might affect the structure and function of hydrophilic proteins.

EcfE, a new essential inner membrane protease: its role in the regulation of heat shock response in Escherichia coli

We have identified a new protease in Escherichia coli, which is required for its viability under normal growth conditions. This protease is anchored in the inner membrane and the gene encoding it has been named ecfE, since it is transcribed by Esigma(E) polymerase. Multicopy expression of the ecfE gene was found to turn down expression of both Esigma(E)- and Esigma(32)-transcribed promoters. Purified EcfE degrades both heat shock sigma factors RpoE and RpoH in vitro. EcfE has a zinc binding domain at the N-terminus, a PDZ-like domain in the middle and a highly conserved tripeptide, LDG, at the C-terminus. These features are characteristic of members of a new class of proteases whose activity occurs close to the inner membrane or within the inner membrane. Temperature-sensitive mutants of this gene were isolated mapping to the catalytic site and other domains that exhibited constitutively elevated levels of both heat shock regulons.

Characterization of the Escherichia coli sigma E regulon

Escherichia coli responds to the accumulation of misfolded proteins by inducing the transcription of heat shock genes. Efinal sigma(E) RNA polymerase controls one of the two heat shock regulons of E. coli. This regulon is activated upon accumulation of misfolded polypeptides in the double membrane envelope of E. coli. final sigma(E) (RpoE) is a member of the extracytoplasmic function subfamily of sigma factors. Here we asked how many genes are activated by Efinal sigma(E) RNA polymerase and what is the identity of these genes. Using two independent genetic approaches, 20 E. coli promoters were identified which activate reporter gene transcription in a final sigma(E)-dependent manner. In all cases examined, a canonical final sigma(E) binding site could be revealed upon mapping transcriptional start sites. 10 identified promoters activated the transcription of previously identified genes with four genes acting directly on the folding of E. coli envelope proteins (dsbC, fkpA, skp, and surA). The remaining promoters transcribed genes that are presumed to encode hitherto unknown extracytoplasmic functions and were named ecf (ecfA-ecfM). Two of these ecf genes were found to be essential for E. coli growth.

Chaperone properties of bacterial elongation factor EF-G and initiation factor IF2

Elongation factor G(EF-G) and initiation factor 2 (IF2) are involved in the translocation of ribosomes on mRNA and in the binding of initiator tRNA to the 30 S ribosomal subunit, respectively. Here we report that the Escherichia coli EF-G and IF2 interact with unfolded and denatured proteins, as do molecular chaperones that are involved in protein folding and protein renaturation after stress. EF-G and IF2 promote the functional folding of citrate synthase and alpha-glucosidase after urea denaturation. They prevent the aggregation of citrate synthase under heat shock conditions, and they form stable complexes with unfolded proteins such as reduced carboxymethyl alpha-lactalbumin. Furthermore, the EF-G and IF2-dependent renaturations of citrate synthase are stimulated by GTP, and the GTPase activity of EF-G and IF2 is stimulated by the permanently unfolded protein, reduced carboxymethyl alpha-lactalbumin. The concentrations at which these chaperone-like functions occur are lower than the cellular concentrations of EF-G and IF2. These results suggest that EF-G and IF2, in addition to their role in translation, might be implicated in protein folding and protection from stress.

Polypeptide flux through bacterial Hsp70: DnaK cooperates with trigger factor in chaperoning nascent chains

A role for DnaK, the major E. coli Hsp70, in chaperoning de novo protein folding has remained elusive. Here we show that under nonstress conditions DnaK transiently associates with a wide variety of nascent and newly synthesized polypeptides, with a preference for chains larger than 30 kDa. Deletion of the nonessential gene encoding trigger factor, a ribosome-associated chaperone, results in a doubling of the fraction of nascent polypeptides interacting with DnaK. Combined deletion of the trigger factor and DnaK genes is lethal under normal growth conditions. These findings indicate important, partially overlapping functions of DnaK and trigger factor in de novo protein folding and explain why the loss of either chaperone can be tolerated by E. coli.

Linkage map of Escherichia coli K-12, edition 10: the traditional map

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.

A new heat-shock gene, ppiD, encodes a peptidyl-prolyl isomerase required for folding of outer membrane proteins in Escherichia coli

We have identified a new folding catalyst, PpiD, in the periplasm of Escherichia coli. The gene encoding PpiD was isolated as a multicopy suppressor of surA, a mutation which severely impairs the folding of outer membrane proteins (OMPs). The ppiD gene was also identified based on its ability to be transcribed by the two-component system CpxR-CpxA. PpiD was purified to homogeneity and shown to have peptidyl-prolyl isomerase (PPIase) activity in vitro. The protein is anchored to the inner membrane via a single transmembrane segment, and its catalytic domain faces the periplasm. In addition, we have identified by site-directed mutagenesis some of the residues essential for its PPIase activity. A null mutation in ppiD leads to an overall reduction in the level and folding of OMPs and to the induction of the periplasmic stress response. The combination of ppiD and surA null mutations is lethal. This is the first time two periplasmic folding catalysts have been shown to be essential. Another unique aspect of PpiD is that its gene is regulated by both the Cpx two-component system and the sigma32 heat shock factor, known to regulate the expression of cytoplasmic chaperones.

Chaperone properties of bacterial elongation factor EF-Tu

Elongation factor Tu (EF-Tu) is involved in the binding and transport of the appropriate codon-specified aminoacyl-tRNA to the aminoacyl site of the ribosome. We report herewith that the Escherichia coli EF-Tu interacts with unfolded and denatured proteins as do molecular chaperones that are involved in protein folding and protein renaturation after stress. EF-Tu promotes the functional folding of citrate synthase and alpha-glucosidase after urea denaturation. It prevents the aggregation of citrate synthase under heat shock conditions, and it forms stable complexes with several unfolded proteins such as reduced carboxymethyl alpha-lactalbumin and unfolded bovine pancreatic trypsin inhibitor. The EF-Tu.GDP complex is much more active than EF-Tu.GTP in stimulating protein renaturation. These chaperone-like functions of EF-Tu occur at concentrations that are at least 20-fold lower than the cellular concentration of this factor. These results suggest that EF-Tu, in addition to its function in translation elongation, might be implicated in protein folding and protection from stress.

GeneMark.hmm: new solutions for gene finding

The number of completely sequenced bacterial genomes has been growing fast. There are computer methods available for finding genes but yet there is a need for more accurate algorithms. The GeneMark. hmm algorithm presented here was designed to improve the gene prediction quality in terms of finding exact gene boundaries. The idea was to embed the GeneMark models into naturally derived hidden Markov model framework with gene boundaries modeled as transitions between hidden states. We also used the specially derived ribosome binding site pattern to refine predictions of translation initiation codons. The algorithm was evaluated on several test sets including 10 complete bacterial genomes. It was shown that the new algorithm is significantly more accurate than GeneMark in exact gene prediction. Interestingly, the high gene finding accuracy was observed even in the case when Markov models of order zero, one and two were used. We present the analysis of false positive and false negative predictions with the caution that these categories are not precisely defined if the public database annotation is used as a control.

The complete genome sequence of Escherichia coli K-12

The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.

Chaperone properties of the bacterial periplasmic substrate-binding proteins

Bacterial periplasmic substrate-binding proteins are initial receptors in the process of active transport across cell membranes and/or chemotaxis. Each of them binds a specific substrate (e.g. sugar, amino acid, or ion) with high affinity. For transport, each binding protein interacts with a cognate membrane complex consisting of two hydrophobic proteins and two subunits of a hydrophilic ATPase. For chemotaxis, binding proteins interact with specific membrane chemotaxis receptors. We report, herewith, that the oligopeptide-binding protein OppA of Escherichia coli, the maltose-binding protein MalE of E. coli, and the galactose-binding protein MglB of Salmonella typhimurium interact with unfolded and denatured proteins, such as the molecular chaperones that are involved in protein folding and protein renaturation after stress. These periplasmic substrate-binding proteins promote the functional folding of citrate synthase and alpha-glucosidase after urea denaturation. They prevent the aggregation of citrate synthase under heat shock conditions, and they form stable complexes with several unfolded proteins, such as reduced carboxymethyl alpha-lactalbumin and unfolded bovine pancreatic trypsin inhibitor. These chaperone-like functions are displayed by both the liganded and ligand-free forms of binding proteins, and they occur at binding protein concentrations that are 10-100-fold lower than their periplasmic concentration. These results suggest that bacterial periplasmic substrate-binding proteins, in addition to their function in transport and chemotaxis, might be implicated in protein folding and protection from stress in the periplasm.

DnaJ potentiates the interaction between DnaK and alpha-helical peptides

Molecular chaperones bind selectively to nascent, unfolded, misfolded, or aggregated polypeptides, and are involved in protein folding, protein targeting to membranes, and protein renaturation after stress. The DnaK chaperone of Escherichia coli is known to interact preferentially with positively charged hydrophobic peptides in an extended conformation. Accordingly, we show in the present study that DnaK has a low affinity for alpha-helical peptides. In the presence of its co-chaperone DnaJ and ATP, however, DnaK interacts more efficiently with alpha-helical peptides. This suggests that DnaJ triggers a conformational change in DnaK which improves its interaction with these peptides. The ability of the DnaK/DnaJ/GrpE chaperone machine to interact with alpha-helical peptides (which represent the most frequent secondary structure in proteins) should be an important part of its role in protein folding and renaturation.

Specificity of DnaK for arginine/lysine and effect of DnaJ on the amino acid specificity of DnaK

Molecular chaperones form a class of proteins that bind selectively to nascent, unfolded, misfolded, or aggregated polypeptides and are involved in protein folding, protein targeting to membranes, and protein renaturation after stress. Chaperones70, including the DnaK chaperone of Escherichia coli, interact specifically with peptides enriched in internal hydrophobic residues, with a preference for positively charged peptides. We previously reported that DnaK interacts with the hydrophobic amino acids Ile, Leu, Val, Ala, Phe, Trp, and Tyr. In the present study, we show that DnaK also possesses a specific binding site for the positively charged amino acids arginine and lysine. Furthermore, the binding of arginine and lysine to DnaK is strengthened when its hydrophobic binding sites are occupied. The specificity of DnaK for Arg/Lys is supported by DnaK-peptide binding studies; the homopolypeptides poly-Arg and poly-Lys interact with DnaK, contrasting with other hydrophilic homopolypeptides, and hydrophobic peptides interact more strongly with DnaK if they contain Arg/Lys at their N terminus. Interestingly, the cochaperone DnaJ attenuates the interaction of DnaK with hydrophobic amino acids while strengthening its interaction with arginine or lysine. The interaction of DnaK with both hydrophobic sequences and with arginine and lysine, and its modulation by DnaJ, may have important implications in both protein folding and protein insertion into membranes.

Combined effects of the signal sequence and the major chaperone proteins on the export of human cytokines in Escherichia coli

We have studied the export of two human proteins in the course of their production in Escherichia coli. The coding sequences of the granulocyte-macrophage colony-stimulating factor and of interleukin 13 were fused to those of two synthetic signal sequences to direct the human proteins to the bacterial periplasm. We found that the total amount of protein varies with the signal peptide-cytokine combination, as does the fraction of it that is soluble in a periplasmic extract. The possibility that the major chaperone proteins such as SecB and the GroEL-GroES and DnaK-DnaJ pairs are limiting factors for the export was tested by overexpressing one or the other of these chaperones concomitantly with the heterologous protein. The GroEL-GroES chaperone pair had no effect on protein production. Overproduction of SecB or DnaK plus DnaJ resulted in a marked increase of the quantity of human proteins in the periplasmic fraction, but this increase depends on the signal peptide-heterologous protein-chaperone association involved.

Multicopy plasmid suppression of stationary phase chaperone toxicity in Escherichia coli by phosphogluconate dehydratase and the N-terminus of DnaK

Overproduction of DnaK in Escherichia coli results in a bacteriocidal effect. This effect is most acute in stationary phase cells. A selection scheme was developed to isolate multicopy suppressors from an E. coli plasmid expression library, which overcome the stationary phase toxicity of excess DnaK. Two suppressor plasmids were recovered which contained inserts of 1.85 kb and 2.69 kb, respectively. Rearranged and deleted plasmid derivatives were constructed and used to further localize the suppressors. DNA sequence analysis demonstrated that one suppressor encoded phosphogluconate dehydratase (Edd) while the other suppressor encoded the N-terminal 237 amino acids of DnaK itself (DnaK'). Strains bearing the suppressor plasmids constitutively overproduced proteins with apparent masses of 66 kDa (Edd) and 37 kDa (DnaK') as determined by gel electrophoresis. Western blot analysis using polyclonal antisera specific for either Edd or DnaK confirmed the identity of these overproduced proteins. Suppression of DnaK toxicity was eliminated by the introduction of a + 1 frameshift mutation early in the respective coding regions of either of the two suppressors. These results suggest that suppressor gene translation plays a role in the mechanism of DnaK suppression.

A novel function of Escherichia coli chaperone DnaJ. Protein-disulfide isomerase

Molecular chaperones, protein-disulfide isomerases, and peptidyl prolyl cis-trans isomerases assist protein folding in both prokaryotes and eukaryotes. The DnaJ protein of Escherichia coli and the DnaJ-like proteins of eukaryotes are known as molecular chaperones and specific regulators of DnaK-like proteins and are involved in protein folding and renaturation after stress. In this study we show that DnaJ, like thioredoxin, protein-disulfide isomerase, and DsbA, possesses an active dithiol/disulfide group and catalyzes protein disulfide formation (oxidative renaturation of reduced RNase), reduction (reduction of insulin disulfides), and isomerization (refolding of randomly oxidized RNase). These results suggest that, in addition to its known function as a chaperone, DnaJ might be involved in controlling the redox state of cytoplasmic, membrane, or exported proteins.

An essential role for the Escherichia coli DnaK protein in starvation-induced thermotolerance, H2O2 resistance, and reductive division

During a 3-day period, glucose starvation of wild-type Escherichia coli produced thermotolerant, H2O2-resistant, small cells with a round morphology. These cells contained elevated levels of the DnaK protein, adjusted either for total protein or on a per-cell basis. Immunoprecipitation of [35S]methionine-labeled protein produced by such starving cells demonstrated that DnaK underwent continuous synthesis but at decreasing rates throughout this time. Glucose resupplementation of starving cells resulted in rapid loss of thermotolerance, H2O2 resistance, and the elevated DnaK levels. A dnaK deletion mutant, but not an otherwise isogenic wild-type strain, failed to develop starvation-induced thermotolerance or H2O2 resistance. The filamentous phenotype associated with DnaK deficiency was suppressed by cultivation in a defined glucose medium. When starved for glucose, the nonfilamentous and rod-shaped dnaK mutant strain failed to convert into the small spherical form typical of starving wild-type cells. The dnaK mutant retained the ability to develop adaptive H2O2 resistance during growth but not adaptive resistance to heat. Complementation of DnaK deficiency by using Ptac-regulated dnaK+ and dnaK+J+ expression plasmids confirmed a specific role for the DnaK molecular chaperone in these starvation-induced phenotypes.

The rpoE gene encoding the sigma E (sigma 24) heat shock sigma factor of Escherichia coli

Previous work has established that the transcription factor sigma E (sigma 24) is necessary for maintaining the induction of the heat shock response of Escherichia coli at high temperatures. We have identified the gene encoding sigma E using a genetic screen designed to isolate trans-acting mutations that abolish expression from either htrA or rpoHP3, two promoters recognized uniquely by sigma E-containing RNA polymerase. Such a screen was achieved by transducing strains carrying a single copy of either phtrA-lacZ or rpoHP3-lacZ fusions with mutagenized bacteriophage P1 lysates and screening for Lac- mutant colonies at 22 degrees C. Lac- mutants were subsequently tested for inability to grow at 43 degrees C (Ts- phenotype). Only those Lac- Ts- mutants that were unable to accumulate heat shock proteins at 50 degrees C were retained for further characterization. In a complementary approach, those genes which when cloned on a multicopy plasmid led to higher constitutive expression of the sigma E regulon were characterized and mapped. Both approaches identified the same gene, rpoE, mapping at 55.5 min on the E.coli genetic map and encoding a polypeptide of 191 amino acid residues. The wild-type and a mutant rpoE gene products were over-expressed and purified. It was found that the purified wild-type sigma E protein, when used in in vitro run-off transcription assays in combination with core RNA polymerase, was able to direct transcription from the htrA and rpoHP3 promoters, but not from known sigma 70-dependent promoters. In vivo and in vitro analyses of rpoE transcriptional regulation showed that the rpoE gene is transcribed from two major promoters, one of which is positively regulated by sigma E itself.

The conserved G/F motif of the DnaJ chaperone is necessary for the activation of the substrate binding properties of the DnaK chaperone

The universally conserved DnaK and DnaJ molecular chaperone proteins bind in a coordinate manner to protein substrates to prevent aggregation, to disaggregate proteins, or to regulate proper protein function. To further examine their synergistic mechanism of action, we constructed and characterized two DnaJ deletion proteins. One has an 11-amino-acid internal deletion that spans amino acid residues 77-87 (DnaJ delta 77-87) and the other amino acids 77-107 (DnaJ delta 77-107). The DnaJ delta 77-87 mutant protein, was normal in all respects analyzed. The DnaJ delta 77-107 mutant protein has its entire G/F (Gly/Phe) motif deleted. This motif is found in most, but not all DnaJ family members. In vivo, DnaJ delta 77-107 supported bacteriophage lambda growth, albeit at reduced levels, demonstrating that at least some protein function was retained. However, DnaJ delta 77-107 did not exhibit other wild type properties, such as proper down-regulation of the heat-shock response, and had an overall poisoning effect of cell growth. The purified DnaJ delta 77-107 protein was shown to physically interact and stimulate DnaK's ATPase activity at wild type levels, unlike the previously characterized DnaJ259 point mutant (DnaJH33Q). Moreover, both DnaJ delta 77-107 and DnaJ259 bound to substrate proteins, such as sigma 32, at similar affinities as DnaJ+. However, DnaJ delta 77-107 was found to be largely defective in activating the ATP-dependent substrate binding mode of DnaK. In vivo, the ability of the mutant DnaJ proteins to down-regulate the heat-shock response was correlated only with their in vitro ability to activate DnaK to bind sigma 32, in an ATP-dependent manner, and not with their ability to bind sigma 32. We conclude, that although the G/F motif of DnaJ does not directly participate in the stimulation of DnaK's ATPase activity, nevertheless, it is involved in an important manner in modulating DnaK's substrate binding activity.

Nucleotide sequence of the Escherichia coli groE promoter

The promoter region of the Escherichia coli groE operon was cloned using the polymerase chain reaction (PCR). The 118-bp nucleotide sequence of the cloned groE promoter was determined on both strands of DNA. Two bp were found between the -10 and -35 regions of this promoter that have not been reported in previous publications of this sequence.

Molecular cloning of two new heat shock genes related to the hsp70 genes in Staphylococcus aureus

We have identified two new heat shock protein genes, orf37 and orf35, in Staphylococcus aureus, located upstream and downstream of grpE(hsp20), dnaK(hsp70), and dnaJ(hsp40) homologous genes in the order orf37-hsp20-hsp70-hsp40-orf35. The transcripts of both orf37 and orf35 were increased by thermal upshift of the culture from 37 to 46 degrees C. The heat shock promoters were located upstream of orf37 and upstream of hsp40. The deduced peptide of orf37 showed similarity with those of orfA in Clostridium acetobutylicum and orf39 in Bacillus subtilis. orf35 was unique in S. aureus and has not yet been described in other bacteria.

Cloning and molecular characterization of a Legionella pneumophila gene induced by intracellular infection and by various in vitro stress conditions

The synthesis of a global stress protein (GspA) of Legionella pneumophila is induced in the intracellular environment of the phagocytic cell and by various in vitro stress stimuli. We used techniques of reverse genetics to isolate the gspA gene from a genomic library of L. pneumophila. Sequence analysis of approximately 1700 bp of a representative clone (pBSP1) showed the presence of two open reading frames (ORFs). ORF1 encoded for a polypeptide with an inferred molecular mass of 19 kDa and an isoelectric point of 6.1. These predictions correlated with the migration of the GspA protein on two-dimensional SDS-polyacrylamide gels. The predicted amino acid sequence of the GspA protein was identical to 22/23 residues of the N-terminal amino acid sequence derived by Edman degradation of the purified protein. The GspA protein was 41.3% and 36.5% identical to the 16 kDa IbpA and IbpB heat-shock proteins, respectively, of Escherichia coli. Primer extension from mRNA isolated from L. pneumophila showed that transcription of the gspA gene was controlled by two overlapping promoters. One of the promoters was a sigma 70 promoter, while the other was a heat-shock promoter and was regulated by the sigma 32 transcription factor in E. coli. Northern blot analysis showed that the level of gspA mRNA was elevated 3.4-, 5.0-, and 6.7-fold after exposure of L. pneumophila to heat shock, oxidative stress and osmotic shock, respectively. The gspA gene was conserved among 13 serogroups of L. pneumophila. Our data showed that the gspA gene of L. pneumophila, which is induced by intracellular infection and by various stress stimuli, is controlled transcriptionally by two overlapping and separately regulated promoters.