Bhag Singh

Phylogenetic analysis of 70 kD heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleus

BACKGROUND The evolutionary relationships between archaebacteria, eubacteria and eukaryotic cells are of central importance in biology. The current view is that each of these three groups of organisms constitutes a monophyletic domain, and that eukaryotic cells have evolved fom an archaebacterial ancestor. Recent studies on a number of highly conserved protein sequences do not, however, support this view and raise important questions concerning the evolutionary relationships between all extant organisms, particularly regarding the origin of eukaryotic cells. RESULTS RESULTS We have used sequences of 70 kD heat shock protein (hsp70)--the most conserved protein found to date in all species--to examine the evolutionary relationship between various species. We have obtained two new archaebacterial hsp70 sequences from the species, Thermoplasma acidophilum and Halobacterium cutirubrum. A global comparison of hsp70 sequences, including our two new sequences, shows that all known archaebacterial homologs share a number of sequence signatures with the Gram-positive group of bacteria that are not found in any other prokaryotic or eukaryotic species. In contrast, the eukaryotic homologs are shown to share a number of unique sequence features with the Gram-negative bacteria that are not present in any archaebacteria. Detailed phylogenetic analyses of hsp70 sequences strongly support a specific evolutionary relationship between archaebacteria and Gram-positive bacteria on the one hand, and Gram-negative bacteria and eukaryotes on the other. The phylogenetic analyses also indicate a polyphyletic branching of archaebacteria within the Gram-positive species. The possibility that the observed relationships are due to horizontal gene transfers can be excluded on the basis of sequence characteristics of different groups of homologs. CONCLUSIONS Our results do not support the view that archaebacteria constitute a monophyletic domain, but instead suggest a close evolutionary linkage between archaebacteria and Gram-positive bacteria. Furthermore, in contrast to the presently accepted view, eukaryotic hsp70s show a close and specific relationship to those from Gram-negative species. To explain the phylogenies based on different gene sequences, a chimeric model for the origin of the eukaryotic cell nucleus involving fusion between an archaebacterium and a Gram-negative eubacterium is proposed. Several predictions from the chimeric model are discussed.

Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis

The presence of shared conserved insertions or deletions in proteins (referred to as signature sequences) provides a powerful means to deduce the evolutionary relationships among prokaryotic organisms. This approach was used in the present work to deduce the branching orders of various eubacterial taxa consisting of photosynthetic organisms. For this purpose, portions of the Hsp60 and Hsp70 genes, covering known signature sequence regions, were PCR‐amplified and sequenced from Heliobacterium chlorum, Chloroflexus aurantiacus and Chlorobium tepidum. This information was integrated with sequence data for several other proteins from numerous species to deduce the branching orders of different photosynthetic taxa. Based on signature sequences that are present in different proteins, it is possible to infer that the various eubacterial phyla evolved from a common ancestor in the following order: low G+C Gram‐positive (H. chlorum ) → high G+C Gram‐positive → Deinococcus–Thermus → green non‐sulphur bacteria (Cf. aurantiacus ) → cyanobacteria → spirochaetes →Chlamydia–Cytophaga–Aquifex–flavobacteria–green sulphur bacteria (Cb. tepidum ) → proteobacteria (α, δ and ε) and → proteobacteria (β and γ). The members of the Heliobacteriaceae family that contain a Fe–S type of reaction centre (RC‐1) and represent the sole photosynthetic phylum from the Gram‐positive or monoderm group of prokaryotes are indicated to be the most ancestral of the photosynthetic lineages. Among the Gram‐negative bacteria or diderm prokaryotes, green non‐sulphur bacteria such as Cf. aurantiacus, which contains a pheophytin–quinone type of reaction centre (RC‐2), are indicated to have evolved very early. Thus, the organisms containing either RC‐1 or RC‐2 existed before the evolution of cyanobacteria, which contain both these reaction centres to carry out oxygenic photosynthesis. The eubacterial divisions consisting of green sulphur bacteria and proteobacteria are indicated to have diverged after cyanobacteria. Some implications of these results concerning the origin of photosynthesis and the earliest prokaryotic fossils are discussed.

Conserved inserts in the Hsp60 (GroEL) and Hsp70 (DnaK) proteins are essential for cellular growth

The Hsp60 and Hsp70 chaperones contain a number of conserved inserts that are restricted to particular phyla of bacteria. A one aa insert in the E. coli GroEL and a 21–23 insert in the DnaK proteins are specific for most Gram-negative bacteria. Two other inserts in DnaK are limited to certain groups of proteobacteria. The requirement of these inserts for cellular growth was examined by carrying out complementation studies with temperature-sensitive (Ts) mutants of E. coligroEL or dnaK. Our results demonstrate that deletion or most changes in these inserts completely abolished the complementation ability of the mutant proteins. Studies with GroEL and DnaK from some other species that either lacked or contained these inserts also indicated that these inserts are essential for growth of E. coli. The DnaK from some bacteria contains a two aa insert that is not found in E. coli. Introduction of this insert into the E. coli DnaK also led to its inactivation, indicating that these inserts are specific for different groups. We postulate that these conserved inserts that are localized in loop regions on protein surfaces, are involved in some ancillary functions that are essential for the groups of bacteria where they are found.

Mutagenic responses of five independent geentic loci in CHO cells to a variety of mutagens: Development and characteristics of a mutagen screening system based on selection of multiple drug-resistant markers

With the aim of developing a sensitive mutagen screening system, the responses of 15 different chemical mutagens at 5 independent genetic loci in Chinese hamster ovary (CHO) cells have been determined. The genetic markers which have been employed include resistance to thioguanine (Thgr), ouabain (OuaR), the protein synthesis inhibitor emetine (Emtr), the polyamine synthesis inhibitor methylglyoxal bisguanylhydrazone (Mbgr) and the nucleoside analog 5,6-dichlororibofuranosyl benzimidazole (DrbR). The optimal selection conditions for all of these genetic markers in CHO cells have been described. The chemicals whose response was investigated in these studies include direct-acting alkylating agents (ethyl methane-sulfonate, methyl methanesulfonate, beta-propiolactone, ethyleneimine, N-nitrosomethylurea and 4-nitroquinoline-N-oxide), DNA intercalating and cross-linking agents (ICR-170, acridine orange, ethidium bromide, mitomycin C and actinomycin D), polycyclic hydrocarbons (benzo[a]pyrene (B(a)P) and 7,12-dimethylbenz[a]anthracene (DMBA)) and aromatic amines (benzidine and beta-naphthylamine). Simultaneous examination of the response of the set of genetic markers to these chemicals revealed that although all of these chemicals caused a dose-dependent increase in the frequency of mutations at many of the above genetic loci, the magnitude of the mutagenic response at different genetic loci varied greatly depending upon the chemical. Of the genetic loci examined, no one single locus showed higher response to all of the above chemicals, instead, depending upon the chemical, specific loci were found to be more responsive than others. The polycyclic hydrocarbons and aromatic amines were weakly mutagenic in this system at several genetic loci even without any exogenous microsomal activation, although in the presence of a rat liver S9 fraction similar toxic and mutagenic effects of B(a)P and DMBA were observed at 5-20-fold lower concentrations. These results indicate that CHO cells may possess significant capacity for the metabolic activation of many procarcinogens, and also underscore the merits of measuring the mutagenic response at multiple genetic loci in mutagen screening studies.

Cloning of HSP70 (dnaK) gene from Clostridium perfringens using a general polymerase chain reaction based approach

A general method to clone the HSP70 gene from any species employing polymerase chain reaction and degenerate oligonucleotide primers for conserved regions of this protein family is described. Using this method, a clone containing the entire coding sequence for the HSP70 gene from Clostridium perfringens, has been isolated and sequenced. The HSP70s from C. perfringens as well as other Gram-positive groups of bacteria contain a large deletion of 25 amino acids, near the N-terminal end, which is not seen in HSP70 from other sources.

Subcellular localization of adenosine kinase in mammalian cells: The long isoform of AdK is localized in the nucleus

Two isoforms of adenosine kinase (AdK) have been identified in mammalian organisms with the long isoform (AdK-long) containing extra 20-21 amino acids at the N-terminus (NTS). The subcellular localizations of these isoforms are not known and they contain no identifiable targeting sequence. Immunofluorescence labeling of mammalian cells expressing either only AdK-long or both isoforms with AdK-specific antibody showed only nuclear labeling or both nucleus and cytoplasmic labeling, respectively. The AdK-long and -short isoforms fused at the C-terminus with c-myc epitope also localized in the nucleus and cytoplasm, respectively. Fusion of the AdK-long NTS to green fluorescent protein also resulted in its nuclear localization. AdK-long NTS contains a cluster of conserved amino acids (PKPKKLKVE). Replacement of KK in this sequence with either AA or AD abolished its nuclear localization capability, indicating that this cluster likely serves as a nuclear localization signal. AdK in nucleus is likely required for sustaining methylation reactions.

Nucleotide sequences of three different isoforms of β-tubulin cDNA from Chinese hamster ovary cells

The complete cDNA sequences of two clones encoding beta-tubulin isotypes and the partial sequence of a third isoform from Chinese hamster ovary cells have been determined. The deduced amino acid sequences of the three isoforms show extensive homology to each other as well as with other alpha and beta-tubulin sequences from various species. These results provide evidence for the expression of three different isoforms of beta-tubulin in Chinese hamster ovary cells.

Cloning of hsp60 groel operon from clostridium perfringens using a polymerase chain reaction based approach

Using degenerate oligonucleotide primers for conserved regions of HSP60, a 0.6 kilobase fragment of Clostridium perfringens DNA was amplified by the polymerase chain reaction. The amplified fragment was used as a probe to isolate a genomic clone containing the C. perfringens HSP60 operon. The clone contained two open reading frames homologous to the GroES and GroEL (or HSP60) family of bacterial and eukaryotic proteins as well as other upstream and downstream sequences. The approach described here, employing this set of degenerate oligonucleotide primers, could be used to clone HSP60 gene/cDNA from any species.

The influence of inorganic phosphate on the activity of adenosine kinase.

The enzyme adenosine kinase (AK; EC 2.7.1.20) shows a dependence upon inorganic phosphate (Pi) for activity. The degree of dependence varies among enzyme sources and the pH at which the activity is measured. At physiological pH, recombinant AK from Chinese hamster ovary (CHO) cells and AK from beef liver (BL) show higher affinities for the substrate adenosine (Ado), larger maximum velocities and lower sensitivities to substrate inhibition in the presence of Pi. At pH 6.2, both BL and CHO AK exhibit almost complete dependence on the presence of Pi for activity. The data show that both enzymes exhibit increasing relief from substrate inhibition upon increasing Pi and the inhibition of BL AK is almost completely alleviated by the addition of 50 mM Pi. The affinity of CHO AK for Ado increases asymptotically from K(m) 6.4 microM to a limit of 0.7 microM upon the addition of increasing Pi from 1 to 50 mM. The concentration of Ado necessary to invoke substrate inhibition also increases asymptotically from K(i) 32 microM to a limit of 69 microM at saturating concentrations of phosphate. In the presence of increasing amounts of Pi, the maximal velocity of activity increases hyperbolically. The effect that phosphate exerts on AK may be either to protect the enzyme from inactivation at high adenosine and H(+) concentrations or to stabilize substrate binding at the active site.

Identification and characterization of human ribokinase and comparison of its properties with E. coli ribokinase and human adenosine kinase.

The gene responsible for ribokinase (RK) in human/eukaryotic cells has not yet been identified/characterized. Blast searches with E. coli RK have identified a human protein showing significant similarity to the bacterial RK. The cDNA for this protein was expressed in E. coli and the recombinant protein efficiently phosphorylated ribose to ribose‐5‐phosphate using ATP, confirming its identity as RK. In contrast to ribose, the enzyme exhibited very little to no phosphorylation of d‐arabinose, d‐xylose, d‐fructose and d‐galactose. The catalytic activity of human RK was dependent upon the presence of inorganic phosphate, as observed previously for E. coli RK and mammalian adenosine kinases (AK). A number of activators and inhibitors of human AK, produced very similar effects on the human and E. coli RKs, indicating that the catalytic mechanism of RK is very similar to that of the AKs.