Secondary literature sources for the SMR domain

For each of the hand selected primary papers associated with the SMR domain, 100 neighbouring papers are retrieved from PubMed. If one of these neighbouring papers is referenced by more than two primary papers, it is shown in the table below.

The amino acid/auxin:proton symport permease family.

Young GB, Jack DL, Smith DW, Saier MH Jr
Biochim Biophys Acta. 1999; 1415: 306-22

Amino acids and their derivatives are transported into and out of cells by a variety of permease types which comprise several distinct protein families. We here present a systematic analysis of a group of homologous transport proteins which together comprise the eukaryotic-specific amino acid/auxin permease (AAAP) family (TC #2. 18). In characterizing this family, we have (1) identified all sequenced members of the family, (2) aligned their sequences, (3) identified regions of striking conservation, (4) derived a family-specific signature sequence, and (5) proposed a topological model that appears to be applicable to all members of the family. We have also constructed AAAP family phylogenetic trees and dendrograms using six different programs that allow us to trace the evolutionary history of the family, estimate the relatedness of proteins from dissimilar organismal phyla, and evaluate the reliability of the different programs available for phylogenetic studies. The TREE and neighbor-joining programs gave fully consistent results while CLUSTAL W gave similar but non-identical results. Other programs gave less consistent results. The phylogenetic analyses reveal (1) that many plant AAAP family proteins arose recently by multiple gene duplication events that occurred within a single organism, (2) that some plant members of the family with strikingly different specificities diverged early in evolutionary history, and (3) that AAAP family proteins from fungi and animals diverged from the plant proteins long ago, possibly when animals, plants and fungi diverged from each other. The Neurospora protein nevertheless exhibits overlapping specificity with those found in plants. Preliminary evidence is presented suggesting that proteins of the AAAP family are distantly related to proteins of the large ubiquitous amino acid/polyamine/choline family (TC #2.3) as well as to those of two small bacterial amino acid transporter families, the ArAAP family (TC #2.42) and the STP family (TC #2.43).

Similarity between putative ATP-binding sites in land plant plastid ORF2280 proteins and the FtsH/CDC48 family of ATPases.

Wolfe KH
Curr Genet. 1994; 25: 379-83

Plastid ORF2280 proteins from five species of land plant are shown to have limited amino-acid sequence similarity to a family of proteins that includes the yeast CDC48, SEC18, PAS1 and SUG1 proteins, three subunits of the mammalian 26S protease, and the Escherichia coli FtsH protein. These proteins all contain one or two ATPase domains and many are involved in cell division, transport of proteins across membranes, or proteolysis. Similarity with the ORF2280 proteins is restricted to a single region of about 130 amino acids that contains: (1) sequences resembling a nucleotide binding site but lacking two normally conserved residues, and (2) a downstream conserved motif with the consensus sequence VIX2TX2PX3DPALX2P. Most of the rest of ORF2280 is very poorly conserved among land plants, even though other family members such as CDC48 have slow rates of protein sequence evolution. In contrast, a protein encoded by plastid DNA of the rhodophyte alga Porphyra purpurea is very similar to E. coli FtsH. Phylogenetic analysis suggests that the red and green plastid genes are not true homologues (orthologues) but distinct members of an ancient gene family.

Sequences and expression of six new members of the tetraspanin/TM4SF family.

Todd SC, Doctor VS, Levy S
Biochim Biophys Acta. 1998; 1399: 101-4

Tetraspanins (or TM4SF) are expressed in a wide variety of species and regulate cell adhesion, migration, proliferation and differentiation. We have identified and sequenced six new members of the tetraspanin family, called Tspan-1-6, from human cDNA. Amino acid sequence analysis of the Tspans highlights conserved residues which may be critical to tetraspanin structure and function. The Tspans are differentially expressed in human tissues.

Mutational analysis of the RecJ exonuclease of Escherichia coli: identification of phosphoesterase motifs.

Sutera VA Jr, Han ES, Rajman LA, Lovett ST
J Bacteriol. 1999; 181: 6098-102

The recJ gene, identified in Escherichia coli, encodes a Mg(+2)-dependent 5'-to-3' exonuclease with high specificity for single-strand DNA. Genetic and biochemical experiments implicate RecJ exonuclease in homologous recombination, base excision, and methyl-directed mismatch repair. Genes encoding proteins with strong similarities to RecJ have been found in every eubacterial genome sequenced to date, with the exception of Mycoplasma and Mycobacterium tuberculosis. Multiple genes encoding proteins similar to RecJ are found in some eubacteria, including Bacillus and Helicobacter, and in the archaea. Among this divergent set of sequences, seven conserved motifs emerge. We demonstrate here that amino acids within six of these motifs are essential for both the biochemical and genetic functions of E. coli RecJ. These motifs may define interactions with Mg(2+) ions or substrate DNA. A large family of proteins more distantly related to RecJ is present in archaea, eubacteria, and eukaryotes, including a hypothetical protein in the MgPa adhesin operon of Mycoplasma, a domain of putative polyA polymerases in Synechocystis and Aquifex, PRUNE of Drosophila, and an exopolyphosphatase (PPX1) of Saccharomyces cereviseae. Because these six RecJ motifs are shared between exonucleases and exopolyphosphatases, they may constitute an ancient phosphoesterase domain now found in all kingdoms of life.

An Edwardsiella tarda strain containing a mutation in a gene with homology to shlB and hpmB is defective for entry into epithelial cells in culture.

Strauss EJ, Ghori N, Falkow S
Infect Immun. 1997; 65: 3924-32

Edwardsiella tarda is an enteric pathogen that causes diarrhea, wound infections, and death due to septicemia. This species is capable of invading human epithelial cell lines, and we have now been able to follow the entry and replication of E. tarda within tissue culture host cells. E. tarda escapes from the endocytic vacuole within minutes of entry and then replicates within the cytoplasm. Unlike other well-studied bacteria that replicate and reside in the cytoplasm, we never observed this organism moving directly from cell to cell; instead the bacteria spread by lysing the plasma membrane after several rounds of replication. Efforts to study the interactions of E. tarda with tissue culture cells are complicated by the presence of a potent cytotoxin that the bacterium produces. Using transposon mutagenesis, we isolated a noncytotoxic strain of E. tarda. This mutant is also defective for hemolysin production. The dual phenotype of this strain is consistent with the hypothesis that cytotoxicity is due to the previously characterized E. tarda hemolysin activity. The nonhemolytic strain is also unable to enter HEp-2 cells. The disrupted gene has sequence similarity to members of a family of genes required for transport and activation of the hemolysin genes, shlA and hpmA. A cosmid bearing 40 kb of E. tarda DNA, including wild-type copies of the E. tarda homologs of the transporter-activator protein and the hemolysin itself, confers hemolytic, cytotoxic, and invasive abilities upon normally nonhemolytic, noncytotoxic, and noninvasive strains of Escherichia coli. Sequence data indicate that the genes required for hemolytic activity are linked to a transposable element, suggesting that they arose in the E. tarda genome by horizontal transfer.

A glycyl radical solution: oxygen-dependent interconversion of pyruvate formate-lyase.

Sawers G, Watson G
Mol Microbiol. 1998; 29: 945-54

Pyruvate formate-lyase (PFL) catalyses the non-oxidative dissimilation of pyruvate to formate and acetyl-CoA using a radical-chemical mechanism. The enzyme is enzymically interconverted between inactive and active forms, the active form contains an organic free radical located on a glycyl residue in the C-terminal portion of the polypeptide chain. Introduction of the radical into PFL only occurs anaerobically, and the activating enzyme responsible is an iron-sulphur protein that uses S-adenosyl methionine as cofactor and reduced flavodoxin as reductant. As the radical form of PFL is inactivated by molecular oxygen it is safeguarded during the transition to aerobiosis by conversion back to the radical-free, oxygen-stable form. This reaction is catalysed by the anaerobically induced multimeric enzyme alcohol dehydrogenase. The genes encoding PFL and its activating enzyme are adjacent on the chromosome but form discrete transcriptional units. This genetic organization is highly conserved in many, but not all, organisms that have PFL. Recent studies have shown that proteins exhibiting significant similarity to PFL and its activating enzyme are relatively widespread in facultative and obligate anaerobic eubacteria, as well as archaea. The physiological function of many of these PFL-like enzymes remains to be established. It is becoming increasingly apparent that glycyl radical enzymes are more prevalent than previously surmised. They represent a class of enzymes with unusual biochemistry and probably predate the appearance of molecular oxygen.

Mitochondrial DNA of the coral Sarcophyton glaucum contains a gene for a homologue of bacterial MutS: a possible case of gene transfer from the nucleus to the mitochondrion.

Pont-Kingdon G, Okada NA, Macfarlane JL, Beagley CT, Watkins-Sims CD, Cavalier-Smith T, Clark-Walker GD, Wolstenholme DR
J Mol Evol. 1998; 46: 419-31

The nucleotide sequences of two segments of 6,737 ntp and 258 nto of the 18.4-kb circular mitochondrial (mt) DNA molecule of the soft coral Sarcophyton glaucum (phylum Cnidaria, class Anthozoa, subclass Octocorallia, order Alcyonacea) have been determined. The larger segment contains the 3' 191 ntp of the gene for subunit 1 of the respiratory chain NADH dehydrogenase (ND1), complete genes for cytochrome b (Cyt b), ND6, ND3, ND4L, and a bacterial MutS homologue (MSH), and the 5' terminal 1,124 ntp of the gene for the large subunit rRNA (1-rRNA). These genes are arranged in the order given and all are transcribed from the same strand of the molecule. The smaller segment contains the 3' terminal 134 ntp of the ND4 gene and a complete tRNA(f-Met) gene, and these genes are transcribed in opposite directions. As in the hexacorallian anthozoan, Metridium senile, the mt-genetic code of S. glaucum is near standard: that is, in contrast to the situation in mt-genetic codes of other invertebrate phyla, AGA and AGG specify arginine, and ATA specifies isoleucine. However, as appears to be universal for metazoan mt-genetic codes, TGA specifies tryptophan rather than termination. Also, as in M. senile the mt-tRNA(f-Met) gene has primary and secondary structural features resembling those of Escherichia coli initiator tRNA, including standard dihydrouridine and T psi C loop sequences, and a mismatched nucleotide pair at the top of the amino-acyl stem. The presence of a mutS gene homologue, which has not been reported to occur in any other known mtDNA, suggests that there is mismatch repair activity in S. glaucum mitochondria. In support of this, phylogenetic analysis of MutS family protein sequences indicates that the S. glaucum mtMSH protein is more closely related to the nuclear DNA-encoded mitochondrial mismatch repair protein (MSH1) of the yeast Saccharomyces cerevisiae than to eukaryotic homologues involved in nuclear function, or to bacterial homologues. Regarding the possible origin of the S. glaucum mtMSH gene, the phylogenetic analysis results, together with comparative base composition considerations, and the absence of an MSH gene in any other known mtDNA best support the hypothesis that S. glaucum mtDNA acquired the mtMSH gene from nuclear DNA early in the evolution of octocorals. The presence of mismatch repair activity in S. glaucum mitochondria might be expected to influence the rate of evolution of this organism's mtDNA.

A novel family of ubiquitous heavy metal ion transport proteins.

Paulsen IT, Saier MH Jr
J Membr Biol. 1997; 156: 99-103

We describe a novel diverse family of metal ion transporter (CDF) proteins (the cation diffusion facilitator (CDF) family) with members occurring in both prokaryotes and eukaryotes. Thirteen sequenced protein members of the CDF family have been identified, several of which have been shown to transport cobalt, cadmium and/or zinc. All members of the CDF family possess six putative transmembrane spanners with strongest conservation in the four N-terminal spanners, and on the basis of the analyses, we present a unified structural model. Members of the family are shown to exhibit an unusual degree of size variation, sequence divergence, and differences in cell localization and polarity. The phylogenetic tree for the CDF family reveals that prokaryotic and eukaryotic proteins cluster separately. It allows functional predictions for some uncharacterized members of this family. A signature sequence specific for the CDF family is derived.

MutK may be a 32 kDa protein and be widespread among proteobacteria.

Moreira D
Mol Microbiol. 1999; 33: 220-2

Dual recognition-incision enzymes might be involved in mismatch repair and meiosis.

Malik HS, Henikoff S
Trends Biochem Sci. 2000; 25: 414-8

Mismatch repair in many organisms depends on three proteins: the mismatch-recognition protein MutS, a nicking endonuclease MutH, and MutL, which acts as a scaffold between these. However, many genomes lack MutL but possess MutS. In one of these cases, in a coral mitochondrial genome, a gene is present that encodes a MutS protein fused to an HNH nicking endonuclease, potentially eliminating the requirement for MutL. Likewise, many prokaryotes could operate similarly, independently of MutL by encoding a fused MutS-Smr (MutS2) protein. Smr, which is proposed to be a nicking endonuclease, can also be found separately in many eukaryotes, where it might play a role in mismatch repair or meiotic chromosome crossing-over.

Specific expansion of protein families in the radioresistant bacterium Deinococcus radiodurans.

Makarova KS, Aravind L, Daly MJ, Koonin EV
Genetica. 2000; 108: 25-34

Computer analysis of the complete genome of Deinococcus radiodurans R1 reveals a number of protein families, which are over-represented in this organism, compared to most other bacteria with known genome sequences. These families include both previously characterized and uncharacterized proteins. Most of the families whose functions are known or could be predicted seem to be related to stress-response and elimination of damage products (cell-cleaning). The two most prominent family expansions are the Nudix (MutT) family of pyrophosphohydrolases and a previously unnoticed family of proteins related to Bacillus subtilis DinB that could possess a metal-dependent enzymatic activity whose exact nature remains to be determined. Several proteins of the expanded families, particularly the Nudix family, are fused to other domains and form multidomain proteins that are so far unique for Deinococcus. The domain composition of some of these proteins indicates that they could be involved in novel DNA-repair pathways. Such unique proteins are good targets for knock-out and gene expression studies, which are aimed to shed light on the unusual features of this interesting bacterium.

A notable example of an evolutionary conserved gene: studies on a putative DNA helicase TIP49.

Kurokawa Y, Kanemaki M, Makino Y, Tamura TA
DNA Seq. 1999; 10: 37-42

TIP49a (just called as simply TIP49 in previous reports [Kanemaki et al., 1997; Makino et al., 1998]) was found in a rat nuclear protein complex that included the TATA-binding protein. TIP49a possesses multiple sequence motifs for ATPase and DNA helicase. Since TIP49a structurally resembles prokaryotic DNA helicase RuvB, TIP49a is resumed to be a putative DNA helicase. We demonstrated TIP49a-related gene(s) in variety organisms from human to archaea. Amino acid identities expressed as aligned scores of human, yeast, and A. fulgidus TIP49a gene counterparts to the rat sequence were 99, 67, and 46, respectively. Strikingly, two homologous regions of mammalian TIP49a and bacterial RuvB exhibited an aligned score of 17-38. We demonstrated that the eukaryotic TIP49a counterparts were immunologically conserved. These lines of evidence show that the TIP49a gene is a notable example of a highly conserved gene among organisms. An extensive homology search revealed another class of TIP49-related gene in the eukaryotes, designated as TIP49b. Moreover, a phylogenetical study suggested that archaeal TIP49 genes belong to the TIP49b ancestor but not to the TIP49a one and that TIP49a evolved from TIP49b in accordance with divergence of archaea and eukarya. The TIP49 gene family is thought to play a fundamental role in a biological activity.

Phylogenetic relationships among prokaryotic and eukaryotic catalases.

Klotz MG, Klassen GR, Loewen PC
Mol Biol Evol. 1997; 14: 951-8

Seventy-four catalase protein sequences, including 29 bacterial, 8 fungal, 7 animal, and 30 plant sequences, were compiled, and 70 were used for phylogenetic reconstruction. The core of the resulting tree revealed unique, separate groups of plant and animal catalases, two groups of fungal catalases, and three groups of bacterial catalases. The only overlap of kingdoms occurred within one branch and involved fungal and bacterial large-subunit enzymes. The other fungal branch was closely linked to the group of animal enzymes. Group I bacterial catalases were more closely related to the plant enzymes and contained such diverse taxa as the Gram-positive Listeria seeligeri, Deinocococcus radiodurans, and gamma-proteobacteria. Group III bacterial sequences were more closely related to fungal and animal sequences and included enzymes from a broad range of bacteria including high- and low-GC Gram positives, proteobacteria, and a bacteroides species. Group II was composed of large-subunit catalases from diverse sources including Gram positives (low-GC Bacilli and high-GC Mycobacteria), proteobacteria, and species of the filamentous fungus Aspergillus. These data can be interpreted in terms of two gene duplication events that produced a minimum of three catalase gene family members that subsequently evolved in response to environmental demands. Horizontal gene transfer may have been responsible for the group II mixture of bacterial and fungal large-subunit catalases.

The CorA magnesium transporter gene family.

Kehres DG, Lawyer CH, Maguire ME
Microb Comp Genomics. 1998; 3: 151-69

The CorA transport system is the primary Mg2+ influx system of Salmonella typhimurium and Escherichia coli. The CorA protein has no homology to any other known family of proteins. It has an unusual membrane topology, with a large, soluble, highly charged periplasmic N-terminal domain with three transmembrane segments in a shorter, hydrophobic C-terminal domain. Previous phenotypic and molecular data had suggested that this transport system was widespread in the Bacteria. In this report we show that CorA is virtually ubiquitous in the Bacteria and Archaea, forming a distinct family of transport proteins. Genomic sequences to date have revealed at least 22 members of the CorA family in the Bacteria and the Archaea, with 6 more distant members in the yeasts. Only three of the smallest bacterial genomes lack a CorA homologue. Strikingly, phylogenetic analysis does not show clustering by related species or even within kingdom. Several species of Bacteria contain two or even three CorA paralogues. Within species, these paralogues are not closely related, however, and we suggest that they might have distinct transport functions. A multiple alignment suggests three extended consensus regions within the N-terminal soluble domain of CorA, which is predicted to be virtually all alpha-helical. A fourth consensus region includes the last 20 residues of the soluble domain and continues through the entire membrane domain. The first half of this last consensus domain may form an amphipathic alpha-helix that extends from the soluble domain into the first transmembrane segment. The degree of charge in the first transmembrane segment is quite variable, and we suggest that this transport family may include members with only two rather than three transmembrane segments. If so, this would place the N-terminal soluble domain on different sides of the membrane in different members of the family. We suggest that the CorA Mg2+ transport system forms the major Mg2+ uptake system in the Bacteria and Archaea but that some family members may have a function other than Mg2+ transport.

Isolation and characterization of AtMLH1, a MutL homologue from Arabidopsis thaliana.

Jean M, Pelletier J, Hilpert M, Belzile F, Kunze R
Mol Gen Genet. 1999; 262: 633-42

DNA mismatch repair systems play an essential role in the maintenance of genetic information in living organisms and are also implicated in genetic recombination and genome stability. Using degenerate primers, we have cloned the first plant homologue of the E. coli MutL gene, which we have called AtMLH1 for Arabidopsis thaliana MutL-homologue 1. AtMLH1 is present as a single-copy gene in the Arabidopsis genome and is located on the top arm of chromosome 4. Sequence analysis revealed that the product of this gene shows extensive sequence homology with other eukaryotic MLH1 proteins. As mlh1-deficient lines would be useful for studying the biological function of this gene, several populations that had been mutagenized using T-DNA and transposon insertions were screened to identify such mutants. One line that carries a T-DNA insertion in the promoter region of the AtMLH1 gene was isolated. Surprisingly, although the insertion occurred only approximately 80 bp upstream of the putative transcription start site, Northern analyses revealed very low but similar amounts of AtMLH1 transcript in both the wild type and the T-DNA insertion lines. RT-PCR analyses suggest, however, that transcription is initiated further upstream in the insertion line and that the T-DNA may supply this novel initiation site. Finally, no increase in microsatellite instability - a phenotype often associated with mutations in mismatch repair genes - was observed in plants homozygous for this insertion.

Signature sequences in diverse proteins provide evidence of a close evolutionary relationship between the Deinococcus-thermus group and cyanobacteria.

Gupta RS, Johari V
J Mol Evol. 1998; 46: 716-20

A number of proteins have been identified that contain prominent sequence signatures that are uniquely shared by the members of the Deinococcus-Thermus genera and the cyanobacterial species but which are not found in any of the other eubacterial or archaebacterial homologs. The proteins containing such sequence signatures include (1) the DnaJ/Hsp40 family of proteins, (2) DNA polymerase I, (3) the protein synthesis elongation factor EF-Tu, and (4) the elongation factor EF-Ts. A strong affinity of the Deinococcus-Thermus species to cyanobacteria is also seen in the phylogenetic trees based on Hsp70 and DnaJ sequences. These results provide strong evidence of a close and specific evolutionary relationship between species belonging to these two eubacterial divisions.

A protein related to eucaryal and bacterial DNA-motor proteins in the hyperthermophilic archaeon Sulfolobus acidocaldarius.

Elie C, Baucher MF, Fondrat C, Forterre P
J Mol Evol. 1997; 45: 107-14

We have isolated a new gene encoding a putative 103-kDa protein from the hyperthermophilic archaeon Sulfolobus acidocaldarius. Analysis of the deduced amino-acid sequence shows an extended central domain, predicted to form coiled-coil structures, and two terminal domains that display purine NTPase motifs. These features are reminiscent of mechanochemical motor proteins which use the energy of ATP hydrolysis to move specific cellular components. Comparative analysis of the amino-acid sequence of the terminal domains and predicted structural organization of this putative purine NTPase show that it is related both to eucaryal proteins from the "SMC family" involved in the condensation of chromosomes and to several bacterial and eucaryal proteins involved in DNA recombination/repair. Further analyses revealed that these proteins are all members of the so called "UvrA-related NTP-binding proteins superfamily" and form a large subgroup of motor-like NTPases involved in different DNA processing mechanisms. The presence of such protein in Archaea, Bacteria, and Eucarya suggests an early origin of DNA-motor proteins that could have emerged and diversified by domain shuffling.

Evolutionary origin, diversification and specialization of eukaryotic MutS homolog mismatch repair proteins.

Culligan KM, Meyer-Gauen G, Lyons-Weiler J, Hays JB
Nucleic Acids Res. 2000; 28: 463-71

Most eubacteria, and all eukaryotes examined thus far, encode homologs of the DNA mismatch repair protein MutS. Although eubacteria encode only one or two MutS-like proteins, eukaryotes encode at least six distinct MutS homolog (MSH) proteins, corresponding to conserved (orthologous) gene families. This suggests evolution of individual gene family lines of descent by several duplication/specialization events. Using quantitative phylogenetic analyses (RASA, or relative apparent synapomorphy analysis), we demonstrate that comparison of complete MutS protein sequences, rather than highly conserved C-terminal domains only, maximizes information about evolutionary relationships. We identify a novel, highly conserved middle domain, as well as clearly delineate an N-terminal domain, previously implicated in mismatch recognition, that shows family-specific patterns of aromatic and charged amino acids. Our final analysis, in contrast to previous analyses of MutS-like sequences, yields a stable phylogenetic tree consistent with the known biochemical functions of MutS/MSH proteins, that now assigns all known eukaryotic MSH proteins to a monophyletic group, whose branches correspond to the respective specialized gene families. The rooted phylogenetic tree suggests their derivation from a mitochondrial MSH1-like protein, itself the descendent of the MutS of a symbiont in a primitive eukaryotic precursor.

Primary structure of a multimeric protein, homologous to the PEP-utilizing enzyme family and isolated from a hyperthermophilic archaebacterium.

Cicicopol C, Peters J, Kellermann J, Baumeister W
FEBS Lett. 1994; 356: 345-50

A large protein complex (approx. 2000 kDa) was found in the cytosol of the hyperthermophilic archaebacterium Staphylothermus marinus. The purified protein was shown to be a homomultimer of 93 kDa subunits, the primary structure of which was determined by nucleotide sequence analysis. The protein belongs to the family of phosphoenolpyruvate-utilizing enzymes and represents the first member characterized in archaebacteria. Its homomultimeric organisation differs from the typically dimeric structure of its eubacterial and eukaryotic counterparts.

Identification and characterization of a thermostable MutS homolog from Thermus aquaticus.

Biswas I, Hsieh P
J Biol Chem. 1996; 271: 5040-8

Recognition of mispaired or unpaired bases during DNA mismatch repair is carried out by the MutS protein family. Here, we describe the isolation and characterization of a thermostable MutS homolog from Thermus aquaticus YT-1. Sequencing of the mutS gene predicts an 89.3-kDa polypeptide sharing extensive amino acid sequence homology with MutS homologs from both prokaryotes and eukaryotes. Expression of the T. aquaticus mutS gene in Escherichia coli results in a dominant mutator phenotype. Initial biochemical characterization of the thermostable MutS protein, which was purified to apparent homogeneity, reveals two thermostable activities, an ATP hydrolysis activity in which ATP is hydrolyzed to ADP and Pi and a specific DNA mismatch binding activity with affinities for heteroduplex DNAs containing either an insertion/deletion of one base or a GT mismatch. The ATPase activity exhibits a temperature optimum of approximately 80 degrees C. Heteroduplex DNA binding by the T. aquaticus MutS protein requires Mg2+ and occurs over a broad temperature range from 0 degrees C to at least 70 degrees C. The thermostable MutS protein may be useful for further biochemical and structural studies of mismatch binding and for applications involving mutation detection.

Evolution of glutamate dehydrogenase genes: evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life.

Benachenhou-Lahfa N, Forterre P, Labedan B
J Mol Evol. 1993; 36: 335-46

The existence of two families of genes coding for hexameric glutamate dehydrogenases has been deduced from the alignment of 21 primary sequences and the determination of the percentages of similarity between each pair of proteins. Each family could also be characterized by specific motifs. One family (Family I) was composed of gdh genes from six eubacteria and six lower eukaryotes (the primitive protozoan Giardia lamblia, the green alga Chlorella sorokiniana, and several fungi and yeasts). The other one (Family II) was composed of gdh genes from two eubacteria, two archaebacteria, and five higher eukaryotes (vertebrates). Reconstruction of phylogenetic trees using several parsimony and distance methods confirmed the existence of these two families. Therefore, these results reinforced our previously proposed hypothesis that two close but already different gdh genes were present in the last common ancestor to the three Ur-kingdoms (eubacteria, archaebacteria, and eukaryotes). The branching order of the different species of Family I was found to be the same whatever the method of tree reconstruction although it varied slightly according the region analyzed. Similarly, the topological positions of eubacteria and eukaryotes of Family II were independent of the method used. However, the branching of the two archaebacteria in Family II appeared to be unexpected: (1) the thermoacidophilic Sulfolobus solfataricus was found clustered with the two eubacteria of this family both in parsimony and distance trees, a situation not predicted by either one of the contradictory trees recently proposed; and (2) the branching of the halophilic Halobacterium salinarium varied according to the method of tree construction: it was closer to the eubacteria in the maximum parsimony tree and to eukaryotes in distance trees. Therefore, whatever the actual position of the halophilic species, archaebacteria did not appear to be monophyletic in these gdh gene trees. This result questions the firmness of the presently accepted interpretation of previous protein trees which were supposed to root unambiguously the universal tree of life and place the archaebacteria in this tree.

An archaebacterial homologue of the essential eubacterial cell division protein FtsZ.

Baumann P, Jackson SP
Proc Natl Acad Sci U S A. 1996; 93: 6726-30

Life falls into three fundamental domains--Archaea, Bacteria, and Eucarya (formerly archaebacteria, eubacteria, and eukaryotes,. respectively). Though Archaea lack nuclei and share many morphological features with Bacteria, molecular analyses, principally of the transcription and translation machineries, have suggested that Archaea are more related to Eucarya than to Bacteria. Currently, little is known about the archaeal cell division apparatus. In Bacteria, a crucial component of the cell division machinery is FtsZ, a GTPase that localizes to a ring at the site of septation. Interestingly, FtsZ is distantly related in sequence to eukaryotic tubulins, which also interact with GTP and are components of the eukaryotic cell cytoskeleton. By screening for the ability to bind radiolabeled nucleotides, we have identified a protein of the hyperthermophilic archaeon Pyrococcus woesei that interacts tightly and specifically with GTP. Furthermore, through screening an expression library of P. woesei genomic DNA, we have cloned the gene encoding this protein. Sequence comparisons reveal that the P. woesei GTP-binding protein is strikingly related in sequence to eubacterial FtsZ and is marginally more similar to eukaryotic tubulins than are bacterial FtsZ proteins. Phylogenetic analyses reinforce the notion that there is an evolutionary linkage between FtsZ and tubulins. These findings suggest that the archaeal cell division apparatus may be fundamentally similar to that of Bacteria and lead us to consider the evolutionary relationships between Archaea, Bacteria, and Eucarya.

The distance between bacterial species in sequence space.

Ambler RP
J Mol Evol. 1996; 42: 617-30

Despite the revolution caused by information from macromolecular sequences, the basis of bacterial classification remains the genus and the species. How do these terms relate to the variety of bacteria that exist on earth? In this paper, the inter- and intraspecies differences in amino acid sequence of several bacterial electron transport proteins, cytochromes c, and blue copper proteins are compared. For the soil and water organisms studied, bacterial species can be classed as "tight" when there is little intraspecies variation, or "loose" when this variation is large. For this set of proteins and organisms, interspecies variation is much larger than that within a species. Examples of "tight" species are Pseudomonas aeruginosa and Rhodobacter sphaeroides, while Pseudomonas stutzeri and Rhodopseudomonas palustris are loose species. The results are discussed in the context of the origin and age of bacterial species, and the distribution of genomes in "sequence space." The situation is probably different for commensal or pathogenic bacteria, whose population structure and evolution are linked to the properties of another organism.

Oxidoreductase-type enzymes and redox proteins involved in fermentative metabolisms of hyperthermophilic Archaea.

Adams MW, Kletzin A
Adv Protein Chem. 1996; 48: 101-80