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PubMed2003

Macrophage migration inhibitory factor (MIF) of jawed and jawless fishes: implications for its evolutionary origin.

The macrophage migration inhibitory factor (MIF) is a cytokine produced by T lymphocytes and macrophages in response to inflammatory stimuli. We sequenced MIF cDNA clones of two jawless fishes, the sea lamprey (Petromyzon marinus) and the North Atlantic hagfish (Myxine glutinosa), as well as of the jawed (cichlid) fish Paralabidochromis chilotes. The fish MIF-encoding genes have the same exon-intron organization as the mammalian MIF genes and are present in one copy per haploid genome. Secondary and tertiary structure predictions suggest that the fish MIF proteins have a topology characteristic of the entire MIF-family of proteins. Phylogenetic analysis separates the known nematode members of the family into two groups, one having a sister group relationship with the mammalian D-dopachrome tautomerase (DDT) proteins and the other being related to vertebrate MIFs. It also reveals a high degree of convergent evolution among the members of the family. Finally, it suggests that the divergence of MIF and DDT occurred before the emergence of nematodes in metazoan evolution.

Amino Acid Sequence↗
PubMed1999

Visual circuits of the avian telencephalon: evolutionary implications.

Birds and primates are vertebrates that possess the most advanced, efficient visual systems. Although lineages leading to these two classes were separated about 300 million years ago, there are striking similarities in their underlying neural mechanisms for visual processing. This paper discusses such similarities with special emphasis on the visual circuits in the avian telencephalon. These similarities include: (1) the existence of two parallel visual pathways and their distinct telencephalic targets, (2) anatomical and functional segregation within the visual pathways, (3) laminar organization of the telencephalic targets of the pathways (e.g. striate cortex in primates), and (4) possible interactions between multiple visual areas. Additional extensive analyses are necessary to determine whether these similarities are due to inheritance from a common ancestral stock or the consequences of convergent evolution based on adaptive response to similar selective pressures. Nevertheless, such a comparison is important to identify the general and specific principles of visual processing in amniotes (reptiles, birds, and mammals). Furthermore, these principles in turn will provide a critical foundation for understanding the evolution of the brain in amniotes.

Animals↗
PubMed1997

Structure and function of the low Mr phosphotyrosine protein phosphatases.

Phosphotyrosine protein phosphatases (PTPases) catalyse the hydrolysis of phosphotyrosine residues in proteins and are hence implicated in the complex mechanism of the control of cell proliferation and differentiation. The low Mr PTPases are a group of soluble PTPases displaying a reduced molecular mass; in addition, a group of low molecular mass dual specificity (ds)PTPases which hydrolyse phosphotyrosine and phosphoserine/threonine residues in proteins are known. The enzymes belonging to the two groups are unrelated to each other and to other PTPase classes except for the presence of a CXXXXXRS/T sequence motif containing some of the catalytic residues (active site signature) and for the common catalytic mechanism, clearly indicating convergent evolution. The low Mr PTPases have a long evolutionary history since microbial (prokaryotic and eukaryotic) counterparts of both tyrosine-specific and dsPTPases have been described. Despite the relevant number of data reported on the structural and catalytic features of a number of low Mr PTPases, only limited information is presently available on the substrate specificity and the true biological roles of these enzymes, in prokaryotic, yeast and eukaryotic cells.

Amino Acid Sequence↗
PubMed1999

Mitogenomics: digging deeper with complete mitochondrial genomes.

Mitochondrial genomes are being used to study increasingly ancient divergences among animal groups. Recent studies of complete mitochondrial DNA sequences have arrived at somewhat heretical conclusions, raising questions about the use of mitochondrial gene sequences for studying the relationships among highly divergent lineages. Other studies have documented convergent evolution of mitochondrial gene order, casting doubt on the use of these characters for phylogenetic analysis. The use of mitochondrial genomes for studying such deep divergences is coming under increased scrutiny, and these novel results need to be confirmed with data from nuclear genes.

Journal Article↗
PubMed1997

An atypical diencephalic nucleus in actinopterygian fishes: visual connections and sporadic phylogenetic distribution.

Nucleus rostrolateralis is a distinctive diencephalic nucleus in some ray-finned fishes. In the osteoglossomorph Pantodon, it is a large ovoid nucleus with visual system connections. A topologically and cytoarchitectonically similar nucleus has been found in six species of non-osteoglossomorph fishes, two species of gars and four euteleosts. Of the latter, two are ostariophysans of the genus Danio, one an atherinomorph, and one a notothenioid percomorph. A variety of characteristic similarities can be found in nucleus rostrolateralis among all these species. The present study reports on these similarities in Danio and in the euteleost Xiphophorus as compared with the nucleus in Pantodon. While this nucleus has a phylogenetic distribution that might imply convergent evolution, the high degree of similarity in its features across species strongly suggests that its genetic basis may be the same despite the lack of phenotypic homology.

Animals↗
PubMed2001

The occurrence and taxonomic distribution of the anthrones aloin, aloinoside and microdontin in Aloe.

A chemotaxonomic survey of 380 species of Aloe indicated the presence of the anthrone isomers aloin A and B together with the aloinoside isomers and microdontin A and B in 36 (10%) species of Aloe. This group, referred to as the microdontin chemotype, is thus characterised by a combination of exudate compounds and not merely a single phytochemical marker, implying taxonomic significance of leaf exudate compounds. The 36 representatives of the group occupy disparate taxonomic positions in the largely artificial hierarchy of the present classification system. Although many of the species have previously been considered as related (based on macromorphology only), a large number of species have not been associated with one another before. The chemical profiles and leaf exudate compositions of the species are presented, followed by a brief summary of the morphological diversity. Whilst conceding the possibility of convergent evolution, the geographical distribution of the species and thoughts on possible relationships between the taxa are discussed.

Journal Article↗
PubMed2001

Molecular phylogeny of Myomys/Stenocephalemys complex and its relationships with related African genera.

Partial 16S rRNA mitochondrial gene sequences were used to infer the phylogenetic relationships among Stenocephalemys albocaudata, S. griseicauda and Myomys albipes, three closely related Ethiopian endemic murines and a selection of related species (Myomys daltoni, Praomys delectorum, Mastomys natalensis, Hylomyscus kaimosae, and Colomys goslingi) from other African regions. The obtained phylogeny confirms the close relationship between M. albipes and the two Stenocephalemys species, but it also suggests that both the genera Myomys and Stenocephalemys are paraphyletic, as M. albipes is closer to Stenocephalemys than to M. daltoni and S. griseicauda is more closely related to M. albipes than to S. albocaudata. These data, if confirmed, would argue that M. albipes should be renamed S. albipes. In conclusion, our study suggests that morphological similarity is not always a reliable measure for close genetic relationship in murines. Morphological similarity among species that evolved under similar ecological conditions can be the result of convergent evolution rather than a consequence of recent common ancestry.

Journal Article↗
PubMed2001

Characterization of Spiroplasma citri adhesion related protein SARP1, which contains a domain of a novel family designated sarpin.

Transmission of the plant pathogen Spiroplasma citri by its leafhopper vector, Circulifer tenellus, involves adherence to and invasion of insect host cells. The S. citri adhesion related protein P89 (SARP1) was purified by immunoprecipitation using anti-SARP1 monoclonal antibodies. The protein's N-terminal amino acid sequence was determined and used to design a degenerate oligonucleotide. The labeled oligonucleotide hybridized to a 3.5 kb MboI fragment from S. citri DNA, which was then cloned and sequenced. Additionally, a 1.9 kb RsaI fragment of S. citri DNA, partially overlapping the MboI fragment, was isolated and characterized. Sequence analysis of the two clones revealed four open reading frames. ORF1 (675 bp) encodes the C-terminal part of a Soj-like protein. ORFs 1 and 2 were separated from ORFs 3 and 4 by a putative transcription termination site, indicated by a hairpin structure. ORF3 encodes an amphiphilic 798 amino acid long protein with a cleavable signal peptide and a predicted transmembrane helix near the C-terminus. The mature protein of 85.96 kDa has a calculated pI value of 5.5 and has an N-terminal amino acid sequence consistent with that determined from the purified SARP1. At the N-terminus of this protein is a region consisting of six repeats, each 39-42 amino acids, a motif belonging to a previously unrecognized family of repeats found in a variety of bacterial proteins. The taxonomically spotty presence of this 'sarpin' domain and the relationship of the repeats to each other suggests a convergent evolution in multiple lineages.

Amino Acid Sequence↗
PubMed2001

Phosphoserine/threonine-binding domains.

Phosphorylation of proteins on serine and threonine residues has traditionally been viewed as a means to allosterically regulate catalytic activity. Research within the past five years, however, has revealed that serine/threonine phosphorylation can also directly result in the formation of multimolecular signaling complexes through specific interactions between phosphoserine/threonine (pSer/Thr)-binding modules and phosphorylated sequence motifs. pSer/Thr-binding proteins and domains currently include 14-3-3, WW domains, forkhead-associated domains, and, tentatively, WD40 repeats and leucine-rich regions. It seems likely that additional modules will be found in the future. The amino acid sequences recognized by these pSer/Thr-binding modules show partial overlap with the optimal phosphorylation motifs for different protein kinase subfamilies, allowing the formation of specific signaling complexes to be controlled through combinatorial interactions between particular upstream kinases and a particular binding module. The structural basis for pSer/Thr binding differs dramatically between 14-3-3 proteins, WW domains and forkhead-associated domains, suggesting that their pSer/Thr binding function was acquired through convergent evolution.

Animals↗
PubMed1996

Inositol phosphates - whither bound? Intracellular signalling.

Many proteins are being found to bind inositol phosphates with varying degrees of specificity; the variety of domains that can bind inositol phosphates suggests convergent evolution, but the functions of most of the binding sites are not yet clear.

Amino Acid Sequence↗
PubMed2001

Crystal structure of Streptococcus mutans pyrophosphatase: a new fold for an old mechanism.

BACKGROUND: Streptococcus mutans pyrophosphatase (Sm-PPase) is a member of a relatively uncommon but widely dispersed sequence family (family II) of inorganic pyrophosphatases. A structure will answer two main questions: is it structurally similar to the family I PPases, and is the mechanism similar? RESULTS: The first family II PPase structure, that of homodimeric Sm-PPase complexed with metal and sulfate ions, has been solved by X-ray crystallography at 2.2 A resolution. The tertiary fold of Sm-PPase consists of a 189 residue alpha/beta N-terminal domain and a 114 residue mixed beta sheet C-terminal domain and bears no resemblance to family I PPase, even though the arrangement of active site ligands and the residues that bind them shows significant similarity. The preference for Mn2+ over Mg2+ in family II PPases is explained by the histidine ligands and bidentate carboxylate coordination. The active site is located at the domain interface. The C-terminal domain is hinged to the N-terminal domain and exists in both closed and open conformations. CONCLUSIONS: The active site similiarities, including a water coordinated to two metal ions, suggest that the family II PPase mechanism is "analogous" (not "homologous") to that of family I PPases. This is a remarkable example of convergent evolution. The large change in C-terminal conformation suggests that domain closure might be the mechanism by which Sm-PPase achieves specificity for pyrophosphate over other polyphosphates.

Binding Sites↗
PubMed1998

Crystal structure of quinolinic acid phosphoribosyltransferase from Mmycobacterium tuberculosis: a potential TB drug target.

BACKGROUND: . Mycobacterium tuberculosis is the single most deadly human pathogen and is responsible for nearly three million deaths every year. Recent elucidation of the mode of action of isoniazid, a frontline antimycobacterial drug, suggests that NAD metabolism is extremely critical for this microorganism. M. tuberculosis depends solely on the de novo pathway to meet its NAD demand. Quinolinic acid phosphoribosyltransferase (QAPRTase), a key enzyme in the de novo biosynthesis of NAD, provides an attractive target for designing novel antitubercular drugs. RESULTS: . The X-ray crystal structure of the M. tuberculosis QAPRTase apoenzyme has been determined by multiple isomorphous replacement at 2.4 A resolution. Structures of the enzyme have also been solved in complex with the substrate quinolinic acid (QA), the inhibitory QA analog phthalic acid (PA), the product nicotinate mononucleotide (NAMN), and as a ternary complex with PA and a substrate analog, 5-phosphoribosyl-1-(beta-methylene)pyrophosphate (PRPCP). The structure of the nonproductive QAPRTase-PA-PRPCP Michaelis complex reveals a 5-phosphoribosyl-1-pyrophosphate-binding site that is different from the one observed in type I phosphoribosyltransferases (PRTases). The type II PRTase active site of QAPRTase undergoes conformational changes that appear to be important in determining substrate specificity and eliciting productive catalysis. CONCLUSIONS: . QAPRTase is the only known representative of the type II PRTase fold, an unusual alpha/beta barrel, and appears to represent convergent evolution for PRTase catalysis. The active site of type II PRTase bears little resemblance to the better known type I enzymes.

Amino Acid Sequence↗
PubMed1999

Mutational analysis of active-site residues of the enterococcal D-ala-D-Ala dipeptidase VanX and comparison with Escherichia coli D-ala-D-Ala ligase and D-ala-D-Ala carboxypeptidase VanY.

BACKGROUND: Vancomycin-resistant enterococci are pathogenic bacteria that attenuate antibiotic sensitivity by producing peptidoglycan precursors that terminate in D-Ala-D-lactate rather than D-Ala-D-Ala. A key enzyme in effecting antibiotic resistance is the metallodipeptidase VanX, which reduces the cellular pool of the D-Ala-D-Ala dipeptide. RESULTS: We constructed eleven mutants, using the recently determined VanX structure as a basis, to investigate residue function. Mutating Asp142 or Ser114 showed a large effect principally on KM, consistent with roles in recognition of the D-Ala-D-Ala termini. The drastic reduction or absence of activity in the Arg71 mutants correlates with a role in the stabilization of an anionic tetrahedral transition state. Three residues of the Escherichia coli D-Ala-D-Ala ligase (Ddl), Glu15, Ser 281 and Arg255, are similarly conserved and have equivalent functions with respect to VanX, consistent with a convergent evolution of active sites to bind D-Ala-D-Ala and lower energy barriers for formation of the tetrahedral intermediate and transition states. In the N-acyl-D-Ala-D-Ala carboxypeptidase VanY, all active-site residues are conserved (except for the two responsible for recognition of the dipeptide amino terminus). CONCLUSIONS: The mutagenesis results support structure-based functional predictions and explain why the VanX dipeptidase and Ddl ligase show narrow specificity for the D,D-dipeptide substrate. The results reveal that VanX and Ddl, two enzymes that use the same substrate but proceed in opposite directions driven by distinct cofactors (zinc versus ATP), evolved similar architectural solutions to substrate recognition and catalysis acceleration. VanY sequence analysis predicts an active site and mechanism of reaction similar to VanX.

Anti-Bacterial Agents↗
PubMed2002

Escherichia coli in disguise: molecular origins of Shigella.

Shigella, which still stands as a genus with four species today, in reality belongs to the extremely diverse species Escherichia coli. There are several lineages of Shigella strains derived through independent acquisition of the pINV virulence plasmid. The chromosomally determined phenotypic properties of Shigella result from convergent evolution during niche adaptation, most due to loss of function, some from negative selection pressure.

Adaptation, Biological↗
PubMed2001

Thermal hysteresis proteins.

Extreme environments present a wealth of biochemical adaptations. Thermal hysteresis proteins (THPs) have been found in vertebrates, invertebrates, plants, bacteria and fungi and are able to depress the freezing point of water (in the presence of ice crystals) in a non-colligative manner by binding to the surface of nascent ice crystals. The THPs comprise a disparate group of proteins with a variety of tertiary structures and often no common sequence similarities or structural motifs. Different THPs bind to different faces of the ice crystal, and no single mechanism has been proposed to account for THP ice binding affinity and specificity. Experimentally THPs have been used in the cryopreservation of tissues and cells and to induce cold tolerance in freeze susceptible organisms. THPs represent a remarkable example of parallel and convergent evolution with different proteins being adapted for an anti-freeze role.

Adaptation, Biological↗
PubMed1997

Structural, catalytic, and functional properties of low M(r), phosphotyrosine protein phosphatases. Evidence of a long evolutionary history.

The PTPase family comprises a number of classes of functionally and structurally unrelated enzymes; it represents an important component of the protein-tyrosine phosphorylation/dephosphorylation machinery, which regulates the level of tyrosine phosphorylation of a number of intracellular proteins. A wealth of recently reported data indicates growing interest in a group of PTPases characterized by low (near 20 kDa) molecular weight and high sequence homology (low M(r), PTPases). These enzymes are present in organisms spanning the philogenetic scale, from prokaryotes to yeast and mammals. The sequence homology of the low M(r), PTPases with other classes of PTPases is limited to the active site sequence CXXXXXRS/T, containing the Cys and Arg residues involved in enzyme catalysis found in all PTPases. The X-ray structural data of three enzymes belonging to different classes of PTPases, a bovine liver low M(r), PTPase isoenzyme, PTP1B, and Yersinia PTPase, show that all these enzymes maintain the same active site and overall catalytic mechanism, though displaying different chain foldings and topologies, supporting convergent evolution. Limited findings on the in vivo function of the low M(r), PTPases are presently available; however, an involvement of the mammalian enzymes in the membrane growth factor receptor signal transduction is emerging. The distribution of these enzymes in philogenetically distant unicellular and multicellular organisms supports their participation in important cell functions.

Amino Acid Sequence↗
PubMed1997

Molecular cloning of diadenosine tetraphosphatase from pig small intestinal mucosa and identification of sequence blocks common to diadenosine polyphosphate hydrolases and phosphorylases.

Diadenosine 5',5"'-P1,P4-tetraphosphate (Ap4A) pyrophosphohydrolase is the enzyme responsible for reducing intracellular levels of the stress-responsive nucleotide diadenosine 5',5"'-P1,P4-tetraphosphate. In order to gain more information on the relationships between the enzymes hydrolysing diadenosine polyphosphates in different eukaryotes, the Ap4A hydrolase and a corresponding cDNA have been isolated from pig small intestinal mucosa by standard procedures. The enzyme is a typical mammalian Ap4A hydrolase (Km = 0.8 microM) being sensitive to inhibition by fluoride (Ki = 24 microM) and adenosine 5'-tetraphosphate (Ki = 10 nM) and yielding ATP and AMP as products. A low Km Ap4A hydrolase (Km = 0.3 microM) was also isolated from rabbit small intestinal mucosa. These enzymes differ from the rat intestinal mucosal hydrolase, which has much higher values of Km for Ap4A and Ki for adenosine 5'-tetraphosphate. A cDNA encoding the pig enzyme was isolated from a pig ileum cDNA library. The derived amino acid sequence of the 16.8 kDa gene product shows 88% identity and 96% similarity to that of the human enzyme. The sequence has the same modification of the MutT motif found in the human enzyme in which a threonine residue replaces a hydrophobic amino acid. Sequences comparisons among eukaryotic diadenosine polyphosphate hydrolases and phosphorylases reveal two blocks of amino acid similarity, including a motif, Z[AD]Gx[ED]AGQ, which may be involved in polyphosphate binding by the hydrolases, and an invariant histidine residue that may be involved in catalysis. These sequence similarities may have arisen by convergent evolution.

Acid Anhydride Hydrolases↗