CPR-C4 is a highly conserved novel protease from the Candidate Phyla Radiation with remote structural homology to human vasohibins

The Candidate Phyla Radiation is a recently uncovered and vast expansion of the bacterial domain of life, made up of largely uncharacterized phyla that lack isolated representatives. This unexplored territory of genetic diversity presents an abundance of novel proteins with potential applications in the life-science sectors. Here, we present the structural and functional elucidation of CPR-C4, a hypothetical protein from the genome of a thermophilic Candidate Phyla Radiation organism, identified through metagenomic sequencing. Our analyses revealed that CPR-C4 is a member of a family of highly conserved proteins within the Candidate Phyla Radiation. The function of CPR-C4 as a cysteine protease was predicted through remote structural similarity to the Homo sapiens vasohibins and subsequently confirmed experimentally with fluorescence-based activity assays. Furthermore, detailed structural and sequence alignment analysis enabled identification of a noncanonical cysteine-histidine-leucine(carbonyl) catalytic triad. The unexpected structural and functional similarities between CPR-C4 and the human vasohibins suggest an evolutionary relationship undetectable at the sequence level alone.     

Identifying conserved gene clusters in the presence of homology families.

The study of conserved gene clusters is important for understanding the forces behind genome organization and evolution, as well as the function of individual genes or gene groups. In this paper, we present a new model and algorithm for identifying conserved gene clusters from pairwise genome comparison. This generalizes a recent model called "gene teams." A gene team is a set of genes that appear homologously in two or more species, possibly in a different order yet with the distance of adjacent genes in the team for each chromosome always no more than a certain threshold. We remove the constraint in the original model that each gene must have a unique occurrence in each chromosome and thus allow the analysis on complex prokaryotic or eukaryotic genomes with extensive paralogs. Our algorithm analyzes a pair of chromosomes in O(mn) time and uses O(m+n) space, where m and n are the number of genes in the respective chromosomes. We demonstrate the utility of our methods by studying two bacterial genomes, E. coli K-12 and B. subtilis. Many of the teams identified by our algorithm correlate with documented E. coli operons, while several others match predicted operons, previously suggested by computational techniques. Our implementation and data are publicly available at euler.slu.edu/ approximately goldwasser/homologyteams/.     

CENP-B is a highly conserved mammalian centromere protein with homology to the helix-loop-helix family of proteins

CENP-B is a centromere associated protein originally identified in human cells as an 80 kDa autoantigen recognized by sera from patients with anti-centromere antibodies (ACA). Recent evidence indicates that CENP-B interacts with centromeric heterochromatin in human chromosomes and may bind to a specific subset of human alphoid satellite DNA. CENP-B has not been unambiguously identified in non-primates and could, in principal, be a primate-specific alphoid DNA binding protein. In this work, a human genomic DNA segment containing the CENP-B gene was isolated and subjected to DNA sequence analysis. In vitro expression identified the site for translation initiation of CENP-B, demonstrating that it is encoded by an intronless open reading frame (ORF) in human DNA. A homologous mouse gene was also isolated and characterized. It was found to possess a high degree of homology with the human gene, containing an intronless ORF coding for a 599 residue polypeptide with 96% sequence similarity to human CENP-B. 5 and 3 flanking and untranslated sequences were conserved at a level of 94.6% and 82.7%, respectively, suggesting that the regulatory properties of CENP-B may be conserved as well. CENP-B mRNA was detected in mouse cells and tissues and an immunoreactive nuclear protein identical in size to human CENP-B was detected in mouse 3T3 cells using human ACA. Analysis of the sequence of CENP-B revealed a segment of significant similarity to a DNA binding motif identified for the helix-loop-helix (HLH) family of DNA binding proteins. These data demonstrate that CENP-B is a highly conserved mammalian protein that may be a member of the HLH protein family and suggest that it plays a role in a conserved aspect of centromere structure or function.     

The carrot secreted glycoprotein gene EP1 is expressed in the epidermis and has sequence homology to Brassica S-locus glycoproteins

Non-embryogenic carrot suspension cells secrete the EP1 glycoprotein. A cDNA clone encoding EP1 was isolated and sequenced. The EP1 sequence revealed a region of homology with Brassica S-locus glycoprotein genes, an Arabidopsis S-like gene and putative S-like receptor protein kinases from maize and Arabidopsis. EP1 gene expression, analysed by in situ mRNA localization, was detected in cells located at the surface of the seedling: in the epidermis of the root, the hypocotyl and the cotyledons, in the root cap, and in a crescent of cells in the apical dome of the shoot. In developing seeds, expression was most pronounced in both the inner and outer integument epidermis.     

Sheep neuropeptide Y. A third structural type of a highly conserved peptide

Mammalian forms of neuropeptide Y (NPY) for which the amino acid sequences have previously been determined, are the human, pig, ox, rabbit, rat, and guinea-pig polypeptides. The only difference among these forms is at position 17, where pig and ox NPY have Leu and the others Met. We now show that sheep NPY differs from all the earlier characterized mammalian forms of NPY by having Asp instead of Glu at position 10. At position 17 it has Leu as do both pig and ox NPY. Consequently, 3 different structural types of mammalian NPY are now known.     

Defining structural homology between the mammalian and avian hippocampus through conserved gene expression patterns observed in the chick embryo

The mammalian hippocampus, a center of neurogenesis in the adult brain, is involved in critical functions such as learning and memory processing. Although there is an overall functional conservation between birds and mammals in the hippocampal region of the brain, there are several morphological differences. A few different models have been proposed for identifying regional and structural homology between the avian and mammalian hippocampus however a consensus is yet to be reached. In this study we have systematically and comprehensively characterized the developing chicken hippocampus at the molecular level. We have identified the time window of neurogenesis and apoptosis during hippocampal development as well as the likely origin and migration path of neurons of the ventral v-shaped region of chick hippocampus. In addition to this we have identified several genes with expression patterns that are conserved between the hippocampus of chicken and mice. Our study provides molecular data that partially supports one of the models reported in literature for structural homology between the avian and mammalian hippocampus. Functional characterization of the genes found in this study to be specifically expressed in the developing chicken hippocampus is likely to provide valuable information on the mechanisms regulating hippocampus development of birds and perhaps could be extrapolated to mammalian hippocampus development as well.     

A ras-related gene from the lower eukaryote Dictyostelium that is highly conserved relative to the human rap genes.

The cellular slime mold Dictyostelium discoideum contains two ras genes, DdrasG and Ddras that are differentially expressed during development. We have characterized a gene that hybridized to both Ddras and DdrasG under low, but not under high stringency conditions. The deduced amino acid sequence is highly conserved with respect to the human rap (Krev-1, smg21) proteins and the corresponding gene has been designated Ddrap1. The Ddrap1 gene is expressed at all stages during development but is expressed maximally during the aggregation and culmination periods when the expression of Ddras and DdrasG is declining. During vegetative growth and early development Ddrap1 cDNA hybridizes to a single mRNA of 1.1 kb. As development progresses the level of this mRNA declines and messages of 1.0 and 1.3 kb appear.     

A highly conserved microsatellite in the dystrophin gene of diverse mammalian species

The presence of a CA repeat within the 3'-untranslated region (UTR) of the dystrophin gene has been reported previously in several species. Because microsatellites showing high cross-species homology can be conveniently used as markers in those species for which detailed linkage maps have not yet been developed, we evaluated whether the CA repeat could be amplified from a wide variety of mammalian species. Using a single pair of canine-specific oligonucleotide primers, we successfully amplified the 3'-UTR from 18 different carnivore and six additional species (human, chimpanzee, goat, cow, rabbit and mouse) and show conservation of the CA repeat in the dystrophin gene from a wide range of evolutionarily diverse mammalian species.     

Structural homology of lens crystallins. A method to detect protein structural homology from primary sequences

The X-ray crystallographic structure of bovine gamma-crystallin shows four similar folding motifs each composed of about 42 residues arranged as four topologically sequential, anti-parallel beta-strands. Since the beta and gamma-crystallin sequences show good homology, proposals for a four-motif beta-crystallin model have been made. The other bovine eye-lens protein species, alpha-crystallins, are not homologous to beta or gamma-crystallin in primary structure. In the present work, smoothed plots of amino acid sequence number versus a residue characteristic (e.g. hydrophobicity) were calculated for the various crystallins. Cross-correlation coefficients were then determined between pairs of crystallin plots for various registers of the curves. The correlation plots were then combined for several characteristics and for pairwise comparisons between beta or gamma-crystallin and the alpha-crystallins. The resulting plots showed four peaks separated by about 42 residues for the alpha-crystallins, suggesting that they also possess a four-motif beta-barrel structure. The physical parameter comparison technique appears generally applicable in suggesting a structural and functional relationship amongst proteins that show no primary sequence homology.     

A highly evolutionarily conserved mitochondrial protein is structurally related to the protein encoded by the Escherichia coli groEL gene.

We recently reported that a Tetrahymena thermophila 58-kilodalton (kDa) mitochondrial protein (hsp58) was selectively synthesized during heat shock. In this study, we show that hsp58 displayed antigenic similarity with mitochondrially associated proteins from Saccharomyces cerevisiae (64 kDa), Xenopus laevis (60 kDa), Zea mays (62 kDa), and human cells (59 kDa). Furthermore, a 58-kDa protein from Escherichia coli also exhibited antigenic cross-reactivity to an antiserum directed against the T. thermophila mitochondrial protein. The proteins from S. cerevisiae and E. coli antigenically related to hsp58 were studied in detail and found to share several other characteristics with hsp58, including heat inducibility and the property of associating into distinct oligomeric complexes. The T. thermophila, S. cerevisiae, and E. coli macromolecular complexes containing these related proteins had similar sedimentation characteristics and virtually identical morphologies as seen with the electron microscope. The distinctive properties of the E. coli homolog to T. thermophila hsp58 indicate that it is most likely the product of the groEL gene.     

Extensive homology between the herpes simplex virus type 2 glycoprotein F gene and the herpes simplex virus type 1 glycoprotein C gene.

The region of the herpes simplex virus type 2 (HSV-2) genome which maps colinearly with the HSV-1 glycoprotein C (gC) gene has been cloned, and the DNA sequence of a 2.29-kilobase region has been determined. Contained within this sequence is a major open reading frame of 479 amino acids. The carboxyterminal three-fourths of the derived HSV-2 protein sequence showed a high degree of sequence homology to the HSV-1 gC amino acid sequence reported by Frink et al. (J. Virol. 45:634-647, 1983). The amino-terminal region of the HSV-2 sequence, however, showed very little sequence homology to HSV-1 gC. In addition, the HSV-1 gC sequence contained 27 amino acids in the amino-terminal region which were missing from the HSV-2 protein. Computer-assisted analysis of the hydrophilic and hydrophobic properties of the derived HSV-2 sequence demonstrated that the protein contained structures characteristic of membrane-bound glycoproteins, including an amino-terminal signal sequence and carboxy-terminal hydrophobic transmembrane domain and charged cytoplasmic anchor. The HSV-2 protein sequence also contained seven putative N-linked glycosylation sites. These data, in conjunction with mapping studies of Para et al. (J. Virol. 45:1223-1227, 1983) and Zezulak and Spear (J. Virol. 49:741-747, 1984), suggest that the protein sequence derived from the HSV-2 genome corresponds to gF, the HSV-2 homolog of HSV-1 gC.