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PubMed2004

Discovery of sequence motifs related to coexpression of genes using evolutionary computation.

Transcription factors are key regulatory elements that control gene expression. Recognition of transcription factor binding site (TFBS) motifs in the upstream region of coexpressed genes is therefore critical towards a true understanding of the regulations of gene expression. The task of discovering eukaryotic TFBSs remains a challenging problem. Here, we demonstrate that evolutionary computation can be used to search for TFBSs in upstream regions of genes known to be coexpressed. Evolutionary computation was used to search for TFBSs of genes regulated by octamer-binding factor and nuclear factor kappa B. The discovered binding sites included experimentally determined known binding motifs as well as lists of putative, previously unknown TFBSs. We believe that this method to search nucleotide sequence information efficiently for similar motifs will be useful for discovering TFBSs that affect gene regulation.

Algorithms↗
PubMed2008

Investigating divergent mechanisms of mesoderm development in arthropods: the expression of Ph-twist and Ph-mef2 in Parhyale hawaiensis.

The evolution of mesoderm was important for the development of complex body plans as well as key organ systems. Genetic and molecular studies in the fruitfly, Drosophila melanogaster, have provided the majority of information concerning mesoderm development in arthropods. In Drosophila, twist is necessary for the specification and correct morphogenesis of mesoderm and myocyte enhancing factor 2 (mef2) is involved downstream of twist to activate muscle differentiation. In Drosophila, mesoderm is defined by positional cues in the blastoderm embryo, while in another arthropod group, the amphipod crustaceans, cell lineage plays a greater role in defining the mesoderm. It is not known how different mechanistic strategies such as positional information vs. cell-lineage-dependent development affect the timing and use of gene networks. Here we describe the development of the mesoderm in a malacostracan crustacean, Parhyale hawaiensis, and characterize the expression of Parhyale twist and mef2 orthologues. In Parhyale, the mesoderm of the post-mandibular segments arises mainly through the asymmetric division of mesoteloblasts as the germband elongates. Ph-twist expression is seen in a subset of segmental mesoderm during germband development, but not during early cleavages when the specific mesodermal cell lineages first arise. ph-mef2 expression starts after the segmental mesoderm begins to proliferate and persists in developing musculature. While the association of these genes with mesoderm differentiation appears to be conserved across the animal kingdom, the timing of expression and relationship with different mechanisms of mesoderm development may give us greater insight into the ancestral use of these genes during mesoderm differentiation.

Amphipoda↗
PubMed1999

The structure and evolution of the ribosomal proteins encoded in the spc operon of the archaeon (Crenarchaeota) Sulfolobus acidocaldarius.

The genes for nine ribosomal proteins, L24, L5, S14, S8, L6, L18, S5, L30, and L15, have been isolated and sequenced from the spc operon in the archaeon (Crenarchaeota) Sulfolobus acidocaldarius, and the putative amino acid sequence of the proteins coded by these genes has been determined. In addition, three other genes in the spc operon, coding for ribosomal proteins S4E, L32E, and L19E (equivalent to rat ribosomal proteins S4, L32, and L19), were sequenced and the structure of the putative proteins was determined. The order of the ribosomal protein genes in the spc operon of the Crenarchaeota kingdom of Archaea is identical to that present in the Euryarchaeota kingdom of Archaea and also identical to that found in bacteria, except for the genes for r-proteins S4E, L32E, and L19E, which are absent in bacteria. Although AUG is the initiation codon in most of the spc genes, GUG (val) and UUG (leu) are also used as initiation codons in S. acidocaldarius. Over 70% of the codons in the Sulfolobus spc operon have A or U in the third position, reflecting the low GC content of Sulfolobus DNA. Phylogenetic analysis indicated that the archaeal r-proteins are a sister group of their eucaryotic counterparts but did not resolve the question of whether the Archaea is monophyletic, as suggested by the L6P, L15P, and L18P trees, or the question of whether the Crenarchaeota is separate from the Euryarchaeota and closer to the Eucarya, as suggested by the S8P, S5P, and L24P trees. In the case of the three Sulfolobus r-proteins that do not have a counterpart in the bacterial ribosome (S4E, L32E, and L19E), the archaeal r-proteins showed substantial identity to their eucaryotic equivalents, but in all cases the archaeal proteins formed a separate group from the eucaryotic proteins.

Amino Acid Sequence↗
PubMed1990

The structure of the homeodomain and its functional implications.

The three-dimensional structure of the homeodomain, as determined by nuclear magnetic resonance spectroscopy, reveals the presence of a helix-turn-helix motif, similar to the one found in prokaryotic gene regulatory proteins. Isolated homeodomains bind with high affinity to specific DNA sequences. Thus, the structure-function relationship is highly conserved in evolution.

Amino Acid Sequence↗
PubMed1989

The complete nucleotide sequence of the growth-hormone gene from Atlantic salmon (Salmo salar).

We report here the complete genomic nucleotide sequence for the Atlantic salmon growth-hormone gene (asGH), including 600 bp of 5' flanking sequences. The primary transcription (3651 nt) is significantly longer than that of the mammalian genes, mainly because of larger intron sizes, but also because the asGH gene contains an additional intron (intron 5). The coding regions of the asGH gene have been compared to the corresponding regions from rainbow trout (cDNA and genomic), coho salmon (cDNA) and chum salmon (cDNA). With the exception of the rainbow trout cDNA sequence, all results were in agreement with current classification of the four species. The results of a similar comparison with the mRNA leader and trailer regions were also consistent with current classification. Sequences upstream from the transcription start point have been compared to the corresponding regions from rainbow trout and mammalian GH gene (maGH) upstream sequences. The results showed that the upstream sequences in the two fish species were very similar, while short stretches similar to conserved upstream sequences in the maGH genes were also found. Some of these conserved sequences are known to be involved in the specificity of expression of the mammalian genes.

Amino Acid Sequence↗
PubMed2005

PII signal transduction proteins: sensors of alpha-ketoglutarate that regulate nitrogen metabolism.

PII proteins are small homotrimeric signal transduction proteins that regulate the activities of metabolic enzymes and permeases, and control the activities of signal transduction enzymes. The protein family shows high conservation, with examples in eukaryota (plants and eukaryotic algae), archaea, and bacteria. This distribution indicates that PII is one of the most ancient signalling proteins known.

Bacterial Physiological Phenomena↗
PubMed2000

Casein kinase 2 as a potentially important enzyme in the nervous system.

Protein kinase CK2 is a ubiquitous and pleiotropic seryl/threonyl protein kinase which is highly conserved in evolution indicating a vital cellular role for this kinase. The holoenzyme is generally composed of two catalytic (alpha and/or alpha') and two regulatory (beta) subunits, but the free alpha/alpha' subunits are catalytically active by themselves and can be present in cells under some circumstances. Special attention has been devoted to phosphorylation status and structure of these enzymic molecules, however, their regulation and roles remain intriguing. Until recently, CK2 was believed to represent a kinase especially required for cell cycle progression in non-neural cells. At present, with respect to recent findings, four essential features suggest potentially important roles for this enzyme in specific neural functions: (1) CK2 is much more abundant in brain than in any other tissue; (2) there appear to be a myriad of substrates for CK2 in both synaptic and nuclear compartments that have clear implications in development, neuritogenesis, synaptic transmission, synaptic plasticity, information storage and survival; (3) CK2 seems to be associated with mechanisms underlying long-term potentiation in hippocampus; and (4) neurotrophins stimulate activity of CK2 in hippocampus. In addition, some data are suggestive that CK2 might play a role in processes underlying progressive disorders due to Alzheimer's disease, ischemia, chronic alcohol exposure or immunodeficiency virus HIV. The present review focuses mainly on the latest data concerning the regulatory mechanisms and the possible neurophysiological functions of this enzyme.

Animals↗
PubMed2000

Structure of the mouse metalloprotease meprin beta gene (Mep1b): alternative splicing in cancer cells.

The mouse meprin beta gene encodes an integral membrane protease that is expressed in a tissue-specific manner in embryonic and adult epithelial cells, and in carcinoma cells. The meprin beta mRNA in the embryo, kidney and intestinal cells is 2.5kb, whereas the isoform in carcinoma cells (beta' mRNA) is 2.7kb. The work herein was initiated to explore the molecular mechanism responsible for the different isoforms. Overlapping fragments containing the Mep1b gene were obtained from a yeast artificial chromosome clone using polymerase chain reactions. The gene spans approximately 40kb and consists of 18 exons and 17 introns. The first three exons are unique to the 5' end of beta' mRNA; the next two exons correspond to the 5' end of beta mRNA. The rest of the exons (13 total) encode the regions common to both beta and beta' messages. In conjunction with the cDNA sequences, the gene structure establishes that alternative splicing of 5' exons is responsible for the generation of the mRNA isoforms. The DNA regions between beta'- and beta-specific exons and upstream of the first beta' exon have been completely sequenced to identify potential regulatory elements for beta and beta' transcription. There is significant homology between the two regions, indicating that a duplication event occurred during evolution of the Mep1b gene. Potential promoter elements and transcription factor-binding sites were identified from comparisons to sequences in the databanks. This is the first gene structure that has been completed for meprin subunits from all species. The work elucidates molecular mechanisms that regulate differential expression of the Mep1b gene.

Alternative Splicing↗
PubMed1998

The genome sequence of Rickettsia prowazekii and the origin of mitochondria.

We describe here the complete genome sequence (1,111,523 base pairs) of the obligate intracellular parasite Rickettsia prowazekii, the causative agent of epidemic typhus. This genome contains 834 protein-coding genes. The functional profiles of these genes show similarities to those of mitochondrial genes: no genes required for anaerobic glycolysis are found in either R. prowazekii or mitochondrial genomes, but a complete set of genes encoding components of the tricarboxylic acid cycle and the respiratory-chain complex is found in R. prowazekii. In effect, ATP production in Rickettsia is the same as that in mitochondria. Many genes involved in the biosynthesis and regulation of biosynthesis of amino acids and nucleosides in free-living bacteria are absent from R. prowazekii and mitochondria. Such genes seem to have been replaced by homologues in the nuclear (host) genome. The R. prowazekii genome contains the highest proportion of non-coding DNA (24%) detected so far in a microbial genome. Such non-coding sequences may be degraded remnants of 'neutralized' genes that await elimination from the genome. Phylogenetic analyses indicate that R. prowazekii is more closely related to mitochondria than is any other microbe studied so far.

DNA Replication↗
PubMed2001

Evolution of the mitochondrial control region in Palaearctic brown trout (Salmo trutta) populations: the biogeographical role of the Iberian Peninsula.

In order to extend present knowledge of brown trout phylogeography in the Palaearctic, we analysed the complete mitochondrial D-loop sequence (1025-1027 bp) of all mitochondrial haplotypes of Salmo trutta found in the Iberian Peninsula and one North African haplotype. Sequence variation in the mitochondrial control region serves to identify four major haplotype groups within the Iberian Peninsula, i.e. Atlantic, Duero, Mediterranean and Andalusian. Including the Iberian haplotypes, the five main European groups previously established were increased to six: (i) an Atlantic group including two different clusters, South European and North Atlantic; (ii) a group representing an endemism restricted to the Duero basin in the Iberian Peninsula; (iii) an Adriatic-Andalusian group found in two vicariant areas including Adriatic-Ionian populations in the Mediterranean and the Andalusian basins of the southern Iberian Peninsula; (iv) a Mediterranean group with a distribution range that extends from the southwestern basins of the Iberian Peninsula to the Ionian basins of the Greek Peninsula; (v) a Danube group of wide distribution in the Black, Aral and Caspian basins; and (vi) a group comprising the S. t. marmoratus subspecies confined to the Adriatic Sea. The Iberian Peninsula appears to have acted as a physical boundary between haplotypes corresponding to Atlantic- and Mediterranean-draining rivers. Owing to its geographical position, this area has played a major role in present Palaearctic species distribution, as illustrated by its haplotype diversity.

Animals↗
PubMed1993

Sequence analysis of the beta-N-acetylhexosaminidase gene of Vibrio vulnificus: evidence for a common evolutionary origin of hexosaminidases.

DNA cloned from the marine bacterium Vibrio vulnificus into Escherichia coli HB101 can hydrolyze chitin oligomer analogs in the recipient. The nucleotide sequence of the cloned DNA was determined and a single long open reading frame of 2541 base pairs (initiation codon through termination codon) was found. The nucleotide sequence predicts a gene product of 847 amino acids and a molecular mass of 94.3 kDa. In vitro transcription and translation analyses indicated a single protein of 94 kDa encoded by the cloned DNA. The gene product hydrolyzes methylumbelliferyl beta-D conjugates of chitotriose, chitobiose, N-acetylglucosamine, and N-acetylgalactosamine and has, therefore, been termed a beta-N-acetylhexosaminidase. The predicted protein shares a high degree of sequence similarity with the chitobiase of Vibrio harveyi and limited similarity with the alpha chain of human beta-hexosaminidase. Cluster analyses suggest a common evolutionary ancestor for all known hexosaminidase enzymes, with no detectable relationship to known chitinases.

Amino Acid Sequence↗
PubMed2004

Functional and structural characterization of RsbU, a stress signaling protein phosphatase 2C.

RsbU is a positive regulator of the activity of sigmaB, the general stress-response sigma factor of Gram+ microorganisms. The N-terminal domain of this protein has no significant sequence homology with proteins of known function, whereas the C-terminal domain is similar to the catalytic domains of PP2C-type phosphatases. The phosphatase activity of RsbU is stimulated greatly during the response to stress by associating with a kinase, RsbT. This association leads to the induction of sigmaB activity. Here we present data on the activation process and demonstrate in vivo that truncations in the N-terminal region of RsbU are deleterious for the activation of RsbU. This conclusion is supported by comparisons of the phosphatase activities of full-length and a truncated form of RsbU in vitro. Our determination of the crystal structure of the N-terminal domain of RsbU from Bacillus subtilis reveals structural similarities to the regulatory domains from ubiquitous protein phosphatases and a conserved domain of sigma-factors, illuminating the activation processes of phosphatases and the evolution of "partner switching." Finally, the molecular basis of kinase recruitment by the RsbU phosphatase is discussed by comparing RsbU sequences from bacteria that either possess or lack RsbT.

Amino Acid Sequence↗
PubMed1982

Anti-phosphorylcholine antibodies of the T15 idiotype are optimally protective against Streptococcus pneumoniae.

In the mouse, most anti-PC antibody is found in one of the three murine anti-PC idiotype families: T15, M603, or M511. The antibodies within each of these idiotypic families have characteristic fine specificities for phosphorylcholine (PC)-analogues. In this paper we compare the ability of hybridoma IgM anti-PC antibodies of the three idiotype families to protect mice from fatal infection with S. pneumoniae. Antibody bearing the T15 idiotype was approximately 8 times as effective as antibody with the M603 idiotype and approximately 30 times as protective as antibody with the M511 idiotype. Reports by others have shown that the heavy chains of virtually all mouse anti-PC antibodies are produced by translocation of a single variable region gene and that the direct translation of this gene (in the absence of somatic mutations) results in heavy chains characteristic of the T15 idiotype. Thus, our findings suggest that the T15 germ line heavy chain variable region gene may have been selected through evolution to code for antibody binding PC-containing pathogens such as S. pneumoniae. Our observations may also explain the existence of regulatory mechanisms that result in maintenance of T15 idiotype expression in murine anti-PC immune responses.

Animals↗
PubMed2026

Molting in Pancrustacea Is Characterized by Both Deeply Conserved and Recently Evolved Gene Modules.

Arthropods such as insects and crustaceans, which together form the monophyletic group Pancrustacea, possess a rigid chitinous exoskeleton that must be periodically shed through molting to allow growth and morphological change. Although molting is a deeply conserved developmental process across Arthropoda, our understanding of its molecular mechanisms is still largely derived from insect model species. Lineage-specific innovations and losses of molting-related genes raise fundamental questions about the extent of its conservation outside noninsect arthropods. Here, we investigate the evolutionary conservation of molting gene expression across five representative pancrustacean species using publicly available transcriptomic datasets. Changes in gene expression during molting are characterized by both deeply conserved and lineage-specific gene modules. Temporal gene expression analyses reveal that these lineage-specific signatures are not uniformly distributed across the molting process: the middle transitional phase is more lineage-specific, thereby exhibiting an inverse hourglass pattern. This is likely due to life-history-specific processes, development of the cuticle, and specialized structures of the exoskeleton. Overall, this study provides evidence for both the evolutionary conservation and divergence of this key postembryonic developmental process and highlights the modular architecture of the molting program.

Animals↗
PubMed2004

Evolutionary genomics of nuclear receptors: from twenty-five ancestral genes to derived endocrine systems.

Bilaterian animals are notably characterized by complex endocrine systems. The receptors for many steroids, retinoids, and other hormones belong to the superfamily of nuclear receptors, which are transcription factors regulating many aspects of development and homeostasis. Despite a diversity of regulatory mechanisms and physiological roles, nuclear receptors share a common protein organization. To obtain the broad picture of bilaterian nuclear hormone receptor evolution, we have characterized the complete set of nuclear receptor genes from nine animal genome sequences and analyzed it in a phylogenetic framework. In addition, expressed sequence tags from key lineages with no available genome sequence were also searched. This allows us to date the evolutionary events that led from an ancestral nuclear receptor gene, in an early metazoan, to present day diversity. We show that there were approximately 25 nuclear receptor genes in Urbilateria, the ancestor of bilaterians, at which point the fundamental diversity of the subfamily was already established. Surprisingly, differential gene loss played an important role in the evolution of different nuclear receptor sets in bilaterian lineages. The nuclear receptor distribution was also shaped by periods of gene duplication, essentially in vertebrates, as well as a lineage-specific duplication burst in nematodes. Our results imply that the genes for major receptors such as steroid receptors or thyroid hormone receptors were present in Urbilateria.

Animals↗
PubMed1989

Nucleotide sequence of the Xdh region in Drosophila pseudoobscura and an analysis of the evolution of synonymous codons.

The nucleotide sequence of the Xdh region of Drosophila pseudoobscura is presented. The Xdh gene structure and organization are compared with the homologous region in D. melanogaster. This locus is shown to have similar organization in the two species, although an additional intron and three insertion/deletion events are described for the D. pseudoobscura coding region. The encoded proteins are predicted to have very similar charges and hydrophobic/hydrophilic domains even though 11% of the amino acids are different. A gene 5' to Xdh, putative l(3)s12, is suggested from sequence similarity between the species. Synonymous differences at the Xdh locus between the two species are analyzed using a new method described in the preceding paper by Lewontin. This analysis shows that synonymous positions within the Xdh locus are evolving at very different rates, being dependent on level of codon redundancy. A comparison of synonymous divergence between D. melanogaster and D. pseudoobscura in five additional genes reveals variation in the level of synonymous substitution.

Amino Acid Sequence↗