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PubMed2003

Comparative plant development: the time of the leaf?

A key problem in developmental biology is understanding the origin of morphological innovations. Comparative studies in plants with different leaf morphologies indicate that the developmental pathway defined by KNOTTED1-type homeodomain proteins could be involved in generating different leaf forms. The differential expression of regulatory proteins has emerged as an important factor in driving morphological innovations in the plant kingdom--an idea that is well supported by quantitative trait locus analyses.

Biological Evolution↗

PubMed1991

Evolution of placenta-specific gene expression: comparison of the equine and human gonadotropin alpha-subunit genes.

Primate and equine species are thought to be unique among mammals in synthesizing placental gonadotropin glycoprotein hormones. Human chorionic gonadotropin (CG) and equine pregnant mare's serum gonadotropin (PMSG) are produced in placenta by the specific activation of a glycoprotein hormone alpha-subunit gene and a corresponding beta-subunit gene. The evolutionary mechanisms for the apparently independent acquisition of tissue specificity were investigated by cloning the 5' flanking region of the equine alpha-subunit gene and comparing the DNA elements and trans-acting factors involved in placental expression. We find that though the equine gene is expressed and induced by cAMP, it does not contain the elements known to confer tissue-specific expression to the human gene, the cAMP response element (CRE) and the trophoblast-specific element (TSE), nor does it bind to the trans-acting factors CREB and TSEB. Instead, an additional factor (alpha-ACT) is found which binds to the equine and human, but not the murine, alpha-subunit genes in a region between the positions of the CRE and TSE and confers cAMP responsiveness.

Animals↗

PubMed1992

Genetic regulation of secondary metabolic pathways in Streptomyces.

Streptomyces species are (along with the fungi) the best-known antibiotic-producing organisms. Often, they make several different antibiotics. The biosynthesis of each antibiotic is encoded by a complex gene cluster that usually also contains regulatory and resistance genes. Typically, there may be more than one such pathway-specific regulatory gene per cluster. Both activator and repressor genes are known. Some of the regulatory genes for different pathways are related. In S. coelicolor, expression of several such biosynthetic gene clusters also depends on at least 11 globally acting genes, at least one of which is involved in the translation of a rare codon (UUA). A protein phosphorylation cascade also seems to be involved. Gene clusters closely similar to those for the biosynthesis of aromatic polyketide antibiotics determine spore pigment in some species. These genes show different regulation from antibiotic production genes. The evolution of gene clusters for polyketide antibiotics, and the possible adaptive benefits of secondary metabolism, are discussed.

Anti-Bacterial Agents↗

PubMed2004

Adaptation of a South American malaria vector to laboratory colonization suggests faster-male evolution for mating ability.

BACKGROUND: Anopheles (Nyssorhynchus) albitarsis (Diptera: Culicidae) is one of the very few South American mosquito vectors of malaria successfully colonized in the laboratory. These vectors are very hard to breed because they rarely mate in artificial conditions. A few years ago a free-mating laboratory colony of An. albitarsis sensu stricto was established after about 30 generations of artificial-mating. To begin to understand the process of adaptation of these malaria vectors to the laboratory we have compared the insemination rates of colony mosquitoes to those from the original population in both artificial and free-mating crosses. We also carried out crossing experiments between the two types of mosquitoes for a preliminary analysis of the genetic basis of such adaptation. RESULTS: We show that, compared to the original population, colony males but not females have increased their insemination rates in the laboratory in both types of mating, suggesting that faster-male evolution of mating ability might have occurred during the colonization process. CONCLUSIONS: The results are consistent with the faster-male theory, which predicts that sexual selection will cause faster rates of evolution of genes expressed in males. The data also suggests that attempts to colonize other South American malaria mosquitoes will be more successful if special attention is given to the male ability to mate in a confined space.

Acclimatization↗

PubMed1991

The structural biology of expression and function of tissue factor.

Analysis of the structural biology of TF provides insights into the both the expression of the gene and the function of this cell surface receptor in the initiation of the coagulation protease cascades. The advance of information may permit inferential hypotheses for the structural biology of other cofactor regulated catalytic steps in blood coagulation.

Amino Acid Sequence↗

PubMed1997

Xenopus HDm, a maternally expressed histone deacetylase, belongs to an ancient family of acetyl-metabolizing enzymes.

Modification of core histones can alter chromatin structure, facilitating the activation and repression of genes. A key example is the acetylation of N-terminal lysines of the core histones. Recently, the mammalian histone deacetylase HD1 was cloned from Jurkat T cells, and shown to be 60% identical to the yeast global gene regulator Rpd3 (Taunton et al., 1996). Here we report the cloning of HDm, a maternally expressed putative deposition histone deacetylase from Xenopus laevis. Comparison of the amino acid sequences of histone deacetylases from diverse eukaryotes shows high levels of identity within a putative enzyme core region. Further alignment with other types of protein: acetoin-utilizing enzymes from eubacteria; acetylpolyamine hydrolases from mycoplasma and cyanobacteria; and a protein of unknown function from an archaebacterium, reveals an apparently conserved core, and suggests that histone deacetylases belong to an ancient family of enzymes with related functions.

Amino Acid Sequence↗

PubMed1988

A highly conserved mouse gene with a propensity to form pseudogenes in mammals.

A mouse cDNA clone corresponding to an abundantly transcribed poly(A)+ mRNA was found to be represented by 200 copies in mammalian genomes. To understand the origin and nature of this sequence family, we studied two genomic members and two cDNA clones from mouse liver. The DNA sequence of the coding strand of a full-length cDNA clone was shown to have an open reading frame capable of encoding a 25-kilodalton polypeptide that has not been previously described. In vitro transcription-translation experiments verified the presence of an open reading frame encoding a protein of the predicted size. Restriction analysis of genomic DNA and DNA sequence analysis of genomic clones indicated that many of the 200 members of this family represent processed pseudogenes, with one or a small number of active structural genes. The vast majority of the genomic copies are heterogeneous in length, truncated at their 5' ends with respect to the mRNA, and do not appear to have intervening sequences. Two distinct genomic members of this family were sequenced and found to represent incomplete copies of the mRNA. Both are 5' truncated at slightly different points with respect to the mRNA. Both pseudogenes have multiple base changes, insertions, and deletions relative to the mRNA, and one of them encodes the poly(A) tail of the mRNA. The expression of this gene family is highest in rapidly dividing cells such as early mouse embryos and testis, but was seen in all tissues tested. This gene shows extremely high sequence conservation, extending to chicken, amphibian, and nematode genomes. Surprisingly, the gene appears to exist in only one copy in these organisms.

Animals↗

PubMed2005

The expansin superfamily.

The expansin superfamily of plant proteins is made up of four families, designated alpha-expansin, beta-expansin, expansin-like A and expansin-like B. alpha-Expansin and beta-expansin proteins are known to have cell-wall loosening activity and to be involved in cell expansion and other developmental events during which cell-wall modification occurs. Proteins in these two families bind tightly to the cell wall and their activity is typically assayed by their stimulation of cell-wall extension and stress relaxation; no bona fide enzymatic activity has been detected for these proteins. Alpha-expansin proteins and some, but not all, beta-expansin proteins are implicated as catalysts of 'acid growth', the enlargement of plant cells stimulated by low extracellular pH. A divergent group of beta-expansin genes are expressed at high levels in the pollen of grasses but not of other plant groups. They probably function to loosen maternal cell walls during growth of the pollen tube towards the ovary. All expansins consist of two domains; domain 1 is homologous to the catalytic domain of proteins in the glycoside hydrolase family 45 (GH45); expansin domain 2 is homologous to group-2 grass pollen allergens, which are of unknown biological function. Experimental evidence suggests that expansins loosen cell walls via a nonenzymatic mechanism that induces slippage of cellulose microfibrils in the plant cell wall.

Biological Evolution↗

PubMed2006

Selection for more of the same product as a force to enhance concerted evolution of duplicated genes.

The duration of concerted evolution after gene duplication is highly variable across genes. To identify the cause of the variation, we analyzed of duplicated genes in yeast that originate from a whole genome duplication event. There appears to be a strong positive correlation between the duration of concerted evolution and the gene expression level. This observation can be explained by selection favoring more of the same product, which could enhance concerted evolution in dosage-sensitive genes.

Evolution, Molecular↗

PubMed1998

The type II peroxiredoxin gene family of the mouse: molecular structure, expression and evolution.

Peroxiredoxins (Prxs) are a newly defined family of antioxidant proteins that have been implicated, via their antioxidant activity, in a number of cellular functions, including cell proliferation and differentiation, protection of other proteins from oxidative damage, and intracellular signaling. We isolated genomic DNA sequences of the type II Prx (Prx II) gene from the mouse and analyzed their molecular genetic characteristics. In the mouse, the Prx II is found to form a small multigene family with three members. One of them, the Prx II-1 gene, is actively transcribed in a variety of adult tissues as well as in the developing embryos to produce a 1.1-kb mRNA. The Prx II-1 gene consists of six exons and five introns, and the whole transcription unit occupies about 4.5 kb in the mouse genome. The other two genes, Prx II-2 and Prx II-3, are encoded by single exons, and show 97.5 and 87% of nucleotide sequence homology with the Prx II-1 gene, respectively. Structural features of these genes and the results of RT-PCR analysis on RNAs from various tissue sources indicate that the Prx II-2 and Prx II-3 genes could be pseudogenes derived from the Prx II-1 gene by a mechanism involving retrotransposition. These results strongly suggest that only the Prx II-1 gene might be relevant for studying the function of the Prx II gene in the murine system.

Amino Acid Sequence↗

PubMed1997

RNA virus mutations and fitness for survival.

RNA viruses exploit all known mechanisms of genetic variation to ensure their survival. Distinctive features of RNA virus replication include high mutation rates, high yields, and short replication times. As a consequence, RNA viruses replicate as complex and dynamic mutant swarms, called viral quasispecies. Mutation rates at defined genomic sites are affected by the nucleotide sequence context on the template molecule as well as by environmental factors. In vitro hypermutation reactions offer a means to explore the functional sequence space of nucleic acids and proteins. The evolution of a viral quasispecies is extremely dependent on the population size of the virus that is involved in the infections. Repeated bottleneck events lead to average fitness losses, with viruses that harbor unusual, deleterious mutations. In contrast, large population passages result in rapid fitness gains, much larger than those so far scored for cellular organisms. Fitness gains in one environment often lead to fitness losses in an alternative environment. An important challenge in RNA virus evolution research is the assignment of phenotypic traits to specific mutations. Different constellations of mutations may be associated with a similar biological behavior. In addition, recent evidence suggests the existence of critical thresholds for the expression of phenotypic traits. Epidemiological as well as functional and structural studies suggest that RNA viruses can tolerate restricted types and numbers of mutations during any specific time point during their evolution. Viruses occupy only a tiny portion of their potential sequence space. Such limited tolerance to mutations may open new avenues for combating viral infections.

Antiviral Agents↗

PubMed1992

Expression of the myogenic gene MRF4 during Xenopus development.

In a search for myogenic genes in Xenopus, I have cloned homologs of the mammalian myogenic genes MRF4 and myogenin. The myogenin clone is a genomic fragment encoding an amino acid sequence with 62% identity to the N-terminal region of rat myogenin. No myogenin transcript has been detected and no cDNA has been isolated, suggesting that Xenopus myogenin, if it is expressed at all, is likely to be expressed at low levels or transiently during development. A Xenopus MRF4 cDNA has been isolated and encodes an amino acid sequence with 72% identity to rat MRF4. In adult frogs, MRF4 RNA is detectable only in skeletal muscle (whereas MyoD, unexpectedly, is also expressed at low levels in the heart). During embryonic development, MRF4 RNA appears later than MyoD, at a time when the embryonic musculature already shows many differentiated features. This implies that MRF4 is not involved in the commitment or early differentiation of muscle cells. The accumulation of Xenopus MRF4 RNA overlaps with the formation of neuromuscular connections, suggesting that it may be induced by innervation. Consistent with this possibility, the level of Xenopus MRF4, but not MyoD, RNA is reduced in response to denervation of adult frog muscle.

Amino Acid Sequence↗

PubMed1984

[Genetic bases of antibody diversity].

Repertoire of immunoglobulin paratopes is estimated as at least 10(7)-10(8) per individual. This repertoire is created by the variability of paratope coding VH- and VL-genes. Three events contribute to the necessary diversity of VH- and VL-genes: 1. Sets of germline DNA segments: VH, DH, JH and VL, JL containing genetic information for different parts of V-domains amino acid sequence. 2. Ontogenic rearrangements of these segments resulting in generation and expression of complete VH- and VL-genes. These rearrangements create the third hypervariable region diversity. 3. Succeeding hypermutational process leading to numerous substitutions of single amino acids along the V-domain localized essentially in hypervariable (complementary determining) regions. This process possesses the greatest possibilities for generation of somatic diversity of V-genes. Final VH- and VL-genes diversity reaches the necessary paratope repertoire, due to epigenetic mechanism of heavy and light chains combination in immunoglobulin molecules. Mechanisms of somatic generation of V-genes diversity are interpreted to spring up and be maintained in the course of evolution because of the fact that micro-parasites (viruses and bacteria) have much higher changeability rate than their hosts--highest vertebrates. Since future evolution of micro-parasites cannot be foreseen with the past events as a basis, natural selection of many thousands of germline V-genes fails to bring adaptation of the immune system to changeability of infection agents. Optimal evolution strategy of immunoglobulin gene complex of host species is expected to ensure developing somatic mechanisms. These mechanisms would generate de novo broad and random V-gene variability which is able, through structure diversity of corresponding paratopes, to foresee not only arbitrary micro-parasite, but also any arbitrary antigen not known in phylogenesis.

Animals↗

PubMedDate not supplied

The expression of an engrailed protein during embryonic shell formation of the tusk-shell, Antalis entalis (Mollusca, Scaphopoda).

This study presents the first detailed account of the larval and early post-metamorphic development of a scaphopod species, Antalis entalis, since 1883. Special reference is given to the expression pattern of an engrailed protein during the formation of the embryonic (protoconch) and adult shell (teleoconch). We found that in the trochophore-like larva the engrailed protein is expressed in shell-secreting cells at the margin of the protoconch close to the mantle edge. During metamorphosis the growth of the protoconch and expression of the engrailed protein along its margin stop and the teleoconch starts to form. These data suggest a different genetic background regarding protoconch and teleoconch formation in the Scaphopoda and possibly all Conchifera, thus inferring a different evolutionary origin of both organs. The single anlage of the scaphopod protoconch contradicts earlier hypotheses of a monophyletic taxon Diasoma (Scaphopoda + Bivalvia), which has been mainly based on the assumption of a primarily bilobed shell in both taxa. Comparative data on engrailed expression patterns suggest nervous system patterning as the basic function of engrailedin the Bilateria. However, there are several independent gain-of-function events, namely segment compartmentation in the Annelida and Arthropoda, protoconch formation in the Mollusca, skeletogenesis in the Echinodermata, and limb formation in vertebrates. These findings provide further evidence that homologous genes may act in very different pathways of bilaterian body plan formation in various animal phyla.

Animals↗

PubMed1994

Inactivation of gene expression in plants as a consequence of specific sequence duplication.

Numerous examples now exist in plants where the insertion of multiple copies of a transgene leads to loss of expression of some or all copies of the transgene. Where the transgene contains sequences homologous to an endogenous gene, expression of both transgene and endogenous gene is sometimes found to be impaired. Several examples of these phenomena displaying different features are reviewed. Possible explanations for the observed phenomena are outlined, drawing on known cellular processes in Drosophila, fungi, and mammals as well as plants. It is hypothesized that duplicated sequences can, under certain circumstances, become involved in cycles of hybrid chromatin formation or other processes that generate the potential for modification of inherited chromatin structure and cytosine methylation patterns. These epigenetic changes could lead to altered transcription rates or altered efficiencies of mRNA maturation and export from the nucleus. Where the loss of gene expression is posttranscriptional, antisense RNA could be formed on accumulated, inefficiently processed RNAs by an RNA-dependent RNA polymerase or from a chromosomal promoter and cause the observed loss of homologous mRNAs and possibly the modification of homologous genes. It is suggested that the mechanisms evolved to help silence the many copies of transposable elements in plants. Multicopy genes that are part of the normal gene catalog of a plant species must have evolved to avoid these silencing mechanisms or their consequences.

Biological Evolution↗

PubMed1992

MgtA and MgtB: prokaryotic P-type ATPases that mediate Mg2+ influx.

The gram-negative bacterium Salmonella typhimurium possesses three distinct Mg2+ transport systems, encoded by the corA, mgtA, and mgtB loci. The CorA transport system is the constitutive Mg2+ influx system. It can also mediate Mg2+ efflux at very high extracellular Mg2+ concentrations. In contrast, the MgtA and MgtB Mg2+ transport systems are normally expressed only at low extracellular Mg2+ concentrations. A strain of S. typhimurium was constructed by mutagenesis which lacks Mg2+ transport and requires 100 mM Mg2+ for growth. Using this strain, both the MgtA and MgtB transport systems were cloned by complementation of the strains inability to grow without Mg2+ supplementation. After sequencing and further genetic analysis, the MgtB system appears to be an operon composed of the mgtC and mgtB genes (5' to 3'). The downstream mgtB gene encodes the 102 kDa MgtB protein which by sequence analysis is clearly a P-type ATPase. Interestingly, while MgtB has relatively poor homology to other known prokaryotic P-type ATPases, it is highly homologous to mammalian reticular Ca(2+)-ATPases. MgtC is a 22.5 kDa hydrophobic membrane protein that lacks homology to any known protein. Transposon insertions in this gene abolish uptake by the MgtB transport system. We hypothesize that MgtC is a subunit of the MgtB ATPase involved either in proper insertion of MgtB into the membrane or possibly in binding of extracellular Mg2+ for delivery to the ATPase subunit. The sequence of the MgtA gene has recently been completed, and it too is a P-type ATPase more similar to eukaryotic than prokaryotic P-type ATPases. Expression of both MgtA and MgtB are highly regulated by the concentration of extracellular Mg2+. Transcription of mgtB can be increased about 1000 fold by lowering Mg2+ from 1 mM to 1 microM. Likewise, when mgtB is expressed from a multicopy plasmid, a similar decrease in extracellular Mg2+ greatly increases transport. Under growth conditions of limiting Mg2+, MgtB becomes the dominant Mg2+ influx system in S. typhimurium. Even so, since MgtB (and MgtA) mediate only influx of Mg2+, it is unclear why the cell requires energy from ATP to mediate Mg2+ entry into the cell down a large electrochemical gradient. Further studies of the structure-function and energetics of these novel Mg2+ influx P-type ATPases should yield insights into the function of P-type ATPases in general as well as information about the regulation of cellular Mg2+ fluxes.

Adenosine Triphosphatases↗

PubMed2026

A high-quality draft genome assembly of Johnsongrass illuminates relationships between polyploidization, crop-wild hybridization, and reproductive biology.

Johnsongrass [Sorghum halepense (L.) Pers.] is an allopolyploid, rhizomatous, perennial grass species and one of the most troublesome weeds in global agriculture. We assembled the first Johnsongrass genome to clarify poorly understood genetic factors influencing variable rates of crop-wild hybridization with cultivated sorghum [S. bicolor (L.) Moench]. The draft genome assembly has a total size of 3.26 Gb and BUSCO completeness of 95.3%. We also report the first evolutionary analysis of INHIBITION OF ALIEN POLLEN (IAP), the only known cross-(in)compatibility locus in the genus. Our results reveal an evolutionary history of genome instability, including the loss of distinct parental subgenomes, and suggest that Nebraska accession 'J-37,' the genome donor, is a segmental allotetraploid that may function as a diploid or aneuploid during meiosis. Genome instability could explain observations of variable ploidies in Johnsongrass and facilitate ongoing hybridization with sorghum where gamete ploidies and IAP alleles match. Given this information, we provide a suggested research framework for studying evolution and gene expression in the Sorghum genus where crop-wild hybridization occurs and for predicting the potential for hybridization between specific crossing partners. Collectively, this work will bolster efforts to study and manage reproductive biology in other crop-wild polyploid complexes.

Sorghum↗

PubMed2004

Protein networks, pleiotropy and the evolution of senescence.

The number of interactions, or connectivity, among proteins in the yeast protein interaction network follows a power law. I compare patterns of connectivity for subsets of yeast proteins associated with senescence and with five other traits. I find that proteins associated with ageing have significantly higher connectivity than expected by chance, a pattern not seen for most other datasets. The pattern holds even when controlling for other factors also associated with connectivity, such as localization of protein expression within the cell. I suggest that these observations are consistent with the antagonistic pleiotropy theory for the evolution of senescence. In further support of this argument, I find that a protein's connectivity is positively correlated with the number of traits it influences or its degree of pleiotropy, and further show that the average degree of pleiotropy is greatest for proteins associated with senescence. I explain these results with a simple mathematical model combining assumptions of the antagonistic pleiotropy theory for the evolution of senescence with data on network topology. These findings integrate molecular and evolutionary models of senescence, and should aid in the search for new ageing genes.

Aging↗