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PubMed1991

Drosophila has a twitchin/titin-related gene that appears to encode projectin.

The sequences of twitchin and titin identify a superfamily of muscle proteins whose functions are not completely understood. In spite of their shared structural features, twitchin and titin appear to differ in function. Genetic and molecular evidence suggests that twitchin has a regulatory role in muscle contraction, whereas it has been proposed that titin has a structural function. We report here that Drosophila has a single-copy gene containing the two-motif amino acid sequence pattern that characterizes twitchin and titin. This gene appears to encode projectin, a muscle protein that is thought to play a structural role in asynchronous flight muscle but may have a role like that of twitchin in synchronous muscle. Thus Drosophila appears to be a case where the apparently diverged functions of twitchin and titin are encoded by a single gene.

Amino Acid Sequence↗
PubMed1994

Three-dimensional structures of two plant beta-glucan endohydrolases with distinct substrate specificities.

The three-dimensional structures of (1-->3)-beta-glucanase (EC 3.2.1.39) isoenzyme GII and (1-->3,1-->4)-beta-glucanase (EC 3.2.1.73) isoenzyme EII from barley have been determined by x-ray crystallography at 2.2- to 2.3-A resolution. The two classes of polysaccharide endohydrolase differ in their substrate specificity and function. Thus, the (1-->3)-beta-glucanases, which are classified amongst the plant "pathogenesis-related proteins," can hydrolyze (1-->3)- and (1-->3,1-->6)-beta-glucans of fungal cell walls and may therefore contribute to plant defense strategies, while the (1-->3,1-->4)-beta-glucanases function in plant cell wall hydrolysis during mobilization of the endosperm in germinating grain or during the growth of vegetative tissues. Both enzymes are alpha/beta-barrel structures. The catalytic amino acid residues are located within deep grooves which extend across the enzymes and which probably bind the substrates. Because the polypeptide backbones of the two enzymes are structurally very similar, the differences in their substrate specificities, and hence their widely divergent functions, have been acquired primarily by amino acid substitutions within the groove.

Base Sequence↗
PubMed1993

Functional characteristics of QT prediction formulas. The concepts of QTmax and QT rate sensitivity.

A community-based population sample of 14,379 North American children and adults aged from birth to 75 years with normal ECG was used to investigate functional properties of 13 QT prediction formulas over a wide range of heart rates (HR) in normal sinus rhythm. QT measurements were made by a computer program from simultaneously sampled standard 12-lead or orthogonal XYZ leads and all QT measurements were visually verified using a high-resolution display terminal. New concepts of QT rate sensitivity (dQT/dHR) and maximum predicted QT after a long pause (QTmax) are introduced. Drastically diverging functional behavior is documented for different QT prediction formulas regarding QT rate sensitivity and QTmax. The simplest formula for predicted QT (QTp) meeting reasonable physiological constraints regarding QTmax and functional behavior of QT rate sensitivity while producing the best QT prediction accuracy was a function with only one independently adjusted parameter (QTmax) of the form: QTp = QTmax/(1 + 0.01HR), with QTmax = 656 ms. This formula also suggests that QT rate sensitivity is inversely proportional to the square of HR and that individual values of QTmax can be predicted from ambulatory or exercise ECGs using the formula QTmax = 2 x QT100, where QT100 is QT at HR = 100/min.

Adolescent↗
PubMed1980

Lactate dehydrogenases of Atlantic hagfish: physiological and evolutionary implications of a primitive heart isozyme.

Isozymes of lactate dehydrogenase from heart and muscle of Atlantic hagfish show less functional divergence than those from other fishes and higher vertebrates. The enzyme from hagfish heart (B4) displays a higher Michaelis constant for pyruvate and lower substrate inhibition at moderate pyruvate concentrations than heart isozymes from other species. These properties support the hypothesis that the ancestral vertebrate lactate dehydrogenase was a muscle (A4)-type enzyme and also suggest a role for the B4 enzyme in the unusual physiology of hagfish cardiac tissue which functions under sustained hypoxic conditions.

Anaerobiosis↗
PubMedDate not supplied

Divergent structure and function of the bicoid gene in Muscoidea fly species.

We have investigated the evolution of the bicoid (bcd) gene in fly species of the Muscoidea Superfamily. We obtained the complete bcd sequence from the housefly Musca domestica and found polymorphism in the coding region among Musca strains. In addition to Musca, we cloned most of the bcd coding sequences from two blowfly species Calliphora vicina and Lucilia sericata. The 5' and 3' regulatory regions flanking the Musca bcd gene are widely diverged in sequence from Drosophila; however, some important sequence motifs identified in Drosophila bcd are present. The predicted RNA secondary structures of the 3' UTRs are similar, despite sequence divergence. Comparison of Bicoid (Bcd) proteins shows a serine-rich domain of unknown function is present in the Muscoidea species, but is absent in other species. The in vivo function of bcd in Musca was tested by RNAi to mimic loss of function phenotype. We obtained a head defect phenotype similar to weak bcd alleles of Drosophila. Although our comparisons initially suggest functional conservation between species, closer inspection reveals significant differences. Divergence of structural motifs, such as regulatory elements in flanking regions and conservation of protein domains in some species but not in others, points to functional divergence between species. We suggest that the larger embryonic size in Muscoidea species restricts the morphogenetic activity of a weak Bcd activator, which has evolved a more specialized role in head determination and lost some functions in thoracic development.

3' Untranslated Regions↗
PubMed2001

Two cyclophilin A homologs with shared and distinct functions important for growth and virulence of Cryptococcus neoformans.

Cyclophilin A is the target of the immunosuppressant cyclosporin A (CsA) and is encoded by a single unique gene conserved from yeast to humans. In the pathogenic fungus Cryptococcus neoformans, two homologous linked genes, CPA1 and CPA2, were found to encode two conserved cyclophilin A proteins. In contrast to Saccharomyces cerevisiae, in which cyclophilin A mutations confer CsA resistance but few other phenotypes, cyclophilin A mutations conferred dramatic phenotypes in C. neoformans. The Cpa1 and Cpa2 cyclophilin A proteins play a shared role in cell growth, mating, virulence and CsA toxicity. The Cpa1 and Cpa2 proteins also have divergent functions. cpa1 mutants are inviable at 39 degrees C and attenuated for virulence, whereas cpa2 mutants are viable at 39 degrees C and fully virulent. cpa1 cpa2 double mutants exhibited synthetic defects in growth and virulence. Cyclophilin A active site mutants restored growth of cpa1 cpa2 mutants at ambient but not at higher temperatures, suggesting that the prolyl isomerase activity of cyclophilin A has an in vivo function.

Amino Acid Sequence↗
PubMed2025

Phyllosphere microbiomes in grassland plants harbor a vast reservoir of novel antimicrobial peptides and biosynthetic diversity.

INTRODUCTION: The phyllosphere microorganisms colonizing plant surface harbor capacities to synthesize diverse specialized metabolites that mediate communication and interactions with environment and host. However, most known metabolites are derived from a few culturable microorganisms, and the genomic diversity and biosynthetic potential of the vast majority of bacteria associated with plants remain largely unexplored. OBJECTIVES: Here, we aim to explore the genome architecture, biosynthetic ability, and host specific adaptability of grassland ecosystems, uncovering new perspectives on grassland phyllosphere microbial resources. METHODS: We employed ultra-deep metagenomic sequencing, functional analysis, host-associated characterization, and bioactivity assays to explore the phyllosphere microbiome across 221 grassland plant samples representing 45 families. This approach revealed host preference in biosynthetic gene clusters (BGCs) and validated the antimicrobial efficacy of phyllosphere-derived antimicrobial peptides (AMPs). RESULTS: Grassland plant phyllosphere microbiomes encode diverse BGCs. We identified 885,396 potential AMPs from over 68 million non-redundant gene sequences. Then, we reconstructed hundreds of near-complete genomes from phyllosphere metagenomes, and 32.61 % of reconstructed genomes were identified as unclassified genomes, primarily within Pseudomonadota, Actinomycetota, Bacillota and Bacteroidota phyla. Of the near-complete genomes, 91.97 % of the BGCs and 99.76 % of the identified AMPs were previously uncharacterized. Host phylogenetic analysis revealed functional divergence. Poaceae-associated Pseudomonas genomes contain an average of 28 BGCs, significantly higher than those in Asteraceae-associated genomes (mean = 14.76, P = 0.033). Similarly, Poaceae-associated Pantoea genomes carried an average of 9 BGCs, exhibiting significant enrichment compared to genomes from Asteraceae (mean = 7.13, P = 6.1e-05), Lamiaceae (mean = 7, P = 0.015), Ranunculaceae (mean = 8.22, P = 0.0053), and Rosaceae (mean = 7.75, P = 0.00069). ParaFit analyses further confirmed that host phylogeny significantly structures microbial functional repertoires, with intra-family hosts sharing more KEGG pathways than inter-family hosts. These results suggest that host evolutionary relationships are associated with metabolic specialization in phyllosphere microbiomes. All 13 AMPs synthesized via solid-phase peptide synthesis demonstrated antimicrobial activity, inhibiting the growth of at least one tested bacterial strain. CONCLUSION: This study demonstrates the promise of grassland plant phyllosphere microbiome as a rich source for novel antimicrobial agents.

Antimicrobial Peptides↗
PubMed1984

Isolation and characterization of two myoactive neuropeptides: further evidence of an invertebrate peptide family.

The neuropeptide proctolin acts as a neuromuscular co-transmitter in insect skeletal muscle. As a prelude to determining whether other peptides may function in a similar way, we are attempting to isolate and characterize the chemical nature of new myoactive neuropeptides in insects. We examined the corpus cardiacum, a major insect neurosecretory structure of the American cockroach (Periplaneta americana), using a skeletal muscle bioassay and high pressure liquid chromatography fractionation and identified two myoactive factors, MI and MII. They are synthesized in the corpus cardiacum and released from it into the blood by a calcium-dependent mechanism. Amino acid and fast atom bombardment-mass spectroscopy analysis show that MI and MII are structurally related octapeptides representing the major secreted products of the cockroach corpus cardiacum. Both MI and MII are also present in the CNS and in the gut, indicating transmitter as well as hormonal functions in the cockroach. A survey in other species indicates MI may be present in invertebrates other than insects, but neither was found in the rat. The MI and MII peptides have clear chemical affinities to two previously described invertebrate peptides, locust adipokinetic hormone and crustacean red pigment concentrating hormone, as well as sharing biological activity with these peptides. Our results provide further evidence for the existence of a large family of structurally related peptides with divergent functions in a variety of invertebrate types.

Animals↗
PubMed1996

Lambda-interacting protein, a novel protein that specifically interacts with the zinc finger domain of the atypical protein kinase C isotype lambda/iota and stimulates its kinase activity in vitro and in vivo.

The members of the atypical subfamily of protein kinase C (PKC) show dramatic structural and functional differences from other PKC isotypes. Thus, in contrast to the classical or novel PKCs, they are not activated by diacylglycerol or phorbol esters. However, the atypical PKCs are the target of important lipid second messengers such as ceramide, phosphatidic acid, and 3'-phosphoinositides. The catalytic and pseudosubstrate sequences in the two atypical PKCs (lambda/iota PKC and zeta PKC) are identical but are significantly different from those of conventional or novel PKCs. It has been shown that microinjection of a peptide with the sequence of the pseudosubstrate of the atypical PKC isotypes but not of alpha PKC or epsilon PKC dramatically inhibited maturation and NF-kappa B activation in Xenopus oocytes, as well as reinitiation of DNA synthesis in quiescent mouse fibroblasts. This indicates that either or both atypical isoforms are important in cell signalling. Besides the pseudosubstrate, the major differences in the sequence between lambda/iota PKC and zeta PKC are located in the regulatory domain. Therefore, any functional divergence between the two types of atypical PKCs will presumably reside in that region. We report here the molecular characterization of lambda-interacting protein (LIP), a novel protein that specifically interacts with the zinc finger of lambda/iota PKC but not zeta PKC. We show in this paper that this interaction is detected not only in vitro but also in vivo, that LIP activates lambda/iota PKC but not zeta PKC in vitro and in vivo, and that this interaction is functionally relevant. Thus, expression of LIP leads to the transactivation of a kappa B-dependent promoter in a manner that is dependent on lambda/iota PKC. To our knowledge, this is the first report on the cloning and characterization of a protein activator of a PKC that binds to the zinc finger domain, which has so far been considered a site for binding of lipid modulators. The fact that LIP binds to lambda/iota PKC but not to the highly related zeta PKC isoform suggests that the specificity of the activation of the members of the different PKC subfamilies will most probably be accounted for by proteins like LIP rather than by lipid activators.

Amino Acid Sequence↗
PubMed2003

Selection on coding regions determined Hox7 genes evolution.

The important role of Hox genes in determining the regionalization of the body plan of the vertebrates makes them invaluable candidates for evolutionary analyses regarding functional and morphological innovation. Gene duplication and gene loss led to a variable number of Hox genes in different vertebrate lineages. The evolutionary forces determining the conservation or loss of Hox genes are poorly understood. In this study, we show that variable selective pressures acted on Hox7 genes in different evolutionary lineages, with episodes of positive selection occurring after gene duplications. Tests for functional divergence in paralogs detected significant differentiation in a region known to modulate HOX7 protein activity. Our results show that both positive and negative selection on coding regions are influencing Hox7 genes evolution.

Amino Acid Sequence↗
PubMed1995

Function of exon 2 in optimal trans-activation by Tat of HIV type 2.

HIV-1 and HIV-2 are human retroviruses whose life cycles require viral regulatory proteins, one of which is the trans-activator, Tat. Tat of HIV-1 (Tat-1) displays modular function with independent activation function localized to the amino-terminal, cysteine-rich, and core regions and independent RNA-binding function localized to a basic region. These functional domains are contained in the first of two exons encoding Tat-1; deletion of exon 2 does not contribute to functional domains of Tat-1. Tat of HIV-2 (Tat-2) has structurally analogous regions, but the amino terminus, basic region, and carboxy terminus encoded by exon 2 display amino acid sequence and functional divergence compared to Tat-1. We have shown that, in contrast to Tat-1, exon 2 of Tat-2 (residues 100 to 130) is required for optimal trans-activation of HIV-1 and HIV-2 long terminal repeats (LTRs). Here we demonstrate that a series of basic residues in exon 2 are required for these effects. Exon 2 does not alter the level of protein expression of Tat-2. Further, in the context of heterologous DNA binding, exon 2 does not contribute to activation function. These data suggest that full-length Tat-2 results in optimal trans-activation through enhanced RNA-binding function of exon 1 by involvement of a basic region in exon 2. Differential expression of short and full-length Tats during different stages of the HIV-2 life cycle might regulate levels of viral expression, viral replication, and resultant cytopathology.

Amino Acid Sequence↗
PubMed2005

Developmental expression of metalloproteases ADAM 9, 10, and 17 becomes restricted to divergent pancreatic compartments.

The A Disintegrin And Metalloprotease (ADAM) family of metalloproteases affects a variety of proteins with important roles in development and disease, including growth factors and adhesion molecules. We have analyzed the expression patterns of ADAMs 9, 10, and 17 during pancreas ontogeny. All ADAMs investigated were expressed in the pancreatic anlagen but invariably became restricted to divergent pancreatic compartments. ADAM9 and 17 became restricted to the insulin-producing beta-cells and all islet cells, respectively. During embryogenesis, ADAM10 was detected predominantly in acinar cells, but in the adult, it was localized to the cell surface membrane of both endocrine and exocrine cells. In addition to ADAM9, a potential prognostic factor for ductal cancers, we describe the expression of ADAM10 and ADAM17 in the pancreatic ductal epithelium. Altogether, the dynamic expression profile of the ADAM proteases described here may reflect a functional divergence of these as mediators of pancreas biology.

Animals↗
PubMed2004

A novel ubiquitin-like domain in IkappaB kinase beta is required for functional activity of the kinase.

Activation of NF-kappaB requires two highly related kinases named IKKalpha and IKKbeta that share identity in the nature and positioning of their structural domains. Despite their similarity, the kinases are functionally divergent, and we therefore sought to identify any structural features specific for IKKalpha or IKKbeta. We performed bioinformatics analysis, and we identified a region resembling a ubiquitin-like domain (UBL) that exists only in IKKbeta and that we named the UBL-like domain (ULD). Deletion of the ULD rendered IKKbeta catalytically inactive and unable to induce NF-kappaB activity, and overexpression of only the ULD dose-dependently inhibited tumor necrosis factor-alpha-induced NF-kappaB activity. The ULD could not be functionally replaced within IKKbeta by ubiquitin or the corresponding region of IKKalpha, whereas deletion of the equivalent section of IKKalpha did not affect its catalytic activity against IkappaBalpha or its activation by NF-kappaB-inducing kinase. We identified five residues conserved among the larger family of UBL-containing proteins and IKKbeta, and alanine scanning revealed that the leucine at position 353 (Leu(353)) is absolutely critical for IKKbeta-induced NF-kappaB activation. Most intriguingly, the L353A mutant was catalytically active but, unlike wild-type IKKbeta, formed a stable complex with the NF-kappaB p65 subunit. Our findings therefore establish the ULD as a critical functional domain specific for IKKbeta that might play a role in dissociating IKKbeta from p65.

Amino Acid Sequence↗
PubMed1999

The amphioxus rab GDP-dissociation inhibitor (GDI) gene is neural-specific: implications for the evolution of chordate rab GDI genes.

The rab GDP-dissociation inhibitor (rab GDI) proteins are involved in the regulation of vesicle-mediated cellular transport. We isolated the amphioxus rab GDI gene, analyzed its expression during amphioxus development, and performed a phylogenetic analysis of the rab GDI family. In contrast to the two major rab GDI forms in mammals, the alpha and beta forms, there is only one rab GDI isoform in amphioxus. Our analysis indicates that the occurrence of the alpha and beta forms of rab GDI preceded the divergence of lineages leading to birds and mammals, and that the amphioxus rab GDI may have evolved directly from the common ancestor of both forms. While the mammalian rab GDI beta-genes are ubiquitously expressed, the rab GDI alpha genes are predominantly expressed in neural tissues. The expression analysis of the amphioxus rab GDI gene shows predominantly neural expression similar to that of the mammalian rab GDI alpha form, suggesting that the ancestral expression pattern of chordate rab GDI was neural. In addition, the chicken rab GDI beta-like gene also shows neural-specific expression, which indicates that the neural expression was retained in both early postduplication alpha and beta isoforms and that a novel function associated with ubiquitous expression may have evolved uniquely in mammals. These results reveal a likely scenario of functional divergence of the rab GDI genes after duplication of the ancestral gene. A similar pattern of evolution, in which one of the duplicated genes retained a role similar to that of the ancestral one while other genes were recruited into novel roles, was also observed in the analysis of chordate Otx and hedgehog genes. In the rab GDI, hedgehog, and Otx gene families, the gene retaining the ancestral role shows a lower rate of sequence evolution than its counterpart, which was recruited for a novel function.

Amino Acid Sequence↗
PubMed2003

A bacterial conjugation machinery recruited for pathogenesis.

Type IV secretion systems (T4SS) are multicomponent transporters of Gram-negative bacteria adapted to functions as diverse as DNA transfer in bacterial conjugation or the delivery of effector proteins into eukaryotic target cells in pathogenesis. The generally modest sequence conservation between T4SS may reflect their evolutionary distance and/or functional divergence. Here, we show that the establishment of intraerythrocytic parasitism by Bartonella tribocorum requires a putative T4SS, which shares an unprecedented level of sequence identity with the Trw conjugation machinery of the broad-host-range antibiotic resistance plasmid R388 (up to 80% amino acid identity for individual T4SS components). The highly conserved T4SS loci are collinear except for the presence of numerous tandem gene duplications in B. tribocorum, which mostly encode variant forms of presumed surface-exposed pilus subunits. Conservation is not only structural, but also functional: R388 mutated in either trwD or trwH encoding essential T4SS components could be trans-complemented for conjugation by the homologues of the B. tribocorum system. Conservation also includes the transcription regulatory circuit: both T4SS loci encode a highly homologous and interchangeable KorA/KorB repressor system that negatively regulates the expression of all T4SS components. This striking example of adaptive evolution reveals the capacity of T4SS to assume dedicated functions in either DNA transfer or pathogenesis over rather short evolutionary distance and implies a novel role for the conjugation systems of widespread broad-host-range plasmids in the evolution of bacterial pathogens.

Bartonella↗
PubMed1979

Effects of habitual variations in napping on psychomotor performance, memory and subjective states.

Effects of habitual variations in napping on psychomotor performance, short-term memory and subjective states were investigated. The subjects were 32 healthy male university students who napped twice or more weekly in themorning and at night. Sixteen were randomly assigned to a control group and 16 to a nap(treatment) group. The experiment comprised two conditions of electrographically (EEG) recorded sleep for the nap group and two EEG monitored conditions of wakefulness for the controls. These conditions were scheduled from 9:35 to 11:35 a.m. and 12 hr later between 9:35 p.m. and 11:35 p.m. Measurements were obtained from: (a) a continuous 10-min auditory reaction time task, (b) a free recall task of short-term memory, (c) an activation-mood adjective check list, and (d) the Stanford Sleepiness scale. Except for memory the dependent variables of waking function were assessed 20 min before and 20 min after all conditions. Following each sleep condition the nap group as opposed to the controls showed a statistically significant improvement in reaction time performance, higher short-term retention, less reported sleepiness and elevated subjective states reflected by fice factors on the adjective mood-activation check list. Among the correlations computed the largest significant coefficients were of stage 4 and REM with posttreatment Stanford Sleepiness ratings. After naps, increased postdormital sleepiness was correlated with stage 4 and decreased sleepiness with REM sleep. Although few strikingly divergent functional effects were associated with morning and nocturanal naps, these did covary with sleep psychophysiology. It is postulated that the phase, the EEG-sleep stages and possibly the duration of accustomed naps are less salient factors influencing performance when the time since awakening until behavioral assessment can be kept constant.

Adult↗
PubMed2001

M1 muscarinic acetylcholine receptors activate extracellular signal-regulated kinase in CA1 pyramidal neurons in mouse hippocampal slices.

Activation of extracellular signal-regulated kinases (ERK) is crucial for many neural functions, including learning, memory, and synaptic plasticity. As muscarinic acetylcholine receptors (mAChR) modulate many of the same higher brain functions as ERK, we examined mAChR-mediated ERK activation in mouse hippocampal slices. The cholinergic agonist carbachol caused an atropine-sensitive ERK activation in the dendrites and somata CA1 pyramidal neurons. To determine the responsible mAChR subtype, we combined pharmacologic and genetic approaches. Pretreatment with M1 antagonists inhibited ERK activation. Furthermore, mAChR-induced ERK activation was absent in slices from M1 knockout mice. ERK activation was normal in slices derived from other mAChR subtype knockouts (M2, M3, and M4), although these other subtypes are expressed in many of the same neurons. Thus, we demonstrate divergent functions for the different mAChR subtypes. We conclude that M1 is responsible for mAChR-mediated ERK activation, providing a mechanism by which M1 may modulate learning and memory.

Animals↗
PubMed2004

Noncanonical function of glutamyl-prolyl-tRNA synthetase: gene-specific silencing of translation.

Aminoacyl tRNA synthetases (ARS) catalyze the ligation of amino acids to cognate tRNAs. Chordate ARSs have evolved distinctive features absent from ancestral forms, including compartmentalization in a multisynthetase complex (MSC), noncatalytic peptide appendages, and ancillary functions unrelated to aminoacylation. Here, we show that glutamyl-prolyl-tRNA synthetase (GluProRS), a bifunctional ARS of the MSC, has a regulated, noncanonical activity that blocks synthesis of a specific protein. GluProRS was identified as a component of the interferon (IFN)-gamma-activated inhibitor of translation (GAIT) complex by RNA affinity chromatography using the ceruloplasmin (Cp) GAIT element as ligand. In response to IFN-gamma, GluProRS is phosphorylated and released from the MSC, binds the Cp 3'-untranslated region in an mRNP containing three additional proteins, and silences Cp mRNA translation. Thus, GluProRS has divergent functions in protein synthesis: in the MSC, its aminoacylation activity supports global translation, but translocation of GluProRS to an inflammation-responsive mRNP causes gene-specific translational silencing.

Amino Acyl-tRNA Synthetases↗