RESUMEN

The liver has a unique ability to regenerate1,2; however, in the setting of acute liver failure (ALF), this regenerative capacity is often overwhelmed, leaving emergency liver transplantation as the only curative option3-5. Here, to advance understanding of human liver regeneration, we use paired single-nucleus RNA sequencing combined with spatial profiling of healthy and ALF explant human livers to generate a single-cell, pan-lineage atlas of human liver regeneration. We uncover a novel ANXA2+ migratory hepatocyte subpopulation, which emerges during human liver regeneration, and a corollary subpopulation in a mouse model of acetaminophen (APAP)-induced liver regeneration. Interrogation of necrotic wound closure and hepatocyte proliferation across multiple timepoints following APAP-induced liver injury in mice demonstrates that wound closure precedes hepatocyte proliferation. Four-dimensional intravital imaging of APAP-induced mouse liver injury identifies motile hepatocytes at the edge of the necrotic area, enabling collective migration of the hepatocyte sheet to effect wound closure. Depletion of hepatocyte ANXA2 reduces hepatocyte growth factor-induced human and mouse hepatocyte migration in vitro, and abrogates necrotic wound closure following APAP-induced mouse liver injury. Together, our work dissects unanticipated aspects of liver regeneration, demonstrating an uncoupling of wound closure and hepatocyte proliferation and uncovering a novel migratory hepatocyte subpopulation that mediates wound closure following liver injury. Therapies designed to promote rapid reconstitution of normal hepatic microarchitecture and reparation of the gut-liver barrier may advance new areas of therapeutic discovery in regenerative medicine.

Asunto(s)

Fallo Hepático Agudo , Regeneración Hepática , Animales , Femenino , Humanos , Masculino , Ratones , Acetaminofén/farmacología , Linaje de la Célula , Movimiento Celular/efectos de los fármacos , Proliferación Celular/efectos de los fármacos , Enfermedad Hepática Inducida por Sustancias y Drogas/patología , Modelos Animales de Enfermedad , Factor de Crecimiento de Hepatocito/metabolismo , Factor de Crecimiento de Hepatocito/farmacología , Hepatocitos/citología , Hepatocitos/efectos de los fármacos , Hepatocitos/metabolismo , Hepatocitos/patología , Hígado/citología , Hígado/efectos de los fármacos , Hígado/patología , Fallo Hepático Agudo/patología , Fallo Hepático Agudo/inducido químicamente , Regeneración Hepática/efectos de los fármacos , Ratones Endogámicos C57BL , Necrosis/inducido químicamente , Medicina Regenerativa , Análisis de Expresión Génica de una Sola Célula , Cicatrización de Heridas

RESUMEN

Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing.

Asunto(s)

Linfocitos B , Aprendizaje Automático , Análisis de Secuencia de ARN , Análisis de la Célula Individual , Linfocitos T , Transcriptoma , Células Cultivadas , Humanos , Especificidad de Órganos

RESUMEN

Liver cirrhosis is a major cause of death worldwide and is characterized by extensive fibrosis. There are currently no effective antifibrotic therapies available. To obtain a better understanding of the cellular and molecular mechanisms involved in disease pathogenesis and enable the discovery of therapeutic targets, here we profile the transcriptomes of more than 100,000 single human cells, yielding molecular definitions for non-parenchymal cell types that are found in healthy and cirrhotic human liver. We identify a scar-associated TREM2+CD9+ subpopulation of macrophages, which expands in liver fibrosis, differentiates from circulating monocytes and is pro-fibrogenic. We also define ACKR1+ and PLVAP+ endothelial cells that expand in cirrhosis, are topographically restricted to the fibrotic niche and enhance the transmigration of leucocytes. Multi-lineage modelling of ligand and receptor interactions between the scar-associated macrophages, endothelial cells and PDGFRα+ collagen-producing mesenchymal cells reveals intra-scar activity of several pro-fibrogenic pathways including TNFRSF12A, PDGFR and NOTCH signalling. Our work dissects unanticipated aspects of the cellular and molecular basis of human organ fibrosis at a single-cell level, and provides a conceptual framework for the discovery of rational therapeutic targets in liver cirrhosis.

Asunto(s)

Células Endoteliales/patología , Cirrosis Hepática/patología , Hígado/patología , Macrófagos/patología , Análisis de la Célula Individual , Animales , Estudios de Casos y Controles , Linaje de la Célula , Sistema del Grupo Sanguíneo Duffy/metabolismo , Células Endoteliales/metabolismo , Femenino , Células Estrelladas Hepáticas/citología , Células Estrelladas Hepáticas/metabolismo , Células Estrelladas Hepáticas/patología , Hepatocitos/citología , Hepatocitos/metabolismo , Hepatocitos/patología , Humanos , Hígado/citología , Cirrosis Hepática/genética , Macrófagos/metabolismo , Masculino , Glicoproteínas de Membrana/metabolismo , Proteínas de la Membrana/metabolismo , Ratones , Fenotipo , Receptor alfa de Factor de Crecimiento Derivado de Plaquetas/metabolismo , Receptores de Superficie Celular/metabolismo , Receptores Inmunológicos/metabolismo , Tetraspanina 29/metabolismo , Transcriptoma , Migración Transendotelial y Transepitelial

RESUMEN

Single-cell RNA-sequencing has uncovered immune heterogeneity, including novel cell types, states and lineages that have expanded our understanding of the immune system as a whole. More recently, studies involving both immune and non-immune cells have demonstrated the importance of immune microenvironment in development, homeostasis and disease. This review focuses on the single-cell studies mapping cell-cell interactions for variety of tissues in development, health and disease. In addition, we address the need to generate a comprehensive interaction map to answer fundamental questions in immunology as well as experimental and computational strategies required for this purpose.

RESUMEN

BACKGROUND: The Human Cell Atlas is a large international collaborative effort to map all cell types of the human body. Single-cell RNA sequencing can generate high-quality data for the delivery of such an atlas. However, delays between fresh sample collection and processing may lead to poor data and difficulties in experimental design. RESULTS: This study assesses the effect of cold storage on fresh healthy spleen, esophagus, and lung from ≥ 5 donors over 72 h. We collect 240,000 high-quality single-cell transcriptomes with detailed cell type annotations and whole genome sequences of donors, enabling future eQTL studies. Our data provide a valuable resource for the study of these 3 organs and will allow cross-organ comparison of cell types. We see little effect of cold ischemic time on cell yield, total number of reads per cell, and other quality control metrics in any of the tissues within the first 24 h. However, we observe a decrease in the proportions of lung T cells at 72 h, higher percentage of mitochondrial reads, and increased contamination by background ambient RNA reads in the 72-h samples in the spleen, which is cell type specific. CONCLUSIONS: In conclusion, we present robust protocols for tissue preservation for up to 24 h prior to scRNA-seq analysis. This greatly facilitates the logistics of sample collection for Human Cell Atlas or clinical studies since it increases the time frames for sample processing.

Asunto(s)

Análisis de Secuencia de ARN , Análisis de la Célula Individual , Conservación de Tejido/métodos , Frío , Esófago/citología , Humanos , Pulmón/citología , Refrigeración , Bazo/citología

RESUMEN

Attosecond light pulses in the extreme ultraviolet have drawn a great deal of attention due to their ability to interrogate electronic dynamics in real time. Nevertheless, to follow charge dynamics and excitations in materials, element selectivity is a prerequisite, which demands such pulses in the soft X-ray region, above 200 eV, to simultaneously cover several fundamental absorption edges of the constituents of the materials. Here, we experimentally demonstrate the exploitation of a transient phase matching regime to generate carrier envelope controlled soft X-ray supercontinua with pulse energies up to 2.9±0.1 pJ and a flux of (7.3±0.1) × 10(7) photons per second across the entire water window and attosecond pulses with 13 as transform limit. Our results herald attosecond science at the fundamental absorption edges of matter by bridging the gap between ultrafast temporal resolution and element specific probing.

RESUMEN

OBJECTIVE: In some regions of Germany dogs are presented to the veterinarian due to a snake bite, especially during the summer. These patients often show multiple clinical and laboratory deviations. Without a significant history diagnosis is commonly difficult. Aim of this retrospective study was to analyze exposure, physical examination and clinical pathology results as well as course and outcome in dogs presented after European adder bites. MATERIAL AND METHODS: Patient history of 15 dogs diagnosed with European adder bites over a 6.5-year-period were evaluated retrospectively. Normality of data distribution was tested by D'Agostino and Pearson omnibus normality test. Data were analyzed by T-test and Wilcoxon-matched-pairs-signed rank-test. P-values < 0.05 were considered significant. RESULTS: All 15 dogs were presented within 1-48 hours after the snakebite. Most common clinical signs were local swelling and pain. Clinical pathology results on day 1 included haemoconcentration, leukocytosis and coagulopathy. On the second day of hospitalization heart rate and haematocrit declined significantly. Treatment included fluid therapy, antibiotic and antihistaminic drugs, glucocorticosteroids, antivenom and analgesics. One of 15 dogs died on the third day of hospitalization, all others were discharged. Duration of hospitalization was between 1 and 8 days (mean 4.2 ± 1.9 days). CLINICAL RELEVANCE: Dogs affected by European adder bites most often present with swelling and pain at the site of the bite, most frequently on the head and limbs. Patients require intensive symptomatic therapy including antibiotics and analgesics, if indicated. With adequate therapy survival rate is high. For some patients European adder bites may be lethal.

Asunto(s)

Enfermedades de los Perros , Mordeduras de Serpientes , Viperidae , Animales , Antivenenos/uso terapéutico , Enfermedades de los Perros/diagnóstico , Enfermedades de los Perros/fisiopatología , Enfermedades de los Perros/terapia , Perros , Alemania , Pronóstico , Estudios Retrospectivos , Mordeduras de Serpientes/diagnóstico , Mordeduras de Serpientes/fisiopatología , Mordeduras de Serpientes/terapia , Mordeduras de Serpientes/veterinaria

RESUMEN

We investigated nonlinear photoemission from plasmonic films with femtosecond, mid-infrared pulses at 3.1 µm wavelength. Transition between regimes of multi-photon-induced and tunneling emission is demonstrated at an unprecedentedly low intensity of <1 GW/cm(2). Thereby, strong-field nanophysics can be accessed at extremely low intensities by exploiting nanoscale plasmonic field confinement, enhancement and ponderomotive wavelength scaling at the same time. Results agree well with quantum mechanical modelling. Our scheme demonstrates an alternative paradigm and regime in strong-field physics.

RESUMEN

OBJECTIVE: Particularly during household fires, inhalation of hot air and smoke, and the formation of carboxyhaemoglobin and cyanide lead to respiratory tract and lung injury in small animals. Additionally, oxygenation is impaired in most cases. The aim of this retrospective study was to analyse smoke exposure, physical examination findings and clinical pathology results as well as their course in dogs and cats presented after smoke inhalation. MATERIAL AND METHODS: Patient histories of dogs and cats that had been diagnosed with smoke inhalation between January 1, 2008 and August 31, 2013 were analysed retrospectively. Normality was tested using the Shapiro-Wilk test and analyses were performed using t-tests, the Chi-square test and Mann-Whitney U-test. P-values < 0.05 were considered significant. RESULTS: The analysis included data of 13 cats and nine dogs. The animals were presented within 12 hours after a household fire with sooting, coughing and polypnoea. Pretreatment in approximately 50% of patients consisted of oxygen, corticoids and bronchodilators. The most common clinical abnormalities were tachycardia, polypnoea and hypothermia as well as pink mucous membranes. Changes observed from clinical pathology analysis included the haemoconcentration, reticulocytosis, a left shift of the leucogram, mixed acid-base disorders and moderate carboxyhaemoglobinema. Therapy included oxygen and fluid therapy, antibiotic treatment, corticoids, bronchodilators and cleaning of the animal. One cat died and 21 animals were discharged 0-6 days after presentation. CLINICAL RELEVANCE: Dogs and cats suffering from smoke inhalation were presented with respiratory disorders and dehydration. Outcome is good if the animals are treated early and adequately with oxygen and fluid therapy.

Asunto(s)

Enfermedades de los Gatos/epidemiología , Enfermedades de los Perros/epidemiología , Lesión por Inhalación de Humo/veterinaria , Animales , Enfermedades de los Gatos/etiología , Enfermedades de los Gatos/terapia , Gatos , Enfermedades de los Perros/etiología , Enfermedades de los Perros/terapia , Perros , Alemania/epidemiología , Estudios Retrospectivos , Lesión por Inhalación de Humo/epidemiología , Lesión por Inhalación de Humo/terapia

RESUMEN

OBJECTIVE: Heatstroke is a life-threating emergency in dogs. The aim of this retrospective study was to analyse the sources of heat stroke in dogs, predisposing and prognostic factors, results of physical examination and clinical pathology as well as the course of this condition and appropriate treatment. MATERIAL AND METHODS: Patient histories of 12 dogs diagnosed with heat stroke over a 5.5-year period were analysed retrospectively. Normality was tested using the Kolmogrow-Smirnow Test and analysed using T-tests, the Chi-square test and the Mann-Whitney U-test. P-values < 0.05 were considered significant. RESULTS: Heat stroke occurred most frequently during summer, particularly in the afternoon. The most common cause of heat stroke was heat exposition in a car. Brachycephalic breeds were overrepresented. The most common clinical signs were polypnoea, tachycardia, hyperthermia and depression to prostration as well as gastrointestinal and neurological symptoms. Clinical pathology results included haemoconcentration, thrombocytopenia, hyperkalemia, prolonged activated partial thromboplastin time and azotemia. Therapies employed included oxygen application, cooling, fluid therapy and administration of gastrointestinal protectants, antiemetics and antibiotics. Duration of hospitalization was 1-6 days. The overall mortality rate was 50%. Most of the non-survivors died or were euthanized within 24-48 hours after presentation. All animals remaining alive after 3 days survived and could be discharged from hospital. CLINICAL RELEVANCE: Heat stroke is a life-threating condition, which can lead to shock, sepsis, coagulation disorders and multiorgan failure. Early recognition and appropriate treatment are important factors for a positive outcome. Furthermore, intensive monitoring and rapid therapy adaption as required are pivotal.

Asunto(s)

Enfermedades de los Perros/diagnóstico , Golpe de Calor/veterinaria , Animales , Enfermedades de los Perros/fisiopatología , Perros , Alemania , Golpe de Calor/diagnóstico , Golpe de Calor/fisiopatología , Estudios Retrospectivos

RESUMEN

We report on the first table-top high-flux source of coherent soft x-ray radiation up to 400 eV, operating at 1 kHz. This source covers the carbon K-edge with a beam brilliance of (4.3±1.2)×10(15) photons/s/mm(2)/strad/10% bandwidth and a photon flux of (1.85±0.12)×10(7) photons/s/1% bandwidth. We use this source to demonstrate table-top x-ray near-edge fine-structure spectroscopy at the carbon K-edge of a polyimide foil and retrieve the specific absorption features corresponding to the binding orbitals of the carbon atoms in the foil.

RESUMEN

We study ionization of molecules by an intense laser field over a broad wavelength regime, ranging from 0.8 to 1.5 µm experimentally and from 0.6 to 10 µm theoretically. A reaction microscope is combined with an optical parametric amplifier to achieve ionization yields in the near-infrared wavelength regime. Calculations are done using the strong-field S-matrix theory and agreement is found between experiment and theory, showing that ionization of many molecules is suppressed compared to the ionization of atoms with identical ionization potentials at near-infrared wavelengths at around 0.8 µm, but not at longest wavelengths (10 µm). This is due to interference effects in the electron emission that are effective at low photoelectron energies but tend to average out at higher energies. We observe the transition between suppression and nonsuppression of molecular ionization in the near-infrared wavelength regime (1-5 µm).

RESUMEN

Proteins are composed of domains, which are conserved evolutionary units that often also correspond to functional units and can frequently be detected with reasonable reliability using computational methods. Most proteins consist of two or more domains, giving rise to a variety of combinations of domains. Another level of complexity arises because proteins themselves can form complexes with small molecules, nucleic acids and other proteins. The networks of both domain combinations and protein interactions can be conceptualised as graphs, and these graphs can be analysed conveniently by computational methods. In this review we summarise facts and hypotheses about the evolution of domains in multi-domain proteins and protein complexes, and the tools and data resources available to study them.

Asunto(s)

Evolución Molecular , Estructura Terciaria de Proteína/genética , Proteínas/genética , Secuencia de Aminoácidos , Animales , Biología Computacional , Secuencia Conservada/genética , Secuencia Conservada/fisiología , Variación Genética , Humanos , Complejos Multiproteicos/química , Complejos Multiproteicos/genética , Estructura Terciaria de Proteína/fisiología , Proteínas/fisiología

RESUMEN

Escherichia coli has been a popular organism for studying metabolic pathways. In an attempt to find out more about how these pathways are constructed, the enzymes were analysed by defining their protein domains. Structural assignments and sequence comparisons were used to show that 213 domain families constitute approximately 90% of the enzymes in the small-molecule metabolic pathways. Catalytic or cofactor-binding properties between family members are often conserved, while recognition of the main substrate with change in catalytic mechanism is only observed in a few cases of consecutive enzymes in a pathway. Recruitment of domains across pathways is very common, but there is little regularity in the pattern of domains in metabolic pathways. This is analogous to a mosaic in which a stone of a certain colour is selected to fill a position in the picture.

Asunto(s)

Enzimas/química , Enzimas/metabolismo , Escherichia coli/enzimología , Sitios de Unión/fisiología , Coenzimas/metabolismo , Escherichia coli/metabolismo , Evolución Molecular , Fucosa/metabolismo , Nucleósidos/metabolismo , Nucleótidos/metabolismo , Estructura Terciaria de Proteína/fisiología , Purinas/biosíntesis , Pirimidinas/biosíntesis , Ácido Pirúvico/metabolismo , Homología de Secuencia , Especificidad por Sustrato/fisiología , Triptófano/biosíntesis

RESUMEN

Hepatic up-regulation of sterol carrier protein 2 (Scp2) in mice promotes hypersecretion of cholesterol into bile and gallstone formation in response to a lithogenic diet. We hypothesized that Scp2 deficiency may alter biliary lipid secretion and hepatic cholesterol metabolism. Male gallstone-susceptible C57BL/6 and C57BL/6(Scp2(-/-)) knockout mice were fed a standard chow or lithogenic diet. Hepatic biles were collected to determine biliary lipid secretion rates, bile flow, and bile salt pool size. Plasma lipoprotein distribution was investigated, and gene expression of cytosolic lipid-binding proteins, lipoprotein receptors, hepatic regulatory enzymes, and intestinal cholesterol absorption was measured. Compared with chow-fed wild-type animals, C57BL/6(Scp2(-/-)) mice had higher bile flow and lower bile salt secretion rates, decreased hepatic apolipoprotein expression, increased hepatic cholesterol synthesis, and up-regulation of liver fatty acid-binding protein. In addition, the bile salt pool size was reduced and intestinal cholesterol absorption was unaltered in C57BL/6(Scp2(-/-)) mice. When C57BL/6(Scp2(-/-)) mice were challenged with a lithogenic diet, a smaller increase of hepatic free cholesterol failed to suppress cholesterol synthesis and biliary cholesterol secretion increased to a much smaller extent than phospholipid and bile salt secretion. Scp2 deficiency did not prevent gallstone formation and may be compensated in part by hepatic up-regulation of liver fatty acid-binding protein. These results support a role of Scp2 in hepatic cholesterol metabolism, biliary lipid secretion, and intracellular cholesterol distribution.

Asunto(s)

Bilis/metabolismo , Proteínas Portadoras/genética , Colesterol/metabolismo , Metabolismo de los Lípidos , Hígado/metabolismo , Proteínas de Neoplasias , Proteínas del Tejido Nervioso , Proteínas de Plantas , Animales , Peso Corporal , Proteínas Portadoras/metabolismo , Colelitiasis/metabolismo , Proteína de Unión a los Ácidos Grasos 7 , Proteínas de Unión a Ácidos Grasos , Absorción Intestinal , Masculino , Ratones , Ratones Endogámicos C57BL , Modelos Animales , Tamaño de los Órganos , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa

RESUMEN

The 106 small molecule metabolic (SMM) pathways in Escherichia coli are formed by the protein products of 581 genes. We can define 722 domains, nearly all of which are homologous to proteins of known structure, that form all or part of 510 of these proteins. This information allows us to answer general questions on the structural anatomy of the SMM pathway proteins and to trace family relationships and recruitment events within and across pathways. Half the gene products contain a single domain and half are formed by combinations of between two and six domains. The 722 domains belong to one of 213 families that have between one and 51 members. Family members usually conserve their catalytic or cofactor binding properties; substrate recognition is rarely conserved. Of the 213 families, members of only a quarter occur in isolation, i.e. they form single-domain proteins. Most members of the other families combine with domains from just one or two other families and a few more versatile families can combine with several different partners. Excluding isoenzymes, more than twice as many homologues are distributed across pathways as within pathways. However, serial recruitment, with two consecutive enzymes both being recruited to another pathway, is rare and recruitment of three consecutive enzymes is not observed. Only eight of the 106 pathways have a high number of homologues. Homology between consecutive pairs of enzymes with conservation of the main substrate-binding site but change in catalytic mechanism (which would support a simple model of retrograde pathway evolution) occurs only six times in the whole set of enzymes. Most of the domains that form SMM pathways have homologues in non-SMM pathways. Taken together, these results imply a pervasive "mosaic" model for the formation of protein repertoires and pathways.

Asunto(s)

Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Escherichia coli/química , Escherichia coli/metabolismo , Evolución Molecular , Sitios de Unión , Secuencia Conservada , Genes Duplicados , Gluconeogénesis , Glucógeno/metabolismo , Histidina/biosíntesis , Cadenas de Markov , Familia de Multigenes , Nucleótidos/metabolismo , Ácidos Fosfatidicos/biosíntesis , Polisacáridos/biosíntesis , Estructura Terciaria de Proteína , Proteoma , Purinas/biosíntesis , Pirimidinas/biosíntesis , Homología de Secuencia de Aminoácido

RESUMEN

Domains are the building blocks of all globular proteins, and are units of compact three-dimensional structure as well as evolutionary units. There is a limited repertoire of domain families, so that these domain families are duplicated and combined in different ways to form the set of proteins in a genome. Proteins are gene products. The processes that produce new genes are duplication and recombination as well as gene fusion and fission. We attempt to gain an overview of these processes by studying the structural domains in the proteins of seven genomes from the three kingdoms of life: Eubacteria, Archaea and Eukaryota. We use here the domain and superfamily definitions in Structural Classification of Proteins Database (SCOP) in order to map pairs of adjacent domains in genome sequences in terms of their superfamily combinations. We find 624 out of the 764 superfamilies in SCOP in these genomes, and the 624 families occur in 585 pairwise combinations. Most families are observed in combination with one or two other families, while a few families are very versatile in their combinatorial behaviour. This type of pattern can be described by a scale-free network. Finally, we study domain repeats and we compare the set of the domain combinations in the genomes to those in PDB, and discuss the implications for structural genomics.

Asunto(s)

Bases de Datos de Proteínas , Estructura Terciaria de Proteína , Biología Computacional , Genoma , Péptidos/química , Péptidos/genética , Filogenia , Estructura Terciaria de Proteína/genética

RESUMEN

The genome sequencing projects and knowledge of the entire protein repertoires of many organisms have prompted new procedures and techniques for the large-scale determination of protein structure, function and interactions. Recently, new work has been carried out on the determination of the function and evolutionary relationships of proteins by experimental structural genomics, and the discovery of protein-protein interactions by computational structural genomics.

Asunto(s)

Evolución Molecular , Genómica/métodos , Proteínas/fisiología , Orden Génico , Filogenia , Estructura Terciaria de Proteína , Proteínas/química

RESUMEN

There is a limited repertoire of domain families that are duplicated and combined in different ways to form the set of proteins in a genome. Proteins are gene products, and at the level of genes, duplication, recombination, fusion and fission are the processes that produce new genes. We attempt to gain an overview of these processes by studying the evolutionary units in proteins, domains, in the protein sequences of 40 genomes. The domain and superfamily definitions in the Structural Classification of Proteins Database are used, so that we can view all pairs of adjacent domains in genome sequences in terms of their superfamily combinations. We find 783 out of the 859 superfamilies in SCOP in these genomes, and the 783 families occur in 1307 pairwise combinations. Most families are observed in combination with one or two other families, while a few families are very versatile in their combinatorial behaviour; 209 families do not make combinations with other families. This type of pattern can be described as a scale-free network. We also study the N to C-terminal orientation of domain pairs and domain repeats. The phylogenetic distribution of domain combinations is surveyed, to establish the extent of common and kingdom-specific combinations. Of the kingdom-specific combinations, significantly more combinations consist of families present in all three kingdoms than of families present in one or two kingdoms. Hence, we are led to conclude that recombination between common families, as compared to the invention of new families and recombination among these, has also been a major contribution to the evolution of kingdom-specific and species-specific functions in organisms in all three kingdoms. Finally, we compare the set of the domain combinations in the genomes to those in the RCSB Protein Data Bank, and discuss the implications for structural genomics.

Asunto(s)

Archaea , Eubacterium , Células Eucariotas , Evolución Molecular , Proteoma/química , Proteoma/genética , Secuencias Repetitivas de Aminoácido/genética , Animales , Archaea/química , Archaea/genética , Secuencia Conservada/genética , Bases de Datos como Asunto , Eubacterium/química , Eubacterium/genética , Células Eucariotas/química , Células Eucariotas/metabolismo , Duplicación de Gen , Genoma , Genómica , Humanos , Familia de Multigenes/genética , Mutación/genética , Filogenia , Estructura Terciaria de Proteína , Proteoma/clasificación , Recombinación Genética/genética , Secuencias Repetidas en Tándem/genética , Levaduras/química , Levaduras/genética

RESUMEN

As the number of protein folds is quite limited, a mode of analysis that will be increasingly common in the future, especially with the advent of structural genomics, is to survey and re-survey the finite parts list of folds from an expanding number of perspectives. We have developed a new resource, called PartsList, that lets one dynamically perform these comparative fold surveys. It is available on the web at http://bioinfo.mbb.yale.edu/partslist and http://www.partslist.org. The system is based on the existing fold classifications and functions as a form of companion annotation for them, providing 'global views' of many already completed fold surveys. The central idea in the system is that of comparison through ranking; PartsList will rank the approximately 420 folds based on more than 180 attributes. These include: (i) occurrence in a number of completely sequenced genomes (e.g. it will show the most common folds in the worm versus yeast); (ii) occurrence in the structure databank (e.g. most common folds in the PDB); (iii) both absolute and relative gene expression information (e.g. most changing folds in expression over the cell cycle); (iv) protein-protein interactions, based on experimental data in yeast and comprehensive PDB surveys (e.g. most interacting fold); (v) sensitivity to inserted transposons; (vi) the number of functions associated with the fold (e.g. most multi-functional folds); (vii) amino acid composition (e.g. most Cys-rich folds); (viii) protein motions (e.g. most mobile folds); and (ix) the level of similarity based on a comprehensive set of structural alignments (e.g. most structurally variable folds). The integration of whole-genome expression and protein-protein interaction data with structural information is a particularly novel feature of our system. We provide three ways of visualizing the rankings: a profiler emphasizing the progression of high and low ranks across many pre-selected attributes, a dynamic comparer for custom comparisons and a numerical rankings correlator. These allow one to directly compare very different attributes of a fold (e.g. expression level, genome occurrence and maximum motion) in the uniform numerical format of ranks. This uniform framework, in turn, highlights the way that the frequency of many of the attributes falls off with approximate power-law behavior (i.e. according to V(-b), for attribute value V and constant exponent b), with a few folds having large values and most having small values.

Asunto(s)

Perfilación de la Expresión Génica , Genoma , Internet , Pliegue de Proteína , Proteínas/química , Programas Informáticos , Cisteína/análisis , Elementos Transponibles de ADN/genética , Bases de Datos como Asunto , Movimiento (Física) , Unión Proteica , Proteínas/clasificación , Proteínas/metabolismo , Proteoma , Proyectos de Investigación , Alineación de Secuencia