Background: Ceriporiopsis subvermispora is a white-rot fungus that displays a high specificity to... more Background: Ceriporiopsis subvermispora is a white-rot fungus that displays a high specificity towards lignin mineralization when colonizing dead wood or lignocellulosic compounds. The lignocellulose degrading system from C. subvermispora is formed by genes that encode cellulose hydrolytic enzymes, manganese peroxidases, and laccases that catalyze the efficient depolymerization and mineralization of lignin in the presence of Mn3+ through the formation of lipoperoxides from unsaturated lipid acids. This highly specific lignin-degrading system is unique among white-rot fungi. Methods: In order to determine if this metabolic specialization has modified codon usage of the ligninolytic system, leading to an increased adaptation to the fungal translational machine, we analyzed the adaptation to host codon usage (CAI), tRNA pool (tAI, and AAtAI), codon pair bias (CPB) and the number of effective codons (Nc). These indexes were correlated with gene expression of C. subvermispora, as evaluat...
Ceriporiopsis subvermispora is a white-rot fungus with a high specificity towards lignin minerali... more Ceriporiopsis subvermispora is a white-rot fungus with a high specificity towards lignin mineralization when colonizing dead wood or lignocellulosic compounds. Its lignocellulose degrading system is formed by cellulose hydrolytic enzymes, manganese peroxidases, and laccases that catalyze the efficient depolymerization and mineralization of lignocellulose. To determine if this metabolic specialization has modified codon usage of the lignocellulolytic system, improving its adaptation to the fungal translational machine, we analyzed the adaptation to host codon usage (CAI), tRNA pool (tAI, and AAtAI), codon pair bias (CPB), and the number of effective codons (Nc). These indexes were correlated with gene expression of C. subvermispora, in the presence of glucose and Aspen wood. General gene expression was not correlated with the index values. However, in media containing Aspen wood, the induction of expression of lignocellulose-degrading genes, showed significantly (p < 0.001) higher...
Immunoglobulin G (IgG)- and IgM-specific antibody titers against Salmonella typhi Ty2 porins have... more Immunoglobulin G (IgG)- and IgM-specific antibody titers against Salmonella typhi Ty2 porins have been measured in 30 paired typhoid sera by enzyme-linked immunosorbent assay. These studies have found that IgG serum titers of acute and convalescent sera were 625 and 5,000 times higher, respectively than the control serum titers. The same typhoid sera were titrated with S. typhi Ty2 flagellin and S. typhi lipopolysaccharide. The titers against these antigens were considerably lower than those against the porins. The highest IgM-specific titer has also been found against porins in convalescent-phase sera. However, the largest increase in IgM-specific titer compared with the control group titer was obtained against flagellin during the acute phase of typhoid. The lowest increases in antibody titer were obtained with the IgM-specific anti-lipopolysaccharide in both types of sera. This may be because many normal individuals in endemic areas already have IgM titers against lipopolysacchar...
Lignin peroxidase-like genes were PCR amplified from Phanerochaete sordida and Ceriporiopsis subv... more Lignin peroxidase-like genes were PCR amplified from Phanerochaete sordida and Ceriporiopsis subvermispora, fungi lacking lignin peroxidase (LiP) activity. Amplification products were highly similar to previously described LiP genes. Using reverse transcription-coupled PCR a LiP-like cDNA clone was amplified from P. sordida RNA. In contrast, no evidence was obtained for transcription of C. subvermispora LiP genes.
The complete sequences of cDNA MnP13-1 and the corresponding Cs-mnp-1 gene encoding for manganese... more The complete sequences of cDNA MnP13-1 and the corresponding Cs-mnp-1 gene encoding for manganese peroxide isoenzyme secreted by Ceriporiopsis subvermispora have been determined. A cDNA for another isoenzyme of MnP (MnP-2) and its corresponding gene (mnp2), plus a third gene coding for MnP (mnp3) have also been isolated, although mnp2 and mnp3 have only been partially sequenced. In addition, a gene from this fungus coding for laccase (lcs1) was isolated from genomic library and it was completely sequenced.
This review describes the advances in the knowledge about the genetic aspects of common chronic c... more This review describes the advances in the knowledge about the genetic aspects of common chronic complications of diabetes with prognostic significance, such as diabetic nephropathy and cardiovascular diseases. It is well known that the genetic factors responsible for chronic complications are different from those that cause Diabetes Mellitus. Until recently, the studies were limited to the analysis of individual genes associated or related to multifactorial diseases. However at the present time the "genome wide associated studies" lead to agreat advance in knowledge. The analysis of genetic variations or polymorphisms allows the understanding of human individuality and the predisposition towards certain diseases. A new research field appeared in 2004, when small messenger RNAs, called microRNA related to Diabetes mellitus and its chronic complications, were identified. The function of these RNAs is to regulate several target genes. These affect insulin secretion and action...
Laccase is one of the ligninolytic enzymes found in liquid cultures of the fungus Ceriporiopsis s... more Laccase is one of the ligninolytic enzymes found in liquid cultures of the fungus Ceriporiopsis subvermispora in defined medium. As an approach to a clarification of the role of laccases during the attack on lignin by the fungus, the enzyme has been characterized further. The levels of this phenol oxidase increase 2-fold in the presence of p-anisidine and are severely affected when addition of either Mn(II) or Cu(II) ions to the medium is omitted. Isoelectrofocusing allowed the resolution of two laccase isoenzymes, with pIs of 3.65 and 3.59. In rich medium, laccase activity is 10-fold higher than in salt medium, and it is not affected by the external addition of p-anisidine or Mn(II). Four isoenzymes were detected in these cultures, with pIs between 3.76 and 3.60. In a wheat bran medium, four isoenzymes with pIs in the range 3.63-3.46, plus a fifth isoenzyme of high pI (4.82), were also identified. The absorption spectrum of a pool containing the four isoenzymes from rich medium sho...
Two outer membrane proteins of Salmonella typhi Ty 2 were extensively co-purified. According to t... more Two outer membrane proteins of Salmonella typhi Ty 2 were extensively co-purified. According to their migration in dodecylsulfate/polyacrylamide gel electrophoresis and solubility characteristics, these proteins are homologous to the 35-kDa and 36-kDa porins found in Salmonella typhimurium. A porin homologous to the 34-kDa one has not been found in S. typhi Ty 2. A critical step in the purification of porins is heating at 100 degrees C in 2% sodium dodecyl sulfate before Sephadex gel filtration. The absence of detergent in aqueous suspensions enhances porin aggregation, these aggregations inducing human red cell lysis. Porins obtained by an alternative procedure consisting of heating at 60 degrees C instead of 100 degrees C were also hemolytic. Using nanomolar concentration of porins a strong influence of temperature on the hemolytic effect was observed. Porin-induced hemolysis was inhibited with anti-porin serum, as well as by a treatment with phenylglyoxal, which reacts with the arginine residues of proteins. The membrane-disrupting ability of porins aggregates might explain some pathogenic characteristics of gram-negative bacterial infections.
Proceedings of the National Academy of Sciences, 1990
We have identified and partially characterized another human general transcription factor, TFIIG.... more We have identified and partially characterized another human general transcription factor, TFIIG. Using a reconstituted in vitro system comprised of purified RNA polymerase II, TFIIB, TFIID, TFIIE, and TFIIF, we found that TFIIG was essential for specific initiation from all class II genes tested. In this system TFIIA could partially replace TFIIG; however, even at saturating concentrations of TFIIA, addition of TFIIG further stimulated transcription. Since the chromatographic properties of TFIIG differed significantly from those of TFIIA, we concluded that TFIIA and TFIIG are distinct but functionally related transcription factors. Heparin challenge assays showed that TFIIG is required for the assembly of a functional preinitiation complex. However, it must act after template commitment by TFIID, since this step did not require, and was unaffected by, either TFIIG or TFIIA.
Cobre y Selenio son elementos esenciales para la vida humana y animal. Sin embargo, dependiendo d... more Cobre y Selenio son elementos esenciales para la vida humana y animal. Sin embargo, dependiendo de las concentraciones, estos pueden causar problemas de toxicidad, ya sea por deficiencia o exceso. En el presente trabajo se determinaron las concentraciones de cobre y selenio en muestras de distintos componentes de tres ecosistemas agricolas de la region de Valparaiso: agua de lluvia, suelos y alfalfa provenientes de los valles de Puchuncavi y *To whom correspondence should be addressed, Fax: 56-32-273422; e-mail: idegrego@ucv.cl Bol. Soc. Chil. Quim., 45, N 1 (2000) Catemu, lugares donde se realizan actividades mineras metalurgicas de importancia y del valle de Casablanca, lugar considerado como referencia. Las muestras fueron recolectadas en el periodo Abril-Mayo de 1997. Los resultados mostraron que en los tres tipos de muestra las concentraciones de cobre decrecen en funcion de la distancia de la fuente emisora. Este mismo comportamiento fue observado para selenio en agua de lluvia. Sin embargo, las concentraciones de este elemento en suelos y alfalfa son bajas y similares (entre 0,1 y 0,4 mg Kg-1). Se obtuvieron buenas correlaciones entre las concentraciones de cobre en los distintos componentes de los ecosistemas. Por el contrario solo se obtuvo una buena correlacion entre las cantidades de cobre y selenio depositadas por agua de lluvia proveniente de los distintos sitios de muestreo del valle de Puchuncavi.
Proceedings of the National Academy of Sciences of the United States of America, Jan 3, 2012
Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referr... more Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium simultaneously degrades lignin and cellulose, whereas the closely related species, Ceriporiopsis subvermispora, also depolymerizes lignin but may do so with relatively little cellulose degradation. To investigate the basis for selective ligninolysis, we conducted comparative genome analysis of C. subvermispora and P. chrysosporium. Genes encoding manganese peroxidase numbered 13 and five in C. subvermispora and P. chrysosporium, respectively. In addition, the C. subvermispora genome contains at least seven genes predicted to encode laccases, whereas the P. chrysosporium genome contains none. We also observed expansion of the number of C. subvermispora desaturase-encoding genes putatively involved in lipid metabolism. Microarray-based transcriptome analysis showed substantial up-regulation of several desaturase and MnP genes in wood-co...
Total copper and selenium concentrations were determined in rain waters, soils and alfalfa sample... more Total copper and selenium concentrations were determined in rain waters, soils and alfalfa samples collected during April-May 1997 at various sites from different zones of Valparaiso region, in Chile: Puchuncavi and Catemu valleys, (both impacted by mining activities) and Casablanca valley (reference site). In rain waters, Cu and Se concentrations clearly decreased exponentially with distance from the sources and were significantly correlated. The results obtained demonstrate that the mining activities have contributed to increase the contamination by copper in the agricultural ecosystems, particularly those located near the smelters. In all matrices from Puchuncavi and Catemu valleys copper concentrations were higher than in the reference site. In Puchuncavi valley, Cu concentrations in soils and alfalfa show close correlation and were a function of the distance from the smelter. Selenium concentration in soils and alfalfa follows a different pattern, being relatively constant in these matrices and presenting no clear dependency on the distance from the sources. In alfalfa they ranged between 0.10 and 0.40 mg kg-1; these concentrations are not high and do not represent a problem to livestock grazing in these areas.
Studies on Salmonella typhi and Salmonella typhimurium outer membrane proteins have shown that th... more Studies on Salmonella typhi and Salmonella typhimurium outer membrane proteins have shown that the relative position of OmpC porin in sodium dodecyl sulfate.polyacrylamide gel electrophoresis undergoes an important shift when the concentration of ammonium persulfate in the running gel is increased from 6 to 12 mM. The apparent molecular mass at these concentrations was estimated to be 34 and 40 kDa, respectively. Under similar electrophoretic conditions the apparent molecular mass estimated for OmpF was 37.6 and 38.2 kDa. Therefore, OmpC moves from a leading position to a position behind OmpF. For Escherichia coli OmpC the shift observed is less pronounced than that occurring in Salmonellae.
Background: Ceriporiopsis subvermispora is a white-rot fungus that displays a high specificity to... more Background: Ceriporiopsis subvermispora is a white-rot fungus that displays a high specificity towards lignin mineralization when colonizing dead wood or lignocellulosic compounds. The lignocellulose degrading system from C. subvermispora is formed by genes that encode cellulose hydrolytic enzymes, manganese peroxidases, and laccases that catalyze the efficient depolymerization and mineralization of lignin in the presence of Mn3+ through the formation of lipoperoxides from unsaturated lipid acids. This highly specific lignin-degrading system is unique among white-rot fungi. Methods: In order to determine if this metabolic specialization has modified codon usage of the ligninolytic system, leading to an increased adaptation to the fungal translational machine, we analyzed the adaptation to host codon usage (CAI), tRNA pool (tAI, and AAtAI), codon pair bias (CPB) and the number of effective codons (Nc). These indexes were correlated with gene expression of C. subvermispora, as evaluat...
Ceriporiopsis subvermispora is a white-rot fungus with a high specificity towards lignin minerali... more Ceriporiopsis subvermispora is a white-rot fungus with a high specificity towards lignin mineralization when colonizing dead wood or lignocellulosic compounds. Its lignocellulose degrading system is formed by cellulose hydrolytic enzymes, manganese peroxidases, and laccases that catalyze the efficient depolymerization and mineralization of lignocellulose. To determine if this metabolic specialization has modified codon usage of the lignocellulolytic system, improving its adaptation to the fungal translational machine, we analyzed the adaptation to host codon usage (CAI), tRNA pool (tAI, and AAtAI), codon pair bias (CPB), and the number of effective codons (Nc). These indexes were correlated with gene expression of C. subvermispora, in the presence of glucose and Aspen wood. General gene expression was not correlated with the index values. However, in media containing Aspen wood, the induction of expression of lignocellulose-degrading genes, showed significantly (p < 0.001) higher...
Immunoglobulin G (IgG)- and IgM-specific antibody titers against Salmonella typhi Ty2 porins have... more Immunoglobulin G (IgG)- and IgM-specific antibody titers against Salmonella typhi Ty2 porins have been measured in 30 paired typhoid sera by enzyme-linked immunosorbent assay. These studies have found that IgG serum titers of acute and convalescent sera were 625 and 5,000 times higher, respectively than the control serum titers. The same typhoid sera were titrated with S. typhi Ty2 flagellin and S. typhi lipopolysaccharide. The titers against these antigens were considerably lower than those against the porins. The highest IgM-specific titer has also been found against porins in convalescent-phase sera. However, the largest increase in IgM-specific titer compared with the control group titer was obtained against flagellin during the acute phase of typhoid. The lowest increases in antibody titer were obtained with the IgM-specific anti-lipopolysaccharide in both types of sera. This may be because many normal individuals in endemic areas already have IgM titers against lipopolysacchar...
Lignin peroxidase-like genes were PCR amplified from Phanerochaete sordida and Ceriporiopsis subv... more Lignin peroxidase-like genes were PCR amplified from Phanerochaete sordida and Ceriporiopsis subvermispora, fungi lacking lignin peroxidase (LiP) activity. Amplification products were highly similar to previously described LiP genes. Using reverse transcription-coupled PCR a LiP-like cDNA clone was amplified from P. sordida RNA. In contrast, no evidence was obtained for transcription of C. subvermispora LiP genes.
The complete sequences of cDNA MnP13-1 and the corresponding Cs-mnp-1 gene encoding for manganese... more The complete sequences of cDNA MnP13-1 and the corresponding Cs-mnp-1 gene encoding for manganese peroxide isoenzyme secreted by Ceriporiopsis subvermispora have been determined. A cDNA for another isoenzyme of MnP (MnP-2) and its corresponding gene (mnp2), plus a third gene coding for MnP (mnp3) have also been isolated, although mnp2 and mnp3 have only been partially sequenced. In addition, a gene from this fungus coding for laccase (lcs1) was isolated from genomic library and it was completely sequenced.
This review describes the advances in the knowledge about the genetic aspects of common chronic c... more This review describes the advances in the knowledge about the genetic aspects of common chronic complications of diabetes with prognostic significance, such as diabetic nephropathy and cardiovascular diseases. It is well known that the genetic factors responsible for chronic complications are different from those that cause Diabetes Mellitus. Until recently, the studies were limited to the analysis of individual genes associated or related to multifactorial diseases. However at the present time the "genome wide associated studies" lead to agreat advance in knowledge. The analysis of genetic variations or polymorphisms allows the understanding of human individuality and the predisposition towards certain diseases. A new research field appeared in 2004, when small messenger RNAs, called microRNA related to Diabetes mellitus and its chronic complications, were identified. The function of these RNAs is to regulate several target genes. These affect insulin secretion and action...
Laccase is one of the ligninolytic enzymes found in liquid cultures of the fungus Ceriporiopsis s... more Laccase is one of the ligninolytic enzymes found in liquid cultures of the fungus Ceriporiopsis subvermispora in defined medium. As an approach to a clarification of the role of laccases during the attack on lignin by the fungus, the enzyme has been characterized further. The levels of this phenol oxidase increase 2-fold in the presence of p-anisidine and are severely affected when addition of either Mn(II) or Cu(II) ions to the medium is omitted. Isoelectrofocusing allowed the resolution of two laccase isoenzymes, with pIs of 3.65 and 3.59. In rich medium, laccase activity is 10-fold higher than in salt medium, and it is not affected by the external addition of p-anisidine or Mn(II). Four isoenzymes were detected in these cultures, with pIs between 3.76 and 3.60. In a wheat bran medium, four isoenzymes with pIs in the range 3.63-3.46, plus a fifth isoenzyme of high pI (4.82), were also identified. The absorption spectrum of a pool containing the four isoenzymes from rich medium sho...
Two outer membrane proteins of Salmonella typhi Ty 2 were extensively co-purified. According to t... more Two outer membrane proteins of Salmonella typhi Ty 2 were extensively co-purified. According to their migration in dodecylsulfate/polyacrylamide gel electrophoresis and solubility characteristics, these proteins are homologous to the 35-kDa and 36-kDa porins found in Salmonella typhimurium. A porin homologous to the 34-kDa one has not been found in S. typhi Ty 2. A critical step in the purification of porins is heating at 100 degrees C in 2% sodium dodecyl sulfate before Sephadex gel filtration. The absence of detergent in aqueous suspensions enhances porin aggregation, these aggregations inducing human red cell lysis. Porins obtained by an alternative procedure consisting of heating at 60 degrees C instead of 100 degrees C were also hemolytic. Using nanomolar concentration of porins a strong influence of temperature on the hemolytic effect was observed. Porin-induced hemolysis was inhibited with anti-porin serum, as well as by a treatment with phenylglyoxal, which reacts with the arginine residues of proteins. The membrane-disrupting ability of porins aggregates might explain some pathogenic characteristics of gram-negative bacterial infections.
Proceedings of the National Academy of Sciences, 1990
We have identified and partially characterized another human general transcription factor, TFIIG.... more We have identified and partially characterized another human general transcription factor, TFIIG. Using a reconstituted in vitro system comprised of purified RNA polymerase II, TFIIB, TFIID, TFIIE, and TFIIF, we found that TFIIG was essential for specific initiation from all class II genes tested. In this system TFIIA could partially replace TFIIG; however, even at saturating concentrations of TFIIA, addition of TFIIG further stimulated transcription. Since the chromatographic properties of TFIIG differed significantly from those of TFIIA, we concluded that TFIIA and TFIIG are distinct but functionally related transcription factors. Heparin challenge assays showed that TFIIG is required for the assembly of a functional preinitiation complex. However, it must act after template commitment by TFIID, since this step did not require, and was unaffected by, either TFIIG or TFIIA.
Cobre y Selenio son elementos esenciales para la vida humana y animal. Sin embargo, dependiendo d... more Cobre y Selenio son elementos esenciales para la vida humana y animal. Sin embargo, dependiendo de las concentraciones, estos pueden causar problemas de toxicidad, ya sea por deficiencia o exceso. En el presente trabajo se determinaron las concentraciones de cobre y selenio en muestras de distintos componentes de tres ecosistemas agricolas de la region de Valparaiso: agua de lluvia, suelos y alfalfa provenientes de los valles de Puchuncavi y *To whom correspondence should be addressed, Fax: 56-32-273422; e-mail: idegrego@ucv.cl Bol. Soc. Chil. Quim., 45, N 1 (2000) Catemu, lugares donde se realizan actividades mineras metalurgicas de importancia y del valle de Casablanca, lugar considerado como referencia. Las muestras fueron recolectadas en el periodo Abril-Mayo de 1997. Los resultados mostraron que en los tres tipos de muestra las concentraciones de cobre decrecen en funcion de la distancia de la fuente emisora. Este mismo comportamiento fue observado para selenio en agua de lluvia. Sin embargo, las concentraciones de este elemento en suelos y alfalfa son bajas y similares (entre 0,1 y 0,4 mg Kg-1). Se obtuvieron buenas correlaciones entre las concentraciones de cobre en los distintos componentes de los ecosistemas. Por el contrario solo se obtuvo una buena correlacion entre las cantidades de cobre y selenio depositadas por agua de lluvia proveniente de los distintos sitios de muestreo del valle de Puchuncavi.
Proceedings of the National Academy of Sciences of the United States of America, Jan 3, 2012
Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referr... more Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium simultaneously degrades lignin and cellulose, whereas the closely related species, Ceriporiopsis subvermispora, also depolymerizes lignin but may do so with relatively little cellulose degradation. To investigate the basis for selective ligninolysis, we conducted comparative genome analysis of C. subvermispora and P. chrysosporium. Genes encoding manganese peroxidase numbered 13 and five in C. subvermispora and P. chrysosporium, respectively. In addition, the C. subvermispora genome contains at least seven genes predicted to encode laccases, whereas the P. chrysosporium genome contains none. We also observed expansion of the number of C. subvermispora desaturase-encoding genes putatively involved in lipid metabolism. Microarray-based transcriptome analysis showed substantial up-regulation of several desaturase and MnP genes in wood-co...
Total copper and selenium concentrations were determined in rain waters, soils and alfalfa sample... more Total copper and selenium concentrations were determined in rain waters, soils and alfalfa samples collected during April-May 1997 at various sites from different zones of Valparaiso region, in Chile: Puchuncavi and Catemu valleys, (both impacted by mining activities) and Casablanca valley (reference site). In rain waters, Cu and Se concentrations clearly decreased exponentially with distance from the sources and were significantly correlated. The results obtained demonstrate that the mining activities have contributed to increase the contamination by copper in the agricultural ecosystems, particularly those located near the smelters. In all matrices from Puchuncavi and Catemu valleys copper concentrations were higher than in the reference site. In Puchuncavi valley, Cu concentrations in soils and alfalfa show close correlation and were a function of the distance from the smelter. Selenium concentration in soils and alfalfa follows a different pattern, being relatively constant in these matrices and presenting no clear dependency on the distance from the sources. In alfalfa they ranged between 0.10 and 0.40 mg kg-1; these concentrations are not high and do not represent a problem to livestock grazing in these areas.
Studies on Salmonella typhi and Salmonella typhimurium outer membrane proteins have shown that th... more Studies on Salmonella typhi and Salmonella typhimurium outer membrane proteins have shown that the relative position of OmpC porin in sodium dodecyl sulfate.polyacrylamide gel electrophoresis undergoes an important shift when the concentration of ammonium persulfate in the running gel is increased from 6 to 12 mM. The apparent molecular mass at these concentrations was estimated to be 34 and 40 kDa, respectively. Under similar electrophoretic conditions the apparent molecular mass estimated for OmpF was 37.6 and 38.2 kDa. Therefore, OmpC moves from a leading position to a position behind OmpF. For Escherichia coli OmpC the shift observed is less pronounced than that occurring in Salmonellae.
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