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Identification of new sphingomyelinases D in pathogenic fungi and other pathogenic organisms.

Dias-Lopes C, Neshich IA, Neshich G, Ortega JM, Granier C, Chávez-Olortegui C, Molina F, Felicori L - PLoS ONE (2013)

Bottom Line: We suggest that the C-terminal tail is responsible for stabilizing the entire internal structure of the SMase D Tim barrel and that it can be considered an SMase D hallmark in combination with the amino acid residues from the active site.Most of these enzyme sequences were discovered from fungi and the SMase D activity was experimentally confirmed in the fungus Aspergillus flavus.Because most of these novel SMases D are from organisms that are endowed with pathogenic properties similar to those evoked by these enzymes alone, they might be associated with their pathogenic mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Bioquímica-Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.

ABSTRACT
Sphingomyelinases D (SMases D) or dermonecrotic toxins are well characterized in Loxosceles spider venoms and have been described in some strains of pathogenic microorganisms, such as Corynebacterium sp. After spider bites, the SMase D molecules cause skin necrosis and occasional severe systemic manifestations, such as acute renal failure. In this paper, we identified new SMase D amino acid sequences from various organisms belonging to 24 distinct genera, of which, 19 are new. These SMases D share a conserved active site and a C-terminal motif. We suggest that the C-terminal tail is responsible for stabilizing the entire internal structure of the SMase D Tim barrel and that it can be considered an SMase D hallmark in combination with the amino acid residues from the active site. Most of these enzyme sequences were discovered from fungi and the SMase D activity was experimentally confirmed in the fungus Aspergillus flavus. Because most of these novel SMases D are from organisms that are endowed with pathogenic properties similar to those evoked by these enzymes alone, they might be associated with their pathogenic mechanisms.

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Related in: MedlinePlus

Multiple sequence alignment of one SMase D sequence for each genus identified.Consensus sequences and secondary structure of L. laeta SMase D (pdb number:1xx1) are shown underneath the alignment. Conserved catalytic histidines residues are marked with blue boxes (Label H12 and H47 in secondary structure of 1xx1). Residues responsible for Mg+2 coordination are marked with red boxes (Label Mg in secondary structure of 1xx1) and amino acids involved in network of hydrogen bonds are marked with black boxes (label HB in secondary structure of 1xx1). The following sequences were used to build this alignment and were obtained from the NCBI nr protein database: Ajellomyces (GI: 225556466), Arthroderma (GI: 302499957), Trichophyton (GI: 327309460), Uncinocarpus (GI: 258566630), Coccidioides (GI: 119182286), Paracoccidioides (GI: 225681750), Aspergillus (GI: 220691453), Metaseiulus (GI: 391334832), Loxosceles (GI: 60594084), Sicarius (GI: 292630576), Ixodes (GI: 121962650), Amblyomma (GI: 346467405), Rhipicephalus (GI: 427782159), Burkholderia (GI: 116687281), Arcanobacterium (GI: 297571658), Corynebacterium (GI: 300857446), Streptomyces (GI: 254384004) and Austwickia (GI:403190737). Six genera have not entries in NCBI nr protein database, but their protein sequences were translated from in NCBI WGS or dbEST entries:, Fusarium (GI: 144921672, position: 31242-32224), Gibberella (GI: 116139506, position: 93710-94513), Passalora (GI: 407486978, position: 4015-4803) , Metarhizium (GI: 322696462), Stegodyphus (GI: 374247203) and Acanthoscurria (GIs: 68762186 and 68761727). The genera Dermatophagoides, Psoroptes, Varroa and Tetranycus have incomplete sequences and were not used in this analysis.
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pone-0079240-g002: Multiple sequence alignment of one SMase D sequence for each genus identified.Consensus sequences and secondary structure of L. laeta SMase D (pdb number:1xx1) are shown underneath the alignment. Conserved catalytic histidines residues are marked with blue boxes (Label H12 and H47 in secondary structure of 1xx1). Residues responsible for Mg+2 coordination are marked with red boxes (Label Mg in secondary structure of 1xx1) and amino acids involved in network of hydrogen bonds are marked with black boxes (label HB in secondary structure of 1xx1). The following sequences were used to build this alignment and were obtained from the NCBI nr protein database: Ajellomyces (GI: 225556466), Arthroderma (GI: 302499957), Trichophyton (GI: 327309460), Uncinocarpus (GI: 258566630), Coccidioides (GI: 119182286), Paracoccidioides (GI: 225681750), Aspergillus (GI: 220691453), Metaseiulus (GI: 391334832), Loxosceles (GI: 60594084), Sicarius (GI: 292630576), Ixodes (GI: 121962650), Amblyomma (GI: 346467405), Rhipicephalus (GI: 427782159), Burkholderia (GI: 116687281), Arcanobacterium (GI: 297571658), Corynebacterium (GI: 300857446), Streptomyces (GI: 254384004) and Austwickia (GI:403190737). Six genera have not entries in NCBI nr protein database, but their protein sequences were translated from in NCBI WGS or dbEST entries:, Fusarium (GI: 144921672, position: 31242-32224), Gibberella (GI: 116139506, position: 93710-94513), Passalora (GI: 407486978, position: 4015-4803) , Metarhizium (GI: 322696462), Stegodyphus (GI: 374247203) and Acanthoscurria (GIs: 68762186 and 68761727). The genera Dermatophagoides, Psoroptes, Varroa and Tetranycus have incomplete sequences and were not used in this analysis.

Mentions: Structural studies on SMase I (PDB 1XX1), an SMase D from Loxosceles laeta [2], have suggested that the catalytic mechanism of this eight-stranded TIM barrel (or α/β barrel) SMase D involves an acid-base reaction that requires two histidine residues (His12 and His47) and the presence of one Mg+2 ion. The alignment (Figure 2) of one sequence of each genera showed that the catalytic histidine residues (12 and 47) are strictly conserved in all the newly identified sequences, except for the mite Metaseiulus occidentalis, which lacks His12. The residues Glu32, Asp34 and Asp91, which coordinate the Mg+2 ion, are also strictly conserved. In this family of proteins, the catalytic His12 and His47 are supported by a network of hydrogen bonds between Asp34, Asp52, Trp230, Asp233 and Asn252. Asp34 and Trp230 are strictly conserved in the aligned sequences of Figure 2; however, Asp52, Asp233 and Asn252 are not conserved.


Identification of new sphingomyelinases D in pathogenic fungi and other pathogenic organisms.

Dias-Lopes C, Neshich IA, Neshich G, Ortega JM, Granier C, Chávez-Olortegui C, Molina F, Felicori L - PLoS ONE (2013)

Multiple sequence alignment of one SMase D sequence for each genus identified.Consensus sequences and secondary structure of L. laeta SMase D (pdb number:1xx1) are shown underneath the alignment. Conserved catalytic histidines residues are marked with blue boxes (Label H12 and H47 in secondary structure of 1xx1). Residues responsible for Mg+2 coordination are marked with red boxes (Label Mg in secondary structure of 1xx1) and amino acids involved in network of hydrogen bonds are marked with black boxes (label HB in secondary structure of 1xx1). The following sequences were used to build this alignment and were obtained from the NCBI nr protein database: Ajellomyces (GI: 225556466), Arthroderma (GI: 302499957), Trichophyton (GI: 327309460), Uncinocarpus (GI: 258566630), Coccidioides (GI: 119182286), Paracoccidioides (GI: 225681750), Aspergillus (GI: 220691453), Metaseiulus (GI: 391334832), Loxosceles (GI: 60594084), Sicarius (GI: 292630576), Ixodes (GI: 121962650), Amblyomma (GI: 346467405), Rhipicephalus (GI: 427782159), Burkholderia (GI: 116687281), Arcanobacterium (GI: 297571658), Corynebacterium (GI: 300857446), Streptomyces (GI: 254384004) and Austwickia (GI:403190737). Six genera have not entries in NCBI nr protein database, but their protein sequences were translated from in NCBI WGS or dbEST entries:, Fusarium (GI: 144921672, position: 31242-32224), Gibberella (GI: 116139506, position: 93710-94513), Passalora (GI: 407486978, position: 4015-4803) , Metarhizium (GI: 322696462), Stegodyphus (GI: 374247203) and Acanthoscurria (GIs: 68762186 and 68761727). The genera Dermatophagoides, Psoroptes, Varroa and Tetranycus have incomplete sequences and were not used in this analysis.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815110&req=5

pone-0079240-g002: Multiple sequence alignment of one SMase D sequence for each genus identified.Consensus sequences and secondary structure of L. laeta SMase D (pdb number:1xx1) are shown underneath the alignment. Conserved catalytic histidines residues are marked with blue boxes (Label H12 and H47 in secondary structure of 1xx1). Residues responsible for Mg+2 coordination are marked with red boxes (Label Mg in secondary structure of 1xx1) and amino acids involved in network of hydrogen bonds are marked with black boxes (label HB in secondary structure of 1xx1). The following sequences were used to build this alignment and were obtained from the NCBI nr protein database: Ajellomyces (GI: 225556466), Arthroderma (GI: 302499957), Trichophyton (GI: 327309460), Uncinocarpus (GI: 258566630), Coccidioides (GI: 119182286), Paracoccidioides (GI: 225681750), Aspergillus (GI: 220691453), Metaseiulus (GI: 391334832), Loxosceles (GI: 60594084), Sicarius (GI: 292630576), Ixodes (GI: 121962650), Amblyomma (GI: 346467405), Rhipicephalus (GI: 427782159), Burkholderia (GI: 116687281), Arcanobacterium (GI: 297571658), Corynebacterium (GI: 300857446), Streptomyces (GI: 254384004) and Austwickia (GI:403190737). Six genera have not entries in NCBI nr protein database, but their protein sequences were translated from in NCBI WGS or dbEST entries:, Fusarium (GI: 144921672, position: 31242-32224), Gibberella (GI: 116139506, position: 93710-94513), Passalora (GI: 407486978, position: 4015-4803) , Metarhizium (GI: 322696462), Stegodyphus (GI: 374247203) and Acanthoscurria (GIs: 68762186 and 68761727). The genera Dermatophagoides, Psoroptes, Varroa and Tetranycus have incomplete sequences and were not used in this analysis.
Mentions: Structural studies on SMase I (PDB 1XX1), an SMase D from Loxosceles laeta [2], have suggested that the catalytic mechanism of this eight-stranded TIM barrel (or α/β barrel) SMase D involves an acid-base reaction that requires two histidine residues (His12 and His47) and the presence of one Mg+2 ion. The alignment (Figure 2) of one sequence of each genera showed that the catalytic histidine residues (12 and 47) are strictly conserved in all the newly identified sequences, except for the mite Metaseiulus occidentalis, which lacks His12. The residues Glu32, Asp34 and Asp91, which coordinate the Mg+2 ion, are also strictly conserved. In this family of proteins, the catalytic His12 and His47 are supported by a network of hydrogen bonds between Asp34, Asp52, Trp230, Asp233 and Asn252. Asp34 and Trp230 are strictly conserved in the aligned sequences of Figure 2; however, Asp52, Asp233 and Asn252 are not conserved.

Bottom Line: We suggest that the C-terminal tail is responsible for stabilizing the entire internal structure of the SMase D Tim barrel and that it can be considered an SMase D hallmark in combination with the amino acid residues from the active site.Most of these enzyme sequences were discovered from fungi and the SMase D activity was experimentally confirmed in the fungus Aspergillus flavus.Because most of these novel SMases D are from organisms that are endowed with pathogenic properties similar to those evoked by these enzymes alone, they might be associated with their pathogenic mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Bioquímica-Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.

ABSTRACT
Sphingomyelinases D (SMases D) or dermonecrotic toxins are well characterized in Loxosceles spider venoms and have been described in some strains of pathogenic microorganisms, such as Corynebacterium sp. After spider bites, the SMase D molecules cause skin necrosis and occasional severe systemic manifestations, such as acute renal failure. In this paper, we identified new SMase D amino acid sequences from various organisms belonging to 24 distinct genera, of which, 19 are new. These SMases D share a conserved active site and a C-terminal motif. We suggest that the C-terminal tail is responsible for stabilizing the entire internal structure of the SMase D Tim barrel and that it can be considered an SMase D hallmark in combination with the amino acid residues from the active site. Most of these enzyme sequences were discovered from fungi and the SMase D activity was experimentally confirmed in the fungus Aspergillus flavus. Because most of these novel SMases D are from organisms that are endowed with pathogenic properties similar to those evoked by these enzymes alone, they might be associated with their pathogenic mechanisms.

Show MeSH
Related in: MedlinePlus