Cupin: A candidate molecular structure for the Nep1-like protein family

<p>Abstract</p> <p>Background</p> <p>NEP1-like proteins (NLPs) are a novel family of microbial elicitors of plant necrosis. Some NLPs induce a hypersensitive-like response in dicot plants though the basis for this response remains unclear. In addition, the spatial structure and the role of these highly conserved proteins are not known.</p> <p>Results</p> <p>We predict a <it>3d</it>-structure for the <it>β</it>-rich section of the NLPs based on alignments, prediction tools and molecular dynamics. We calculated a consensus sequence from 42 NLPs proteins, predicted its secondary structure and obtained a high quality alignment of this structure and conserved residues with the two Cupin superfamily motifs. The conserved sequence GHRHDWE and several common residues, especially some conserved histidines, in NLPs match closely the two cupin motifs. Besides other common residues shared by dicot Auxin-Binding Proteins (ABPs) and NLPs, an additional conserved histidine found in all dicot ABPs was also found in all NLPs at the same position.</p> <p>Conclusion</p> <p>We propose that the necrosis inducing protein class belongs to the Cupin superfamily. Based on the <it>3d</it>-structure, we are proposing some possible functions for the NLPs.</p

Sarcoidoisis ocular: presentación de un caso / Ocular Sarcoidosis: a case report

La sarcoidosis es una enfermedad granulomatosa multifactorial que afecta principalmente ganglios linfaticos, pulmones, piel, ojos, hígado, bazo y parótidas. Con menor frecuencia también puede afectar el sistema nervioso central, corazón, tracto respiratorio alto y hueso. No es frecuente en Pinar del Río observar  complicaciones oftalmológicas en la sarcoidosis.  Objetivo: Reportar el primer caso de sarcoidosis con complicaciones oculares y tratamiento de las mismas.   Presentación de caso: Paciente masculino de 55 años que fue ingresado por un síndrome general y que se diagnosticó como portador de sarcoidosis en la UCI del  Hospital General Docente Abel Santamaría Cuadrado que además presentaba complicaciones  oftalmológicas graves tales como: atalamia bilateral, hipotonía ocular, ausencia de lágrimas, queratitis, desdoblamiento corneal con degeneración del tercio inferior de la misma, cataratas, sinequias posteriores y disminución de la agudeza visual bilateral.   Ante la gravedad del estado ocular se recurrió a medidas quirúrgicas como la aplicación intra cameral de sustancia visco elástica para reponer el tono ocular; se usaron además lágrimas artificiales, esteroides  sistémicos y tópicos, midriáticos.   Se  logró preservar la morfología ocular y poder posteriormente, tratar las cataratas,  preservándole una visión útil, con alta calidad de vida.Palabras Clave: Sarcoidosis, granuloma, oftalmopatías/complicaciones.ABSTRACTSarcoidosis is a multifactorial granulomatose disease that affects lymphatic ganglia, lungs, skin, eyes, liver, spleen and parotids.  It rarely affects central nervous system, heart, upper respiratory tract and bones. Ophthalmic-sarcoidosis complications are not frequently found in Pinar del Rio province, Cuba. Objective: To report the first case presented with sarcoidosis with ocular complications and treatment. Case: A 55 years-old male patient was admitted in the ICU ("Abel Santamaria Cuadrado" University Hospital) presenting a general syndrome and diagnosed as a carrier of Sarcoidosis with severe ophthalmic complications such as: bilateral athalamia, ocular hypotonia, absence of tears, keratitis, corneal unfold with degeneration of the inferior third of it, cataracts, posterior synechia and decrease of the bilateral visual acuteness. Due to the severity of the ocular conditions surgical measures were taken:  an intra-chamber elastic-viscous substance was applied to replace the ocular tone; using also artificial tears, systemic, topic and mydriatic steroids. Ocular morphology was protected to facilitate the treatment of cataracts and preserving the usefulness of vision with quality of life. Key words: Sarcoidosis, granuloma, eye diseases/complications

Global Analyses Of Ceratocystis Cacaofunesta Mitochondria: From Genome To Proteome.

The ascomycete fungus Ceratocystis cacaofunesta is the causal agent of wilt disease in cacao, which results in significant economic losses in the affected producing areas. Despite the economic importance of the Ceratocystis complex of species, no genomic data are available for any of its members. Given that mitochondria play important roles in fungal virulence and the susceptibility/resistance of fungi to fungicides, we performed the first functional analysis of this organelle in Ceratocystis using integrated omics approaches. The C. cacaofunesta mitochondrial genome (mtDNA) consists of a single, 103,147-bp circular molecule, making this the second largest mtDNA among the Sordariomycetes. Bioinformatics analysis revealed the presence of 15 conserved genes and 37 intronic open reading frames in C. cacaofunesta mtDNA. Here, we predicted the mitochondrial proteome (mtProt) of C. cacaofunesta, which is comprised of 1,124 polypeptides - 52 proteins that are mitochondrially encoded and 1,072 that are nuclearly encoded. Transcriptome analysis revealed 33 probable novel genes. Comparisons among the Gene Ontology results of the predicted mtProt of C. cacaofunesta, Neurospora crassa and Saccharomyces cerevisiae revealed no significant differences. Moreover, C. cacaofunesta mitochondria were isolated, and the mtProt was subjected to mass spectrometric analysis. The experimental proteome validated 27% of the predicted mtProt. Our results confirmed the existence of 110 hypothetical proteins and 7 novel proteins of which 83 and 1, respectively, had putative mitochondrial localization. The present study provides the first partial genomic analysis of a species of the Ceratocystis genus and the first predicted mitochondrial protein inventory of a phytopathogenic fungus. In addition to the known mitochondrial role in pathogenicity, our results demonstrated that the global function analysis of this organelle is similar in pathogenic and non-pathogenic fungi, suggesting that its relevance in the lifestyle of these organisms should be based on a small number of specific proteins and/or with respect to differential gene regulation. In this regard, particular interest should be directed towards mitochondrial proteins with unknown function and the novel protein that might be specific to this species. Further functional characterization of these proteins could enhance our understanding of the role of mitochondria in phytopathogenicity.149

Global analyses of Ceratocystis cacaofunesta mitochondria: from genome to proteome

Abstract Background The ascomycete fungus Ceratocystis cacaofunesta is the causal agent of wilt disease in cacao, which results in significant economic losses in the affected producing areas. Despite the economic importance of the Ceratocystis complex of species, no genomic data are available for any of its members. Given that mitochondria play important roles in fungal virulence and the susceptibility/resistance of fungi to fungicides, we performed the first functional analysis of this organelle in Ceratocystis using integrated “omics” approaches. Results The C. cacaofunesta mitochondrial genome (mtDNA) consists of a single, 103,147-bp circular molecule, making this the second largest mtDNA among the Sordariomycetes. Bioinformatics analysis revealed the presence of 15 conserved genes and 37 intronic open reading frames in C. cacaofunesta mtDNA. Here, we predicted the mitochondrial proteome (mtProt) of C. cacaofunesta, which is comprised of 1,124 polypeptides - 52 proteins that are mitochondrially encoded and 1,072 that are nuclearly encoded. Transcriptome analysis revealed 33 probable novel genes. Comparisons among the Gene Ontology results of the predicted mtProt of C. cacaofunesta, Neurospora crassa and Saccharomyces cerevisiae revealed no significant differences. Moreover, C. cacaofunesta mitochondria were isolated, and the mtProt was subjected to mass spectrometric analysis. The experimental proteome validated 27% of the predicted mtProt. Our results confirmed the existence of 110 hypothetical proteins and 7 novel proteins of which 83 and 1, respectively, had putative mitochondrial localization. Conclusions The present study provides the first partial genomic analysis of a species of the Ceratocystis genus and the first predicted mitochondrial protein inventory of a phytopathogenic fungus. In addition to the known mitochondrial role in pathogenicity, our results demonstrated that the global function analysis of this organelle is similar in pathogenic and non-pathogenic fungi, suggesting that its relevance in the lifestyle of these organisms should be based on a small number of specific proteins and/or with respect to differential gene regulation. In this regard, particular interest should be directed towards mitochondrial proteins with unknown function and the novel protein that might be specific to this species. Further functional characterization of these proteins could enhance our understanding of the role of mitochondria in phytopathogenicity

Cupin: A candidate molecular structure for the Nep1-like protein family-3

15 type II NLPs (second line), 32 dicot ABPs (third line), 9 monocot ABPs (fourth line), (maize ABP), (cysteine dioxygenase type 1, capitalized residues represent 100% conservation in 10 different organisms), (hypothetical protein) and the two main cupin motifs (last line). Solid line boxes represent real , dashed line boxes represent those predicted and dotted line boxes are predicted with low confidence level. Compatible residues are shown in boldface and those residues present in both type I/II NLPs and any of the other sequences are grey boxed. The first two lines follow the convention of Figure 1.<p><b>Copyright information:</b></p><p>Taken from "Cupin: A candidate molecular structure for the Nep1-like protein family"</p><p>http://www.biomedcentral.com/1471-2229/8/50</p><p>BMC Plant Biology 2008;8():50-50.</p><p>Published online 30 Apr 2008</p><p>PMCID:PMC2396628.</p><p></p

Cupin: A candidate molecular structure for the Nep1-like protein family-0

15 type II NLPs (second line), 32 dicot ABPs (third line), 9 monocot ABPs (fourth line), (maize ABP), (cysteine dioxygenase type 1, capitalized residues represent 100% conservation in 10 different organisms), (hypothetical protein) and the two main cupin motifs (last line). Solid line boxes represent real , dashed line boxes represent those predicted and dotted line boxes are predicted with low confidence level. Compatible residues are shown in boldface and those residues present in both type I/II NLPs and any of the other sequences are grey boxed. The first two lines follow the convention of Figure 1.<p><b>Copyright information:</b></p><p>Taken from "Cupin: A candidate molecular structure for the Nep1-like protein family"</p><p>http://www.biomedcentral.com/1471-2229/8/50</p><p>BMC Plant Biology 2008;8():50-50.</p><p>Published online 30 Apr 2008</p><p>PMCID:PMC2396628.</p><p></p

Cupin: A candidate molecular structure for the Nep1-like protein family-1

Sition of some of the conserved residues in the -structure (right side). The sphere in the middle of the structure represents the putative metal ion.<p><b>Copyright information:</b></p><p>Taken from "Cupin: A candidate molecular structure for the Nep1-like protein family"</p><p>http://www.biomedcentral.com/1471-2229/8/50</p><p>BMC Plant Biology 2008;8():50-50.</p><p>Published online 30 Apr 2008</p><p>PMCID:PMC2396628.</p><p></p

Cupin: A candidate molecular structure for the Nep1-like protein family-4

Sition of some of the conserved residues in the -structure (right side). The sphere in the middle of the structure represents the putative metal ion.<p><b>Copyright information:</b></p><p>Taken from "Cupin: A candidate molecular structure for the Nep1-like protein family"</p><p>http://www.biomedcentral.com/1471-2229/8/50</p><p>BMC Plant Biology 2008;8():50-50.</p><p>Published online 30 Apr 2008</p><p>PMCID:PMC2396628.</p><p></p

Cupin: A candidate molecular structure for the Nep1-like protein family-2

Ion for type I NLP consensus sequence (a), type II NLP consensus sequence (b) and cupin (c). The solid line (shaded gray) represents the confidence level for the , and the dashed line for the . SP = signal peptide. IMR = Inter Motif Region. represents the GHRHDWE motif in type I and II NLP consensus sequences and ihrhscee in , respectively.<p><b>Copyright information:</b></p><p>Taken from "Cupin: A candidate molecular structure for the Nep1-like protein family"</p><p>http://www.biomedcentral.com/1471-2229/8/50</p><p>BMC Plant Biology 2008;8():50-50.</p><p>Published online 30 Apr 2008</p><p>PMCID:PMC2396628.</p><p></p