2401
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Holmes DE, Mester T, O'Neil RA, Perpetua LA, Larrahondo MJ, Glaven R, Sharma ML, Ward JE, Nevin KP, Lovley DR. Genes for two multicopper proteins required for Fe(III) oxide reduction in Geobacter sulfurreducens have different expression patterns both in the subsurface and on energy-harvesting electrodes. Microbiology (Reading) 2008; 154:1422-1435. [DOI: 10.1099/mic.0.2007/014365-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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2402
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Dynamic expression pattern of the growth hormone receptor during early development of the Chilean flounder. Comp Biochem Physiol B Biochem Mol Biol 2008; 150:93-102. [DOI: 10.1016/j.cbpb.2008.01.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Revised: 01/30/2008] [Accepted: 01/30/2008] [Indexed: 11/17/2022]
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2403
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Park D, Kim BC, Cho SW, Park SJ, Choi JS, Kim SI, Bhak J, Lee S. MassNet: a functional annotation service for protein mass spectrometry data. Nucleic Acids Res 2008; 36:W491-5. [PMID: 18448467 PMCID: PMC2447811 DOI: 10.1093/nar/gkn241] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Although mass spectrometry has been frequently used to identify proteins, there are no web servers that provide comprehensive functional annotation of those identified proteins. It is necessary to provide such web service due to a rapid increase in the data. We, therefore, introduce MassNet, which provides (i) physico-chemical analysis information, (ii) KEGG pathway assignment (iii) Gene Ontology mapping and (iv) protein-protein interaction (PPI) prediction for the data from MASCOT, Prospector and Profound. MassNet provides the prediction information for PPIs using both 3D structural interaction and experimental interaction deposited in PSIMAP, BIND, DIP, HPRD, IntAct, MINT, CYGD and BioGrid. The web service is freely available at http://massnet.kr or http://sequenceome.kobic.re.kr/MassNet/.
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Affiliation(s)
- Daeui Park
- Korean BioInformation Center, KRIBB, Daejeon 305-806, Korea
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2404
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Expression patterns of engrailed and dpp in the gastropod Lymnaea stagnalis. Dev Genes Evol 2008; 218:237-51. [PMID: 18443822 DOI: 10.1007/s00427-008-0217-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Accepted: 03/20/2008] [Indexed: 10/22/2022]
Abstract
We isolated the full-length cDNAs of engrailed and dpp-BMP2/4 orthologues from the pond snail Lymnaea stagnalis and examined their expression patterns during development by the whole mount in situ hybridization. At the gastrula and trochophore stages, engrailed is expressed in the peripheral ectoderm of the presumptive and invaginating shell gland, corroborating its role in the shell formation that is widely conserved among molluscs. At the same stages, dpp-BMP2/4 is expressed in the right-hand side ectoderm of the shell gland and in the invaginating stomodaeum. Unlike in the gastropod Patella vulgata, our results suggested that dpp-BMP2/4 has a role in the shell formation, rather than in the regional specification and that it could be involved in the specification pathway of the left-right asymmetry of the developing shell in L. stagnalis.
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2405
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Benítez-Páez A, Cárdenas-Brito S. Dissection of functional residues in receptor activity-modifying proteins through phylogenetic and statistical analyses. Evol Bioinform Online 2008; 4:153-69. [PMID: 19204815 PMCID: PMC2614204 DOI: 10.4137/ebo.s705] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Type I and type-II functional divergences have been stated to highlight specific residues carrying out differential functions in evolutionary-divergent protein clusters from a single common ancestor. Briefly, type I analysis is based on residue constraints reflecting a gain of function just in one cluster of an entire family of proteins; while the type-II approach is based on residue constraints showing a different chemical nature in every cluster of a protein family. This last evidence is understood as differential functionality among clusters. The Receptor Activity-Modifying Proteins constitute a family characterized by its paralogous distribution in vertebrates. They are known as G-Protein Coupled Receptor modulators. Although several studies have determined their involvement in ligand binding, specificity, and enhancement of signal transduction, the responsible residues supporting those functions are unclear. Using different bioinformatic approaches, we predicted residues involved in different RAMP functional tasks. Many residues localized in an extracellular coil of RAMP proteins were predicted to be under functional divergence suggesting a gain of function in their respective proteins. Interestingly, the transmembrane region also showed important results for residues playing relevant roles where most of them showed a biased distribution on the structure. A relevant role was conferred by the enrichment of type-II residues observed in their sequences. We show a collection of residues explaining possible gain of function and differential functionality in RAMP proteins. These residues are still experimentally unexplored with regards to functionality. Finally, an evolutionary history could be discerned. Mainly, the RAMP2 cluster has evolved in a higher manner than other RAMP clusters. However, a deacceleration in the aminoacid substitution rate of RAMP2 was observed in mammals. Such effect could be caused by the co-evolution of ligands and receptors interacting with RAMP2 through evolution and/or the specialization of this cluster in GPCR modulation.
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Affiliation(s)
- Alfonso Benítez-Páez
- Bioinformatic Analysis Group-GABi. Centro de Investigación y Desarrollo en Biotecnología-CIDBIO. Bogotá D.C., Colombia.
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2406
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Bauerschmitt H, Funes S, Herrmann JM. The membrane-bound GTPase Guf1 promotes mitochondrial protein synthesis under suboptimal conditions. J Biol Chem 2008; 283:17139-46. [PMID: 18442968 DOI: 10.1074/jbc.m710037200] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recently, the bacterial elongation factor LepA was identified as critical for the accuracy of in vitro translation reactions. Extremely well conserved homologues of LepA are present throughout bacteria and eukaryotes, but the physiological relevance of these proteins is unclear. Here we show that the yeast counterpart of LepA, Guf1, is located in the mitochondrial matrix and tightly associated with the inner membrane. It binds to mitochondrial ribosomes in a GTP-dependent manner. Mutants lacking Guf1 show cold- and heat-sensitive growth defects on non-fermentable carbon sources that are especially pronounced under nutrient-limiting conditions. The cold sensitivity is explained by diminished rates of protein synthesis at low temperatures. At elevated temperatures, Guf1-deficient mutants exhibit defects in the assembly of cytochrome oxidase, suggesting that the polypeptides produced are not functional. Moreover, Guf1 mutants exhibit synthetic growth defects with mutations of the protein insertase Oxa1. These observations show a critical role for Guf1 in vivo. The observed defects in Guf1-deficient mitochondria are consistent with a function of Guf1 as a fidelity factor of mitochondrial protein synthesis.
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Affiliation(s)
- Heike Bauerschmitt
- Institute of Physiological Chemistry, University of Munich, 81377 Munich, Germany
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2407
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Norman A, Hansen LH, She Q, Sørensen SJ. Nucleotide sequence of pOLA52: a conjugative IncX1 plasmid from Escherichia coli which enables biofilm formation and multidrug efflux. Plasmid 2008; 60:59-74. [PMID: 18440636 DOI: 10.1016/j.plasmid.2008.03.003] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Revised: 03/11/2008] [Accepted: 03/13/2008] [Indexed: 12/01/2022]
Abstract
The large conjugative multidrug resistance (MDR) plasmid pOLA52 was sequenced and annotated. The plasmid encodes two phenotypes normally associated with the chromosomes of opportunistic pathogens, namely MDR via a resistance-nodulation-division (RND)-type efflux-pump (oqxAB), and the formation of type 3 fimbriae (mrkABCDF). The plasmid was found to be 51,602 bp long with 68 putative genes. About half of the plasmid constituted a conserved IncX1-type backbone with predicted regions for conjugation, replication and partitioning, as well as a toxin/antitoxin (TA) plasmid addiction system. The plasmid was also classified as IncX1 with incompatibility testing. The conjugal transfer and plasmid maintenance regions of pOLA52 therefore seem to represent IncX1 orthologues of the well-characterized IncX2 plasmid R6K. Sequence homology searches in GenBank also suggested a considerably higher prevalence of IncX1 group plasmids than IncX2. The 21 kb 'genetic load' region of pOLA52 was shown to consist of a mosaic, among other things a fragmented Tn3 transposon encoding ampicillin resistance. Most notably the oqxAB and mrkABCDF cassettes were contained within two composite transposons (Tn6010 and Tn6011) that seemed to originate from Klebsiella pneumoniae, thus demonstrating the capability of IncX1 plasmids of facilitating lateral transfer of gene cassettes between different Enterobacteriaceae.
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Affiliation(s)
- Anders Norman
- Department of Biology, Evolution and Microbiology Section, University of Copenhagen, Sølvgade 83H, DK-1307 Copenhagen K, Denmark
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2408
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Zybailov B, Rutschow H, Friso G, Rudella A, Emanuelsson O, Sun Q, van Wijk KJ. Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. PLoS One 2008; 3:e1994. [PMID: 18431481 PMCID: PMC2291561 DOI: 10.1371/journal.pone.0001994] [Citation(s) in RCA: 501] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Accepted: 03/06/2008] [Indexed: 01/24/2023] Open
Abstract
Characterization of the chloroplast proteome is needed to understand the essential contribution of the chloroplast to plant growth and development. Here we present a large scale analysis by nanoLC-Q-TOF and nanoLC-LTQ-Orbitrap mass spectrometry (MS) of ten independent chloroplast preparations from Arabidopsis thaliana which unambiguously identified 1325 proteins. Novel proteins include various kinases and putative nucleotide binding proteins. Based on repeated and independent MS based protein identifications requiring multiple matched peptide sequences, as well as literature, 916 nuclear-encoded proteins were assigned with high confidence to the plastid, of which 86% had a predicted chloroplast transit peptide (cTP). The protein abundance of soluble stromal proteins was calculated from normalized spectral counts from LTQ-Obitrap analysis and was found to cover four orders of magnitude. Comparison to gel-based quantification demonstrates that ‘spectral counting’ can provide large scale protein quantification for Arabidopsis. This quantitative information was used to determine possible biases for protein targeting prediction by TargetP and also to understand the significance of protein contaminants. The abundance data for 550 stromal proteins was used to understand abundance of metabolic pathways and chloroplast processes. We highlight the abundance of 48 stromal proteins involved in post-translational proteome homeostasis (including aminopeptidases, proteases, deformylases, chaperones, protein sorting components) and discuss the biological implications. N-terminal modifications were identified for a subset of nuclear- and chloroplast-encoded proteins and a novel N-terminal acetylation motif was discovered. Analysis of cTPs and their cleavage sites of Arabidopsis chloroplast proteins, as well as their predicted rice homologues, identified new species-dependent features, which will facilitate improved subcellular localization prediction. No evidence was found for suggested targeting via the secretory system. This study provides the most comprehensive chloroplast proteome analysis to date and an expanded Plant Proteome Database (PPDB) in which all MS data are projected on identified gene models.
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Affiliation(s)
- Boris Zybailov
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
| | - Heidi Rutschow
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
| | - Giulia Friso
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
| | - Andrea Rudella
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
| | - Olof Emanuelsson
- Stockholm Bioinformatics Center, AlbaNova, Stockholm University, Stockholm, Sweden
| | - Qi Sun
- Computation Biology Service Unit, Cornell Theory Center, Cornell University, Ithaca, New York, United States of America
| | - Klaas J. van Wijk
- Department of Plant Biology, Cornell University, Ithaca, New York, United States of America
- * To whom correspondence should be addressed. E-mail:
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2409
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Zhao XM, Chen L, Aihara K. Protein function prediction with high-throughput data. Amino Acids 2008; 35:517-30. [PMID: 18427717 DOI: 10.1007/s00726-008-0077-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2008] [Accepted: 03/13/2008] [Indexed: 12/12/2022]
Abstract
Protein function prediction is one of the main challenges in post-genomic era. The availability of large amounts of high-throughput data provides an alternative approach to handling this problem from the computational viewpoint. In this review, we provide a comprehensive description of the computational methods that are currently applicable to protein function prediction, especially from the perspective of machine learning. Machine learning techniques can generally be classified as supervised learning, semi-supervised learning and unsupervised learning. By classifying the existing computational methods for protein annotation into these three groups, we are able to present a comprehensive framework on protein annotation based on machine learning techniques. In addition to describing recently developed theoretical methodologies, we also cover representative databases and software tools that are widely utilized in the prediction of protein function.
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Affiliation(s)
- Xing-Ming Zhao
- ERATO Aihara Complexity Modelling Project, JST, Tokyo, 151-0064, Japan
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2410
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Grunt M, Žárský V, Cvrčková F. Roots of angiosperm formins: the evolutionary history of plant FH2 domain-containing proteins. BMC Evol Biol 2008; 8:115. [PMID: 18430232 PMCID: PMC2386819 DOI: 10.1186/1471-2148-8-115] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Accepted: 04/22/2008] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Shuffling of modular protein domains is an important source of evolutionary innovation. Formins are a family of actin-organizing proteins that share a conserved FH2 domain but their overall domain architecture differs dramatically between opisthokonts (metazoans and fungi) and plants. We performed a phylogenomic analysis of formins in most eukaryotic kingdoms, aiming to reconstruct an evolutionary scenario that may have produced the current diversity of domain combinations with focus on the origin of the angiosperm formin architectures. RESULTS The Rho GTPase-binding domain (GBD/FH3) reported from opisthokont and Dictyostelium formins was found in all lineages except plants, suggesting its ancestral character. Instead, mosses and vascular plants possess the two formin classes known from angiosperms: membrane-anchored Class I formins and Class II formins carrying a PTEN-like domain. PTEN-related domains were found also in stramenopile formins, where they have been probably acquired independently rather than by horizontal transfer, following a burst of domain rearrangements in the chromalveolate lineage. A novel RhoGAP-related domain was identified in some algal, moss and lycophyte (but not angiosperm) formins that define a specific branch (Class III) of the formin family. CONCLUSION We propose a scenario where formins underwent multiple domain rearrangements in several eukaryotic lineages, especially plants and chromalveolates. In plants this replaced GBD/FH3 by a probably inactive RhoGAP-like domain, preserving a formin-mediated association between (membrane-anchored) Rho GTPases and the actin cytoskeleton. Subsequent amplification of formin genes, possibly coincident with the expansion of plants to dry land, was followed by acquisition of alternative membrane attachment mechanisms present in extant Class I and Class II formins, allowing later loss of the RhoGAP-like domain-containing formins in angiosperms.
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Affiliation(s)
- Michal Grunt
- Department of Plant Physiology, Faculty of Sciences, Charles University, Vinièná 5, CZ 128 43 Praha 2, Czech Republic
| | - Viktor Žárský
- Department of Plant Physiology, Faculty of Sciences, Charles University, Vinièná 5, CZ 128 43 Praha 2, Czech Republic
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojová 135, CZ 165 02 Praha 6, Czech Republic
| | - Fatima Cvrčková
- Department of Plant Physiology, Faculty of Sciences, Charles University, Vinièná 5, CZ 128 43 Praha 2, Czech Republic
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2411
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Viratyosin W, Ingsriswang S, Pacharawongsakda E, Palittapongarnpim P. Genome-wide subcellular localization of putative outer membrane and extracellular proteins in Leptospira interrogans serovar Lai genome using bioinformatics approaches. BMC Genomics 2008; 9:181. [PMID: 18423054 PMCID: PMC2387172 DOI: 10.1186/1471-2164-9-181] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Accepted: 04/21/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In bacterial pathogens, both cell surface-exposed outer membrane proteins and proteins secreted into the extracellular environment play crucial roles in host-pathogen interaction and pathogenesis. Considerable efforts have been made to identify outer membrane (OM) and extracellular (EX) proteins produced by Leptospira interrogans, which may be used as novel targets for the development of infection markers and leptospirosis vaccines. RESULT In this study we used a novel computational framework based on combined prediction methods with deduction concept to identify putative OM and EX proteins encoded by the Leptospira interrogans genome. The framework consists of the following steps: (1) identifying proteins homologous to known proteins in subcellular localization databases derived from the "consensus vote" of computational predictions, (2) incorporating homology based search and structural information to enhance gene annotation and functional identification to infer the specific structural characters and localizations, and (3) developing a specific classifier for cytoplasmic proteins (CP) and cytoplasmic membrane proteins (CM) using Linear discriminant analysis (LDA). We have identified 114 putative EX and 63 putative OM proteins, of which 41% are conserved or hypothetical proteins containing sequence and/or protein folding structures similar to those of known EX and OM proteins. CONCLUSION Overall results derived from the combined computational analysis correlate with the available experimental evidence. This is the most extensive in silico protein subcellular localization identification to date for Leptospira interrogans serovar Lai genome that may be useful in protein annotation, discovery of novel genes and understanding the biology of Leptospira.
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Affiliation(s)
- Wasna Viratyosin
- BIOTEC Central Research Unit, National Center for Genetic Engineering and Biotechnology, Pathumthani, 12120, Thailand.
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2412
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Gasparini F, Franchi N, Spolaore B, Ballarin L. Novel rhamnose-binding lectins from the colonial ascidian Botryllus schlosseri. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2008; 32:1177-1191. [PMID: 18471875 DOI: 10.1016/j.dci.2008.03.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Revised: 03/13/2008] [Accepted: 03/18/2008] [Indexed: 05/26/2023]
Abstract
In a full-length cDNA library from the compound ascidian Botryllus schlosseri, we identified, by BLAST search against UniProt database, five transcripts, each with complete coding sequence, homologous to known rhamnose-binding lectins (RBLs). Comparisons of the predicted amino acid sequences suggest that they represent different isoforms of a novel RBL, called BsRBL-1-5. Four of these isolectins were found in Botryllus homogenate after purification by affinity chromatography on acid-treated Sepharose, analysis by reverse-phase HPLC and mass spectrometry. Analysis of both molecular masses and tryptic digests of BsRBLs indicated that the N-terminal sequence of the purified proteins starts from residue 22 of the putative amino acid sequence, and residues 1-21 represent a signal peptide. Analysis by mass spectrometry of V8-protease digests confirmed the presence and alignments of the eight cysteines involved in the disulphide bridges that characterise RBLs. Functional studies proved the enhancing effect on phagocytosis of the affinity-purified material. Results are discussed in terms of phylogenetic relationships of BsRBLs with orthologous molecules from protostomes and deuterostomes.
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Affiliation(s)
- Fabio Gasparini
- Dipartimento di Biologia and CRIBI, University of Padova, Padova, Italy
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2413
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Ziegler K, Benz R, Schulz GE. A putative alpha-helical porin from Corynebacterium glutamicum. J Mol Biol 2008; 379:482-91. [PMID: 18462756 DOI: 10.1016/j.jmb.2008.04.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Revised: 04/03/2008] [Accepted: 04/03/2008] [Indexed: 11/16/2022]
Abstract
The cell wall of Corynebacterium glutamicum contains a mycolic acid layer, which is a protective nonpolar barrier similar to the outer membrane of Gram-negative bacteria. The exchange of material across this barrier requires porins. Porin B (PorB) is one of them. Recombinant PorB has been produced in Escherichia coli, purified, crystallized and analyzed by X-ray diffraction, yielding 16 independent molecular structures in four different crystal forms at resolutions up to 1.8 A. All 16 molecules have the same globular core, which consists of 70 residues forming four alpha-helices tied together by a disulfide bridge. The 16 structures vary greatly with respect to the 29 residues in the N- and C-terminal extensions. Since corynebacteria belong to the group of mycolata that includes some prominent human pathogens, the observed structure may be of medical relevance. Due to the clearly established solid structure of the core, the native porin has to be oligomeric, and the reported structure is one of the subunits. An alpha-helical porin in a bacterial outer envelope is surprising because all presently known structures of such porins consist of beta-barrels. Since none of the four crystal packing arrangements was compatible with an oligomeric membrane channel, we constructed a model of such an oligomer that was consistent with all available data of native PorB. The proposed model is based on the required polar interior and nonpolar exterior of the porin, on a recurring crystal packing contact around a 2-fold axis, on the assumption of a simple C(n) symmetry (a symmetric arrangement around an n-fold axis), on the experimentally established electric conductivity and anion selectivity and on the generally observed shape of porin channels.
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Affiliation(s)
- Karin Ziegler
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstr. 21, 79104 Freiburg im Breisgau, Germany
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2414
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The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 2008; 452:88-92. [PMID: 18322534 DOI: 10.1038/nature06556] [Citation(s) in RCA: 574] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Accepted: 12/20/2007] [Indexed: 11/08/2022]
Abstract
Mycorrhizal symbioses--the union of roots and soil fungi--are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants. Boreal, temperate and montane forests all depend on ectomycorrhizae. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains approximately 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.
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2415
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Jacob J, Mitreva M, Vanholme B, Gheysen G. Exploring the transcriptome of the burrowing nematode Radopholus similis. Mol Genet Genomics 2008; 280:1-17. [PMID: 18386064 DOI: 10.1007/s00438-008-0340-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Accepted: 03/19/2008] [Indexed: 01/03/2023]
Abstract
Radopholus similis is an important nematode pest on fruit crops in the tropics. Unraveling the transcriptome of this migratory plant-parasitic nematode can provide insight in the parasitism process and lead to more efficient control measures. For the first high throughput molecular characterization of this devastating nematode, 5,853 expressed sequence tags from a mixed stage population were generated. Adding 1,154 tags from the EST division of GenBank for subsequent analysis, resulted in a total of 7,007 ESTs, which represent approximately 3,200 genes. The mean G + C content of the nucleotides at the third codon position (GC3%) was calculated to be as high as 64.8%, the highest for nematodes reported to date. BLAST-searches resulted in about 70% of the clustered ESTs having homology to (DNA and protein) sequences from the GenBank database, whereas one-third of them did not match to any known sequence. Roughly 40% of these latter sequences are predicted to be coding, representing putative novel protein coding genes. Functional annotation of the sequences by GO annotation revealed the abundance of genes involved in reproduction and development, which reflects the nematode population biology. Genes with a role in the parasitism process are identified, as well as genes essential for nematode survival, providing information useful for parasite control. No evidence was found for the presence of trans-spliced leader sequences commonly occurring in nematodes, despite the use of various approaches. In conclusion, we found three different sources for the EST sequences: the majority has a nuclear origin, approximately 1% of the EST sequences are derived from the mitochondrial transcriptome, and interestingly, 1% of the tags are with high probability derived from Wolbachia, providing the first molecular indication for the presence of this endosymbiont in a plant-parasitic nematode.
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Affiliation(s)
- Joachim Jacob
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Ghent, Belgium.
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2416
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Overton IM, van Niekerk CAJ, Carter LG, Dawson A, Martin DMA, Cameron S, McMahon SA, White MF, Hunter WN, Naismith JH, Barton GJ. TarO: a target optimisation system for structural biology. Nucleic Acids Res 2008; 36:W190-6. [PMID: 18385152 PMCID: PMC2447720 DOI: 10.1093/nar/gkn141] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
TarO (http://www.compbio.dundee.ac.uk/taro) offers a single point of reference for key bioinformatics analyses relevant to selecting proteins or domains for study by structural biology techniques. The protein sequence is analysed by 17 algorithms and compared to 8 databases. TarO gathers putative homologues, including orthologues, and then obtains predictions of properties for these sequences including crystallisation propensity, protein disorder and post-translational modifications. Analyses are run on a high-performance computing cluster, the results integrated, stored in a database and accessed through a web-based user interface. Output is in tabulated format and in the form of an annotated multiple sequence alignment (MSA) that may be edited interactively in the program Jalview. TarO also simplifies the gathering of additional annotations via the Distributed Annotation System, both from the MSA in Jalview and through links to Dasty2. Routes to other information gateways are included, for example to relevant pages from UniProt, COG and the Conserved Domains Database. Open access to TarO is available from a guest account with private accounts for academic use available on request. Future development of TarO will include further analysis steps and integration with the Protein Information Management System (PIMS), a sister project in the BBSRC ‘Structural Proteomics of Rational Targets’ initiative
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Affiliation(s)
- Ian M Overton
- School of Life Sciences Research, University of Dundee, Dow Street, Dundee, UK
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2417
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Kleemann J, Takahara H, Stüber K, O'Connell R. Identification of soluble secreted proteins from appressoria of Colletotrichum higginsianum by analysis of expressed sequence tags. Microbiology (Reading) 2008; 154:1204-1217. [DOI: 10.1099/mic.0.2007/014944-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Jochen Kleemann
- Max-Planck-Institute for Plant Breeding Research, Department of Plant–Microbe Interactions, D-50829 Köln, Germany
| | - Hiroyuki Takahara
- Max-Planck-Institute for Plant Breeding Research, Department of Plant–Microbe Interactions, D-50829 Köln, Germany
| | - Kurt Stüber
- Max-Planck-Institute for Plant Breeding Research, Department of Plant–Microbe Interactions, D-50829 Köln, Germany
| | - Richard O'Connell
- Max-Planck-Institute for Plant Breeding Research, Department of Plant–Microbe Interactions, D-50829 Köln, Germany
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2418
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Bröker D, Dietz D, Arenskötter M, Steinbüchel A. The genomes of the non-clearing-zone-forming and natural-rubber- degrading species Gordonia polyisoprenivorans and Gordonia westfalica harbor genes expressing Lcp activity in Streptomyces strains. Appl Environ Microbiol 2008; 74:2288-97. [PMID: 18296529 PMCID: PMC2293141 DOI: 10.1128/aem.02145-07] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Accepted: 02/14/2008] [Indexed: 11/20/2022] Open
Abstract
The latex-clearing protein (Lcp(K30)) from the rubber-degrading bacterium Streptomyces sp. strain K30 is involved in the cleavage of poly(cis-1,4-isoprene), yielding isoprenoid aldehydes and ketones. Lcp homologues have so far been detected in all investigated clearing-zone-forming rubber-degrading bacteria. Internal degenerated oligonucleotides derived from lcp genes of Streptomyces sp. strain K30 (lcp(K30)), Streptomyces coelicolor strain A3(2), and Nocardia farcinica strains IFM10152 and E1 were applied in PCR to investigate whether lcp homologues occur also in the non-clearing-zone-forming rubber-utilizing bacteria Gordonia polyisoprenivorans strains VH2 and Y2K, Gordonia alkanivorans strain 44187, and Gordonia westfalica strain Kb1, which grow adhesively on rubber. The 1,230- and 1,224-bp lcp-homologous genes from G. polyisoprenivorans strain VH2 (lcp(VH2)) and G. westfalica strain Kb1 (lcp(Kb1)) were obtained after screening genomic libraries by degenerated PCR amplification, and their translational products exhibited 50 and 52% amino acid identity, respectively, to Lcp(K30). Recombinant lcp(VH2) and lcp(Kb1) harboring cells of the non-rubber-degrading Streptomyces lividans strain TK23 were able to form clearing zones and aldehydes on latex overlay-agar plates, thus indicating that lcp(VH2) and lcp(Kb1) encode functionally active proteins. Analysis by gel permeation chromatography demonstrated lower polymer concentrations and molecular weights of the remaining polyisoprenoid molecules after incubation with these recombinant S. lividans strains. Reverse transcription-PCR analysis demonstrated that lcp(VH2) was transcribed in cells of G. polyisoprenivorans strain VH2 cultivated in the presence of poly(cis-1,4-isoprene) but not in the presence of sodium acetate. Anti-Lcp(K30) immunoglobulin Gs, which were raised in this study, were rather specific for Lcp(K30) and did not cross-react with Lcp(VH2) and Lcp(Kb1). A lcp(VH2) disruption mutant was still able to grow with poly(cis-1,4-isoprene) as sole carbon source; therefore, lcp(VH2) seems not to be essential for rubber degradation in G. polyisoprenivorans.
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Affiliation(s)
- Daniel Bröker
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, D-48149 Münster, Germany
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2419
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Zhou M, Boekhorst J, Francke C, Siezen RJ. LocateP: genome-scale subcellular-location predictor for bacterial proteins. BMC Bioinformatics 2008; 9:173. [PMID: 18371216 PMCID: PMC2375117 DOI: 10.1186/1471-2105-9-173] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 03/27/2008] [Indexed: 11/10/2022] Open
Abstract
Background In the past decades, various protein subcellular-location (SCL) predictors have been developed. Most of these predictors, like TMHMM 2.0, SignalP 3.0, PrediSi and Phobius, aim at the identification of one or a few SCLs, whereas others such as CELLO and Psortb.v.2.0 aim at a broader classification. Although these tools and pipelines can achieve a high precision in the accurate prediction of signal peptides and transmembrane helices, they have a much lower accuracy when other sequence characteristics are concerned. For instance, it proved notoriously difficult to identify the fate of proteins carrying a putative type I signal peptidase (SPIase) cleavage site, as many of those proteins are retained in the cell membrane as N-terminally anchored membrane proteins. Moreover, most of the SCL classifiers are based on the classification of the Swiss-Prot database and consequently inherited the inconsistency of that SCL classification. As accurate and detailed SCL prediction on a genome scale is highly desired by experimental researchers, we decided to construct a new SCL prediction pipeline: LocateP. Results LocateP combines many of the existing high-precision SCL identifiers with our own newly developed identifiers for specific SCLs. The LocateP pipeline was designed such that it mimics protein targeting and secretion processes. It distinguishes 7 different SCLs within Gram-positive bacteria: intracellular, multi-transmembrane, N-terminally membrane anchored, C-terminally membrane anchored, lipid-anchored, LPxTG-type cell-wall anchored, and secreted/released proteins. Moreover, it distinguishes pathways for Sec- or Tat-dependent secretion and alternative secretion of bacteriocin-like proteins. The pipeline was tested on data sets extracted from literature, including experimental proteomics studies. The tests showed that LocateP performs as well as, or even slightly better than other SCL predictors for some locations and outperforms current tools especially where the N-terminally anchored and the SPIase-cleaved secreted proteins are concerned. Overall, the accuracy of LocateP was always higher than 90%. LocateP was then used to predict the SCLs of all proteins encoded by completed Gram-positive bacterial genomes. The results are stored in the database LocateP-DB [1]. Conclusion LocateP is by far the most accurate and detailed protein SCL predictor for Gram-positive bacteria currently available.
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Affiliation(s)
- Miaomiao Zhou
- Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
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2420
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Treangen TJ, Ambur OH, Tonjum T, Rocha EPC. The impact of the neisserial DNA uptake sequences on genome evolution and stability. Genome Biol 2008; 9:R60. [PMID: 18366792 PMCID: PMC2397512 DOI: 10.1186/gb-2008-9-3-r60] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 01/13/2008] [Accepted: 03/26/2008] [Indexed: 12/03/2022] Open
Abstract
A study of the origin and distribution of the abundant short DNA uptake sequence (DUS) in six genomes of Neisseria suggests that transformation and recombination are tightly linked in evolution and that recombination has a key role in the establishment of DUS. Background Efficient natural transformation in Neisseria requires the presence of short DNA uptake sequences (DUSs). Doubts remain whether DUSs propagate by pure selfish molecular drive or are selected for 'safe sex' among conspecifics. Results Six neisserial genomes were aligned to identify gene conversion fragments, DUS distribution, spacing, and conservation. We found a strong link between recombination and DUS: DUS spacing matches the size of conversion fragments; genomes with shorter conversion fragments have more DUSs and more conserved DUSs; and conversion fragments are enriched in DUSs. Many recent and singly occurring DUSs exhibit too high divergence with homologous sequences in other genomes to have arisen by point mutation, suggesting their appearance by recombination. DUSs are over-represented in the core genome, under-represented in regions under diversification, and absent in both recently acquired genes and recently lost core genes. This suggests that DUSs are implicated in genome stability rather than in generating adaptive variation. DUS elements are most frequent in the permissive locations of the core genome but are themselves highly conserved, undergoing mutation selection balance and/or molecular drive. Similar preliminary results were found for the functionally analogous uptake signal sequence in Pasteurellaceae. Conclusion As do many other pathogens, Neisseria and Pasteurellaceae have hyperdynamic genomes that generate deleterious mutations by intrachromosomal recombination and by transient hypermutation. The results presented here suggest that transformation in Neisseria and Pasteurellaceae allows them to counteract the deleterious effects of genome instability in the core genome. Thus, rather than promoting hypervariation, bacterial sex could be regenerative.
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Affiliation(s)
- Todd J Treangen
- Algorithms and Genetics Group, Department of Computer Science, Technical University of Catalonia, Jordi Girona Salgado, 1-3, E-08034 Barcelona, Spain.
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2421
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Thorsen K, Sørensen KD, Brems-Eskildsen AS, Modin C, Gaustadnes M, Hein AMK, Kruhøffer M, Laurberg S, Borre M, Wang K, Brunak S, Krainer AR, Tørring N, Dyrskjøt L, Andersen CL, Orntoft TF. Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis. Mol Cell Proteomics 2008; 7:1214-24. [PMID: 18353764 DOI: 10.1074/mcp.m700590-mcp200] [Citation(s) in RCA: 180] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing enhances proteome diversity and modulates cancer-associated proteins. To identify tissue- and tumor-specific alternative splicing, we used the GeneChip Human Exon 1.0 ST Array to measure whole-genome exon expression in 102 normal and cancer tissue samples of different stages from colon, urinary bladder, and prostate. We identified 2069 candidate alternative splicing events between normal tissue samples from colon, bladder, and prostate and selected 15 splicing events for RT-PCR validation, 10 of which were successfully validated by RT-PCR and sequencing. Furthermore 23, 19, and 18 candidate tumor-specific splicing alterations in colon, bladder, and prostate, respectively, were selected for RT-PCR validation on an independent set of 81 normal and tumor tissue samples. In total, seven genes with tumor-specific splice variants were identified (ACTN1, CALD1, COL6A3, LRRFIP2, PIK4CB, TPM1, and VCL). The validated tumor-specific splicing alterations were highly consistent, enabling clear separation of normal and cancer samples and in some cases even of different tumor stages. A subset of the tumor-specific splicing alterations (ACTN1, CALD1, and VCL) was found in all three organs and may represent general cancer-related splicing events. In silico protein predictions suggest that the identified cancer-specific splice variants encode proteins with potentially altered functions, indicating that they may be involved in pathogenesis and hence represent novel therapeutic targets. In conclusion, we identified and validated alternative splicing between normal tissue samples from colon, bladder, and prostate in addition to cancer-specific splicing events in colon, bladder, and prostate cancer that may have diagnostic and prognostic implications.
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Affiliation(s)
- Kasper Thorsen
- Molecular Diagnostic Laboratory, Department of Clinical Biochemistry, Aarhus University Hospital, Skejby, DK-8200 Aarhus N, Denmark
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2422
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Proteins found in a CikA interaction assay link the circadian clock, metabolism, and cell division in Synechococcus elongatus. J Bacteriol 2008; 190:3738-46. [PMID: 18344369 DOI: 10.1128/jb.01721-07] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diverse organisms time their cellular activities to occur at distinct phases of Earth's solar day, not through the direct regulation of these processes by light and darkness but rather through the use of an internal biological (circadian) clock that is synchronized with the external cycle. Input pathways serve as mechanisms to transduce external cues to a circadian oscillator to maintain synchrony between this internal oscillation and the environment. The circadian input pathway in the cyanobacterium Synechococcus elongatus PCC 7942 requires the kinase CikA. A cikA null mutant exhibits a short circadian period, the inability to reset its clock in response to pulses of darkness, and a defect in cell division. Although CikA is copurified with the Kai proteins that constitute the circadian central oscillator, no direct interaction between CikA and either KaiA, KaiB, or KaiC has been demonstrated. Here, we identify four proteins that may help connect CikA with the oscillator. Phenotypic analyses of null and overexpression alleles demonstrate that these proteins are involved in at least one of the functions--circadian period regulation, phase resetting, and cell division--attributed to CikA. Predictions based on sequence similarity suggest that these proteins function through protein phosphorylation, iron-sulfur cluster biosynthesis, and redox regulation. Collectively, these results suggest a model for circadian input that incorporates proteins that link the circadian clock, metabolism, and cell division.
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2423
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Moreira CK, Templeton TJ, Lavazec C, Hayward RE, Hobbs CV, Kroeze H, Janse CJ, Waters AP, Sinnis P, Coppi A. The Plasmodium TRAP/MIC2 family member, TRAP-Like Protein (TLP), is involved in tissue traversal by sporozoites. Cell Microbiol 2008; 10:1505-16. [PMID: 18346224 DOI: 10.1111/j.1462-5822.2008.01143.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the apicomplexan protozoans motility and cell invasion are mediated by the TRAP/MIC2 family of transmembrane proteins, members of which link extracellular adhesion to the intracellular actomyosin motor complex. Here we characterize a new member of the TRAP/MIC2 family, named TRAP-Like Protein (TLP), that is highly conserved within the Plasmodium genus. Similar to the Plasmodium sporozoite protein, TRAP, and the ookinete protein, CTRP, TLP possesses an extracellular domain architecture that is comprised of von Willebrand factor A (vWA) and thrombospondin type 1 (TSP1) domains, plus a short cytoplasmic domain. Comparison of the vWA domain of TLP genes from multiple Plasmodium falciparum isolates showed relative low sequence diversity, suggesting that the protein is not under selective pressures of the host immune system. Analysis of transcript levels by quantitative reverse transcription polymerase chain reaction (RT-PCR) showed that TLP is predominantly expressed in salivary gland sporozoites of P. falciparum and P. berghei. Targeted disruption of P. berghei TLP resulted in a decreased capacity for cell traversal by sporozoites, and reduced infectivity of sporozoites in vivo, whereas in vitro sporozoite motility and hepatocyte invasion were unaffected. These results indicate a role of TLP in cell traversal by sporozoites.
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Affiliation(s)
- Cristina K Moreira
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
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2424
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Chessa D, Dorsey CW, Winter M, Baümler AJ. Binding Specificity of Salmonella Plasmid-encoded Fimbriae Assessed by Glycomics. J Biol Chem 2008; 283:8118-24. [DOI: 10.1074/jbc.m710095200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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2425
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Oxford KL, Eberhardt MK, Yang KW, Strelow L, Kelly S, Zhou SS, Barry PA. Protein coding content of the UL)b' region of wild-type rhesus cytomegalovirus. Virology 2008; 373:181-8. [PMID: 18068749 DOI: 10.1016/j.virol.2007.10.040] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Revised: 10/15/2007] [Accepted: 10/31/2007] [Indexed: 11/19/2022]
Abstract
A recent comparison of two rhesus cytomegalovirus (RhCMV) genomes revealed that the region at the right end of the U(L) genome component (U(L)b') undergoes genetic alterations similar to those observed in serially passaged human cytomegalovirus (HCMV). To determine the coding content of authentic wild-type RhCMV in this region, the U(L)b' sequence was amplified from virus obtained from naturally infected rhesus macaques without passage in vitro. A total of 24 open reading frames (ORFs) potentially encoding >99 amino acid residues were identified, 10 of which are related to HCMV ORFs and 15 to previously listed RhCMV ORFs. In addition, the analysis revealed a cluster of three novel alpha chemokine-like ORFs, bringing the number of predicted alpha chemokine genes in this region to six. Three of these six genes exhibit a high level of sequence diversity, as has been observed for the HCMV alpha chemokine gene UL146.
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Affiliation(s)
- Kristie L Oxford
- Center for Comparative Medicine, Department of Pathology and Laboratory Medicine, California National Primate Research Center, University of California, Davis, Davis, CA 95616, USA
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2426
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Outer-membrane proteomic maps and surface-exposed proteins of Legionella pneumophila using cellular fractionation and fluorescent labelling. Anal Bioanal Chem 2008; 390:1861-71. [DOI: 10.1007/s00216-008-1923-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 01/15/2008] [Accepted: 01/28/2008] [Indexed: 12/14/2022]
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2427
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Silverman JM, Chan SK, Robinson DP, Dwyer DM, Nandan D, Foster LJ, Reiner NE. Proteomic analysis of the secretome of Leishmania donovani. Genome Biol 2008; 9:R35. [PMID: 18282296 PMCID: PMC2374696 DOI: 10.1186/gb-2008-9-2-r35] [Citation(s) in RCA: 229] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2007] [Revised: 01/22/2008] [Accepted: 02/18/2008] [Indexed: 12/21/2022] Open
Abstract
Analysis of Leishmania-conditioned medium resulted in the identification of 151 proteins apparently secreted by the parasitic protozoan Leishmania donovani and suggested a vesicle-based secretion system. Background Leishmania and other intracellular pathogens have evolved strategies that support invasion and persistence within host target cells. In some cases the underlying mechanisms involve the export of virulence factors into the host cell cytosol. Previous work from our laboratory identified one such candidate leishmania effector, namely elongation factor-1α, to be present in conditioned medium of infectious leishmania as well as within macrophage cytosol after infection. To investigate secretion of potential effectors more broadly, we used quantitative mass spectrometry to analyze the protein content of conditioned medium collected from cultures of stationary-phase promastigotes of Leishmania donovani, an agent of visceral leishmaniasis. Results Analysis of leishmania conditioned medium resulted in the identification of 151 proteins apparently secreted by L. donovani. Ratios reflecting the relative amounts of each leishmania protein secreted, as compared to that remaining cell associated, revealed a hierarchy of protein secretion, with some proteins secreted to a greater extent than others. Comparison with an in silico approach defining proteins potentially exported along the classic eukaryotic secretion pathway suggested that few leishmania proteins are targeted for export using a classic eukaryotic amino-terminal secretion signal peptide. Unexpectedly, a large majority of known eukaryotic exosomal proteins was detected in leishmania conditioned medium, suggesting a vesicle-based secretion system. Conclusion This analysis shows that protein secretion by L. donovani is a heterogeneous process that is unlikely to be determined by a classical amino-terminal secretion signal. As an alternative, L. donovani appears to use multiple nonclassical secretion pathways, including the release of exosome-like microvesicles.
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Affiliation(s)
- J Maxwell Silverman
- Department of Medicine (Division of Infectious Diseases), University of British Columbia, Faculty of Medicine, 2733 Heather St, Vancouver, British Columbia, V5Z 3J5, Canada.
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2428
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Fleige T, Pfaff N, Gross U, Bohne W. Localisation of gluconeogenesis and tricarboxylic acid (TCA)-cycle enzymes and first functional analysis of the TCA cycle in Toxoplasma gondii. Int J Parasitol 2008; 38:1121-32. [PMID: 18336823 DOI: 10.1016/j.ijpara.2008.01.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Revised: 12/17/2007] [Accepted: 01/21/2008] [Indexed: 12/25/2022]
Abstract
The apicomplexan parasite Toxoplasma gondii displays some unusual localisations of carbohydrate converting enzymes, which is due to the presence of a vestigial, non-photosynthetic plastid, referred to as the apicoplast. It was recently demonstrated that the single pyruvate dehydrogenase complex (PDH) in T. gondii is exclusively localised inside the apicoplast but absent in the mitochondrion. This raises the question about expression, localisation and function of enzymes for the tricarboxylic acid (TCA)-cycle, which normally depends on PDH generated acetyl-CoA. Based on the expression and localisation of epitope-tagged fusion proteins, we show that all analysed TCA cycle enzymes are localised in the mitochondrion, including both isoforms of malate dehydrogenase. The absence of a cytosolic malate dehydrogenase suggests that a typical malate-aspartate shuttle for transfer of reduction equivalents is missing in T. gondii. We also localised various enzymes which catalyse the irreversible steps in gluconeogenesis to a cellular compartment and examined mRNA expression levels for gluconeogenesis and TCA cycle genes between tachyzoites and in vitro bradyzoites. In order to get functional information on the TCA cycle for the parasite energy metabolism, we created a conditional knock-out mutant for the succinyl-CoA synthetase. Disruption of the sixth step in the TCA cycle should leave the biosynthetic parts of the cycle intact, but prevent FADH2 production. The succinyl-CoA synthetase depletion mutant displayed a 30% reduction in growth rate, which could be restored by supplementation with 2 microM succinate in the tissue culture medium. The mitochondrial membrane potential in these parasites was found to be unaltered. The lack of a more severe phenotype suggests that a functional TCA cycle is not essential for T. gondii replication and for maintenance of the mitochondrial membrane potential.
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Affiliation(s)
- Tobias Fleige
- Institute of Medical Microbiology, University of Göttingen, Kreuzbergring 57, Göttingen, Germany
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2429
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Zhou J, Zhu T, Hu C, Li H, Chen G, Xu G, Wang S, Zhou J, Ma D. Comparative genomics and function analysis on BI1 family. Comput Biol Chem 2008; 32:159-62. [PMID: 18440869 DOI: 10.1016/j.compbiolchem.2008.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Revised: 01/29/2008] [Accepted: 01/31/2008] [Indexed: 11/17/2022]
Abstract
Bax inhibitor-1 (BI1) family contains six known genes in human. Some members of BI1 family have been proved to play important roles in cell death. Here we discuss the similarities and differences among the members of BI1 family by comparative genomics and proteomics, and report here the discovery of a novel member, tmbim1b, in Bos taurus. BI1 family is evolutionarily conserved as integral membrane proteins containing multiple membrane-spanning segments and predominantly localized to intracellular membranes, similar to Bcl-2 family proteins. They share multiple motifs and transcriptional factors within the promoter and the coding regions. They may represent regulators of cell death pathways, which are concluded from structure conservation of BI1 family.
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Affiliation(s)
- Jinhua Zhou
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave., Wuhan, Hubei, PR China
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2430
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Using Chou's pseudo amino acid composition based on approximate entropy and an ensemble of AdaBoost classifiers to predict protein subnuclear location. Amino Acids 2008; 34:669-75. [PMID: 18256886 DOI: 10.1007/s00726-008-0034-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Accepted: 01/17/2008] [Indexed: 10/22/2022]
Abstract
The knowledge of subnuclear localization in eukaryotic cells is essential for understanding the life function of nucleus. Developing prediction methods and tools for proteins subnuclear localization become important research fields in protein science for special characteristics in cell nuclear. In this study, a novel approach has been proposed to predict protein subnuclear localization. Sample of protein is represented by Pseudo Amino Acid (PseAA) composition based on approximate entropy (ApEn) concept, which reflects the complexity of time series. A novel ensemble classifier is designed incorporating three AdaBoost classifiers. The base classifier algorithms in three AdaBoost are decision stumps, fuzzy K nearest neighbors classifier, and radial basis-support vector machines, respectively. Different PseAA compositions are used as input data of different AdaBoost classifier in ensemble. Genetic algorithm is used to optimize the dimension and weight factor of PseAA composition. Two datasets often used in published works are used to validate the performance of the proposed approach. The obtained results of Jackknife cross-validation test are higher and more balance than them of other methods on same datasets. The promising results indicate that the proposed approach is effective and practical. It might become a useful tool in protein subnuclear localization. The software in Matlab and supplementary materials are available freely by contacting the corresponding author.
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2431
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Lange PR, Geserick C, Tischendorf G, Zrenner R. Functions of chloroplastic adenylate kinases in Arabidopsis. PLANT PHYSIOLOGY 2008; 146:492-504. [PMID: 18162585 PMCID: PMC2245825 DOI: 10.1104/pp.107.114702] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Accepted: 12/21/2007] [Indexed: 05/02/2023]
Abstract
Adenosine monophosphate kinase (AMK; adenylate kinase) catalyses the reversible formation of ADP by the transfer of one phosphate group from ATP to AMP, thus equilibrating adenylates. The Arabidopsis (Arabidopsis thaliana) genome contains 10 genes with an adenylate/cytidylate kinase signature; seven of these are identified as putative adenylate kinases. Encoded proteins of at least two members of this Arabidopsis adenylate kinase gene family are targeted to plastids. However, when the individual genes are disrupted, the phenotypes of both mutants are strikingly different. Although absence of AMK2 causes only 30% reduction of total adenylate kinase activity in leaves, there is loss of chloroplast integrity leading to small, pale-looking plantlets from embryo to seedling development. In contrast, no phenotype for disruption of the second plastid adenylate kinase was found. From this analysis, we conclude that AMK2 is the major activity for equilibration of adenylates and de novo synthesis of ADP in the plastid stroma.
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Affiliation(s)
- Peter Robert Lange
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany
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2432
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Meinnel T, Giglione C. Tools for analyzing and predicting N-terminal protein modifications. Proteomics 2008; 8:626-49. [DOI: 10.1002/pmic.200700592] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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2433
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Mining the Moraxella catarrhalis genome: identification of potential vaccine antigens expressed during human infection. Infect Immun 2008; 76:1599-607. [PMID: 18227159 DOI: 10.1128/iai.01253-07] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Moraxella catarrhalis is an important cause of respiratory infections in adults and otitis media in children. Developing an effective vaccine would reduce the morbidity, mortality, and costs associated with such infections. An unfinished genome sequence of a strain of M. catarrhalis available in the GenBank database was analyzed, and open reading frames predicted to encode potential vaccine candidates were identified. Three genes encoding proteins having molecular masses of approximately 22, 75, and 78 kDa (designated Msp [Moraxella surface proteins]) (msp22, msp75, and msp78, respectively) were determined to be conserved by competitive hybridization using a microarray, PCR, and sequencing of the genes in clinical isolates of M. catarrhalis. The genes were transcribed when M. catarrhalis was grown in vitro. These genes were amplified by PCR and cloned into Escherichia coli expression vectors. Recombinant proteins were generated and then studied using enzyme-linked immunosorbent assays with preacquisition and postclearance serum and sputum samples from 31 adults with chronic obstructive pulmonary disease (COPD) who acquired and cleared M. catarrhalis. New antibody responses to the three proteins were observed for a small proportion of the patients with COPD, indicating that these proteins were expressed during human infection. These studies indicate that the Msp22, Msp75, and Msp78 proteins, whose genes were discovered using genome mining, are highly conserved among strains, are expressed during human infection with M. catarrhalis, and represent potential vaccine antigens.
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2434
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Levasseur A, Piumi F, Coutinho PM, Rancurel C, Asther M, Delattre M, Henrissat B, Pontarotti P, Asther M, Record E. FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds. Fungal Genet Biol 2008; 45:638-45. [PMID: 18308593 DOI: 10.1016/j.fgb.2008.01.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Revised: 01/14/2008] [Accepted: 01/15/2008] [Indexed: 10/22/2022]
Abstract
The breakdown of lignin by fungi is a key step during carbon recycling in terrestrial ecosystems. This process is of great interest for green and white biotechnological applications. Given the importance of these enzymatic processes, we have classified the enzymes potentially involved in lignin catabolism into sequence-based families and integrated them in a newly developed database, designated Fungal Oxidative Lignin enzymes (FOLy). Families were defined after sequence similarity searches starting from protein sequences and validated by the convergence of results with biochemical experiments reported in the literature. The resulting database was applied as a tool for the functional annotation of genomes from different fungi, namely (i) the Basidiomycota Coprinopsis cinerea, Phanerochaete chrysosporium and Ustilago maydis and (ii) the Ascomycota Aspergillus nidulans and Trichoderma reesei. Genomic comparison of the oxidoreductases of these fungi revealed significant differences in the putative enzyme arsenals. Two Ascomycota fungal genomes were annotated and new candidate genes were identified that could be useful for lignin degradation and (or) melanin synthesis, and their function investigated experimentally. This database efforts aims at providing the means to get new insights for the understanding and biotechnological exploitation of the lignin degradation. A WWW server giving access to the routinely updated FOLy classifications of enzymes potentially involved in lignin degradation can be found at http://foly.esil.univ-mrs.fr.
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Affiliation(s)
- Anthony Levasseur
- UMR 1163 INRA de Biotechnologie des Champignons Filamenteux, IFR86-BAIM, Universités de Provence et de la Méditerranée, ESIL, 163 Avenue de Luminy, Case Postale 925, 13288 Marseille Cedex 09, France
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2435
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Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms. Nat Protoc 2008; 3:153-62. [PMID: 18274516 DOI: 10.1038/nprot.2007.494] [Citation(s) in RCA: 690] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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2436
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Zhang D, Howe DK. Investigation of SnSPR1, a novel and abundant surface protein of Sarcocystis neurona merozoites. Vet Parasitol 2008; 152:210-9. [PMID: 18291589 DOI: 10.1016/j.vetpar.2007.12.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 12/21/2007] [Accepted: 12/26/2007] [Indexed: 11/26/2022]
Abstract
An expressed sequence tag (EST) sequencing project has produced over 15,000 partial cDNA sequences from the equine pathogen Sarcocystis neurona. While many of the sequences are clear homologues of previously characterized genes, a significant number of the S. neurona ESTs do not exhibit similarity to anything in the extensive sequence databases that have been generated. In an effort to characterize parasite proteins that are novel to S. neurona, a seemingly unique gene was selected for further investigation based on its abundant representation in the collection of ESTs and the predicted presence of a signal peptide and glycolipid anchor addition on the encoded protein. The gene was expressed in E. coli, and monospecific polyclonal antiserum against the recombinant protein was produced by immunization of a rabbit. Characterization of the native protein in S. neurona merozoites and schizonts revealed that it is a low molecular weight surface protein that is expressed throughout intracellular development of the parasite. The protein was designated Surface Protein 1 (SPR1) to reflect its display on the outer surface of merozoites and to distinguish it from the ubiquitous SAG/SRS surface antigens of the heteroxenous Coccidia. Interestingly, infection assays in the presence of the polyclonal antiserum suggested that SnSPR1 plays some role in attachment and/or invasion of host cells by S. neurona merozoites. The work described herein represents a general template for selecting and characterizing the various unidentified gene sequences that are plentiful in the EST databases for S. neurona and other apicomplexans. Furthermore, this study illustrates the value of investigating these novel sequences since it can offer new candidates for diagnostic or vaccine development while also providing greater insight into the biology of these parasites.
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Affiliation(s)
- Deqing Zhang
- Department of Veterinary Sciences, University of Kentucky, Gluck Equine Research Center, Lexington, KY 40546-0099, USA
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2437
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Duh D, Nichol ST, Khristova ML, Saksida A, Hafner-Bratkovic I, Petrovec M, Dedushaj I, Ahmeti S, Avsic-Zupanc T. The complete genome sequence of a Crimean-Congo hemorrhagic fever virus isolated from an endemic region in Kosovo. Virol J 2008; 5:7. [PMID: 18197964 PMCID: PMC2266736 DOI: 10.1186/1743-422x-5-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Accepted: 01/15/2008] [Indexed: 01/14/2023] Open
Abstract
The Balkan region and Kosovo in particular, is a well-known Crimean-Congo hemorrhagic fever (CCHF) endemic region, with frequent epidemic outbreaks and sporadic cases occurring with a hospitalized case fatality of approximately 30%. Recent analysis of complete genome sequences of diverse CCHF virus strains showed that the genome plasticity of the virus is surprisingly high for an arthropod-borne virus. High levels of nucleotide and amino acid differences, frequent RNA segment reassortment and even RNA recombination have been recently described. This diversity illustrates the need to determine the complete genome sequence of CCHF virus representatives of all geographically distinct endemic areas, particularly in light of the high pathogenicity of the virus and its listing as a potential bioterrorism threat. Here we describe the first complete CCHF virus genome sequence of a virus (strain Kosova Hoti) isolated from a hemorrhagic fever case in the Balkans. This virus strain was isolated from a fatal CCHF case, and passaged only twice on Vero E6 cells prior to sequence analysis. The virus total genome was found to be 19.2 kb in length, consisting of a 1672 nucleotide (nt) S segment, a 5364 nt M segment and a 12150 nt L segment. Phylogenetic analysis of CCHF virus complete genomes placed the Kosova Hoti strain in the Europe/Turkey group, with highest similarity seen with Russian isolates. The virus M segments are the most diverse with up to 31 and 27% differences seen at the nt and amino acid levels, and even 1.9% amino acid difference found between the Kosova Hoti and another strain from Kosovo (9553-01). This suggests that distinct virus strains can coexist in highly endemic areas.
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Affiliation(s)
- Darja Duh
- Institute of Microbiology and Immunology, Medical Faculty, Ljubljana, Slovenia.
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2438
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Kroth PG, Chiovitti A, Gruber A, Martin-Jezequel V, Mock T, Parker MS, Stanley MS, Kaplan A, Caron L, Weber T, Maheswari U, Armbrust EV, Bowler C. A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis. PLoS One 2008; 3:e1426. [PMID: 18183306 PMCID: PMC2173943 DOI: 10.1371/journal.pone.0001426] [Citation(s) in RCA: 281] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Accepted: 12/11/2007] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Diatoms are unicellular algae responsible for approximately 20% of global carbon fixation. Their evolution by secondary endocytobiosis resulted in a complex cellular structure and metabolism compared to algae with primary plastids. METHODOLOGY/PRINCIPAL FINDINGS The whole genome sequence of the diatom Phaeodactylum tricornutum has recently been completed. We identified and annotated genes for enzymes involved in carbohydrate pathways based on extensive EST support and comparison to the whole genome sequence of a second diatom, Thalassiosira pseudonana. Protein localization to mitochondria was predicted based on identified similarities to mitochondrial localization motifs in other eukaryotes, whereas protein localization to plastids was based on the presence of signal peptide motifs in combination with plastid localization motifs previously shown to be required in diatoms. We identified genes potentially involved in a C4-like photosynthesis in P. tricornutum and, on the basis of sequence-based putative localization of relevant proteins, discuss possible differences in carbon concentrating mechanisms and CO(2) fixation between the two diatoms. We also identified genes encoding enzymes involved in photorespiration with one interesting exception: glycerate kinase was not found in either P. tricornutum or T. pseudonana. Various Calvin cycle enzymes were found in up to five different isoforms, distributed between plastids, mitochondria and the cytosol. Diatoms store energy either as lipids or as chrysolaminaran (a beta-1,3-glucan) outside of the plastids. We identified various beta-glucanases and large membrane-bound glucan synthases. Interestingly most of the glucanases appear to contain C-terminal anchor domains that may attach the enzymes to membranes. CONCLUSIONS/SIGNIFICANCE Here we present a detailed synthesis of carbohydrate metabolism in diatoms based on the genome sequences of Thalassiosira pseudonana and Phaeodactylum tricornutum. This model provides novel insights into acquisition of dissolved inorganic carbon and primary metabolic pathways of carbon in two different diatoms, which is of significance for an improved understanding of global carbon cycles.
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Affiliation(s)
- Peter G Kroth
- Fachbereich Biologie, University of Konstanz, Konstanz, Germany.
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2439
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Couvreur B, Beaufays J, Charon C, Lahaye K, Gensale F, Denis V, Charloteaux B, Decrem Y, Prévôt PP, Brossard M, Vanhamme L, Godfroid E. Variability and action mechanism of a family of anticomplement proteins in Ixodes ricinus. PLoS One 2008; 3:e1400. [PMID: 18167559 PMCID: PMC2151134 DOI: 10.1371/journal.pone.0001400] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Accepted: 12/11/2007] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Ticks are blood feeding arachnids that characteristically take a long blood meal. They must therefore counteract host defence mechanisms such as hemostasis, inflammation and the immune response. This is achieved by expressing batteries of salivary proteins coded by multigene families. METHODOLOGY/PRINCIPAL FINDINGS We report the in-depth analysis of a tick multigene family and describe five new anticomplement proteins in Ixodes ricinus. Compared to previously described Ixodes anticomplement proteins, these segregated into a new phylogenetic group or subfamily. These proteins have a novel action mechanism as they specifically bind to properdin, leading to the inhibition of C3 convertase and the alternative complement pathway. An excess of non-synonymous over synonymous changes indicated that coding sequences had undergone diversifying selection. Diversification was not associated with structural, biochemical or functional diversity, adaptation to host species or stage specificity but rather to differences in antigenicity. CONCLUSIONS/SIGNIFICANCE Anticomplement proteins from I. ricinus are the first inhibitors that specifically target a positive regulator of complement, properdin. They may provide new tools for the investigation of role of properdin in physiological and pathophysiological mechanisms. They may also be useful in disorders affecting the alternative complement pathway. Looking for and detecting the different selection pressures involved will help in understanding the evolution of multigene families and hematophagy in arthropods.
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Affiliation(s)
- Bernard Couvreur
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
| | - Jérôme Beaufays
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
| | - Cédric Charon
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
| | - Kathia Lahaye
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
| | - François Gensale
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
| | - Valérie Denis
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
| | - Benoît Charloteaux
- Centre de Biophysique Moléculaire Numérique, Gembloux Agricultural University, Gembloux, Belgium
| | - Yves Decrem
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
| | - Pierre-Paul Prévôt
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
| | - Michel Brossard
- Institute of Zoology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Luc Vanhamme
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
- Laboratory of Molecular Parasitology, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
| | - Edmond Godfroid
- Laboratory for Molecular Biology of Ectoparasites, Institut de Biologie et de Médecine Moléculaires (IBMM), Université Libre de Bruxelles, Gosselies, Belgium
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2440
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Li L, Sweedler JV. Peptides in the brain: mass spectrometry-based measurement approaches and challenges. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2008; 1:451-483. [PMID: 20636086 DOI: 10.1146/annurev.anchem.1.031207.113053] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The function and activity of almost every circuit in the human brain are modified by the signaling peptides (SPs) surrounding the neurons. As the complement of peptides can vary even in adjacent neurons and their physiological actions can occur over a broad range of concentrations, the required figures of merit for techniques to characterize SPs are surprisingly stringent. In this review, we describe the formation and catabolism of SPs and highlight a range of mass spectrometric techniques used to characterize SPs. Approaches that supply high chemical information content, direct tissue profiling, spatially resolved data, and temporal information on peptide release are also described. Because of advances in measurement technologies, our knowledge of SPs has greatly increased over the last decade, and SP discoveries will continue as the capabilities of modern measurement approaches improve.
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Affiliation(s)
- Lingjun Li
- Department of Chemistry, University of Wisconsin, Madison, 53705-2222, USA.
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2441
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Habib T, Zhang C, Yang JY, Yang MQ, Deng Y. Supervised learning method for the prediction of subcellular localization of proteins using amino acid and amino acid pair composition. BMC Genomics 2008; 9 Suppl 1:S16. [PMID: 18366605 PMCID: PMC2386058 DOI: 10.1186/1471-2164-9-s1-s16] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Occurrence of protein in the cell is an important step in understanding its function. It is highly desirable to predict a protein's subcellular locations automatically from its sequence. Most studied methods for prediction of subcellular localization of proteins are signal peptides, the location by sequence homology, and the correlation between the total amino acid compositions of proteins. Taking amino-acid composition and amino acid pair composition into consideration helps improving the prediction accuracy. RESULTS We constructed a dataset of protein sequences from SWISS-PROT database and segmented them into 12 classes based on their subcellular locations. SVM modules were trained to predict the subcellular location based on amino acid composition and amino acid pair composition. Results were calculated after 10-fold cross validation. Radial Basis Function (RBF) outperformed polynomial and linear kernel functions. Total prediction accuracy reached to 71.8% for amino acid composition and 77.0% for amino acid pair composition. In order to observe the impact of number of subcellular locations we constructed two more datasets of nine and five subcellular locations. Total accuracy was further improved to 79.9% and 85.66%. CONCLUSIONS A new SVM based approach is presented based on amino acid and amino acid pair composition. Result shows that data simulation and taking more protein features into consideration improves the accuracy to a great extent. It was also noticed that the data set needs to be crafted to take account of the distribution of data in all the classes.
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Affiliation(s)
- Tanwir Habib
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Chaoyang Zhang
- School of Computing, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Jack Y Yang
- Harvard Medical School, Harvard University, Cambridge, Massachusetts 02140, USA
| | - Mary Qu Yang
- National Human Genome Research Institute, National Institutes of Health (NIH), U.S. Department of Health and Human Services Bethesda, MD 20852, USA
| | - Youping Deng
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
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2442
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Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Li Y, Shi T. AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology. Nucleic Acids Res 2008; 36:D999-1008. [PMID: 17962307 PMCID: PMC2238993 DOI: 10.1093/nar/gkm844] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Revised: 09/25/2007] [Accepted: 09/25/2007] [Indexed: 12/01/2022] Open
Abstract
Arabidopsis thaliana Protein Interactome Database (AtPID) is an object database that integrates data from several bioinformatics prediction methods and manually collected information from the literature. It contains data relevant to protein-protein interaction, protein subcellular location, ortholog maps, domain attributes and gene regulation. The predicted protein interaction data were obtained from ortholog interactome, microarray profiles, GO annotation, and conserved domain and genome contexts. This database holds 28,062 protein-protein interaction pairs with 23,396 pairs generated from prediction methods. Among the rest 4666 pairs, 3866 pairs of them involving 1875 proteins were manually curated from the literature and 800 pairs were from enzyme complexes in KEGG. In addition, subcellular location information of 5562 proteins is available. AtPID was built via an intuitive query interface that provides easy access to the important features of proteins. Through the incorporation of both experimental and computational methods, AtPID is a rich source of information for system-level understanding of gene function and biological processes in A. thaliana. Public access to the AtPID database is available at http://atpid.biosino.org/.
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Affiliation(s)
- Jian Cui
- College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, Shanghai Information Center for Life Sciences, Chinese Academy of Sciences, Shanghai 200031, Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, Daqing Institute of Biotechnology, Northeast Forestry University, Daqing, Heilongjiang 163316, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234 and Bioinformatics Center, Shanghai University, Shanghai 200444, China
| | - Peng Li
- College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, Shanghai Information Center for Life Sciences, Chinese Academy of Sciences, Shanghai 200031, Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, Daqing Institute of Biotechnology, Northeast Forestry University, Daqing, Heilongjiang 163316, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234 and Bioinformatics Center, Shanghai University, Shanghai 200444, China
| | - Guang Li
- College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, Shanghai Information Center for Life Sciences, Chinese Academy of Sciences, Shanghai 200031, Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, Daqing Institute of Biotechnology, Northeast Forestry University, Daqing, Heilongjiang 163316, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234 and Bioinformatics Center, Shanghai University, Shanghai 200444, China
| | - Feng Xu
- College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, Shanghai Information Center for Life Sciences, Chinese Academy of Sciences, Shanghai 200031, Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, Daqing Institute of Biotechnology, Northeast Forestry University, Daqing, Heilongjiang 163316, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234 and Bioinformatics Center, Shanghai University, Shanghai 200444, China
| | - Chen Zhao
- College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, Shanghai Information Center for Life Sciences, Chinese Academy of Sciences, Shanghai 200031, Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, Daqing Institute of Biotechnology, Northeast Forestry University, Daqing, Heilongjiang 163316, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234 and Bioinformatics Center, Shanghai University, Shanghai 200444, China
| | - Yuhua Li
- College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, Shanghai Information Center for Life Sciences, Chinese Academy of Sciences, Shanghai 200031, Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, Daqing Institute of Biotechnology, Northeast Forestry University, Daqing, Heilongjiang 163316, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234 and Bioinformatics Center, Shanghai University, Shanghai 200444, China
| | - Zhongnan Yang
- College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, Shanghai Information Center for Life Sciences, Chinese Academy of Sciences, Shanghai 200031, Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, Daqing Institute of Biotechnology, Northeast Forestry University, Daqing, Heilongjiang 163316, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234 and Bioinformatics Center, Shanghai University, Shanghai 200444, China
| | - Guang Wang
- College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, Shanghai Information Center for Life Sciences, Chinese Academy of Sciences, Shanghai 200031, Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, Daqing Institute of Biotechnology, Northeast Forestry University, Daqing, Heilongjiang 163316, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234 and Bioinformatics Center, Shanghai University, Shanghai 200444, China
| | - Qingbo Yu
- College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, Shanghai Information Center for Life Sciences, Chinese Academy of Sciences, Shanghai 200031, Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, Daqing Institute of Biotechnology, Northeast Forestry University, Daqing, Heilongjiang 163316, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234 and Bioinformatics Center, Shanghai University, Shanghai 200444, China
| | - Yixue Li
- College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, Shanghai Information Center for Life Sciences, Chinese Academy of Sciences, Shanghai 200031, Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, Daqing Institute of Biotechnology, Northeast Forestry University, Daqing, Heilongjiang 163316, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234 and Bioinformatics Center, Shanghai University, Shanghai 200444, China
| | - Tieliu Shi
- College of Life Sciences, the Northeast Forestry University, Harbin, Heilongjiang 150040, Shanghai Information Center for Life Sciences, Chinese Academy of Sciences, Shanghai 200031, Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, Daqing Institute of Biotechnology, Northeast Forestry University, Daqing, Heilongjiang 163316, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234 and Bioinformatics Center, Shanghai University, Shanghai 200444, China
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2443
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Muralla R, Chen E, Sweeney C, Gray JA, Dickerman A, Nikolau BJ, Meinke D. A bifunctional locus (BIO3-BIO1) required for biotin biosynthesis in Arabidopsis. PLANT PHYSIOLOGY 2008; 146:60-73. [PMID: 17993549 PMCID: PMC2230573 DOI: 10.1104/pp.107.107409] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Accepted: 11/02/2007] [Indexed: 05/20/2023]
Abstract
We identify here the Arabidopsis (Arabidopsis thaliana) gene encoding the third enzyme in the biotin biosynthetic pathway, dethiobiotin synthetase (BIO3; At5g57600). This gene is positioned immediately upstream of BIO1, which is known to be associated with the second reaction in the pathway. Reverse genetic analysis demonstrates that bio3 insertion mutants have a similar phenotype to the bio1 and bio2 auxotrophs identified using forward genetic screens for arrested embryos rescued on enriched nutrient medium. Unexpectedly, bio3 and bio1 mutants define a single genetic complementation group. Reverse transcription-polymerase chain reaction analysis demonstrates that separate BIO3 and BIO1 transcripts and two different types of chimeric BIO3-BIO1 transcripts are produced. Consistent with genetic data, one of the fused transcripts is monocistronic and encodes a bifunctional fusion protein. A splice variant is bicistronic, with distinct but overlapping reading frames. The dual functionality of the monocistronic transcript was confirmed by complementing the orthologous auxotrophs of Escherichia coli (bioD and bioA). BIO3-BIO1 transcripts from other plants provide further evidence for differential splicing, existence of a fusion protein, and localization of both enzymatic reactions to mitochondria. In contrast to most biosynthetic enzymes in eukaryotes, which are encoded by genes dispersed throughout the genome, biotin biosynthesis in Arabidopsis provides an intriguing example of a bifunctional locus that catalyzes two sequential reactions in the same metabolic pathway. This complex locus exhibits several unusual features that distinguish it from biotin operons in bacteria and from other genes known to encode bifunctional enzymes in plants.
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Affiliation(s)
- Rosanna Muralla
- Department of Botany, Oklahoma State University, Stillwater, OK 74078, USA
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2444
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Jianlin Cheng, Tegge A, Baldi P. Machine Learning Methods for Protein Structure Prediction. IEEE Rev Biomed Eng 2008; 1:41-9. [DOI: 10.1109/rbme.2008.2008239] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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2445
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Sakamoto W, Miyagishima SY, Jarvis P. Chloroplast biogenesis: control of plastid development, protein import, division and inheritance. THE ARABIDOPSIS BOOK 2008; 6:e0110. [PMID: 22303235 PMCID: PMC3243408 DOI: 10.1199/tab.0110] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The chloroplast is a multi-copy cellular organelle that not only performs photosynthesis but also synthesizes amino acids, lipids and phytohormones. The plastid also responds to environmental stimuli such as gravitropism. Biogenesis of chloroplasts is initiated from proplastids in shoot meristems, and involves a series of important events. In the last decade, considerable progress has been made towards understanding various aspects of chloroplast biogenesis at the molecular level, via studies in model systems such as Arabidopsis. This review focuses on two important aspects of chloroplast biogenesis, synthesis/assembly and division/transmission. Chloroplasts originated through endosymbiosis from an ancestor of extant cyanobacteria, and thus contain their own genomes. DNA in chloroplasts is organized into complexes with proteins, and these are called nucleoids. The synthesis of chloroplast proteins is regulated at various steps. However, a majority of proteins are synthesized in the cytosol, and their proper import into chloroplast compartments is a prerequisite for chloroplast development. Fundamental aspects of plastid gene expression/regulation and chloroplast protein transport are described, together with recent proteome analyses of the organelle. Chloroplasts are not de novo synthesized, but instead are propagated from pre-existing plastids. In addition, plastids are transmitted from generation to generation with a unique mode of inheritance. Our current knowledge on the division machinery and the inheritance of plastids is described.
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Affiliation(s)
- Wataru Sakamoto
- Research Institute for Bioresources, Okayama University, Kurashiki, Okayama 710-0046, Japan
- Address correspondence to
| | | | - Paul Jarvis
- Department of Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
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2446
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Nair R, Rost B. Protein subcellular localization prediction using artificial intelligence technology. Methods Mol Biol 2008; 484:435-63. [PMID: 18592195 DOI: 10.1007/978-1-59745-398-1_27] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Proteins perform many important tasks in living organisms, such as catalysis of biochemical reactions, transport of nutrients, and recognition and transmission of signals. The plethora of aspects of the role of any particular protein is referred to as its "function." One aspect of protein function that has been the target of intensive research by computational biologists is its subcellular localization. Proteins must be localized in the same subcellular compartment to cooperate toward a common physiological function. Aberrant subcellular localization of proteins can result in several diseases, including kidney stones, cancer, and Alzheimer's disease. To date, sequence homology remains the most widely used method for inferring the function of a protein. However, the application of advanced artificial intelligence (AI)-based techniques in recent years has resulted in significant improvements in our ability to predict the subcellular localization of a protein. The prediction accuracy has risen steadily over the years, in large part due to the application of AI-based methods such as hidden Markov models (HMMs), neural networks (NNs), and support vector machines (SVMs), although the availability of larger experimental datasets has also played a role. Automatic methods that mine textual information from the biological literature and molecular biology databases have considerably sped up the process of annotation for proteins for which some information regarding function is available in the literature. State-of-the-art methods based on NNs and HMMs can predict the presence of N-terminal sorting signals extremely accurately. Ab initio methods that predict subcellular localization for any protein sequence using only the native amino acid sequence and features predicted from the native sequence have shown the most remarkable improvements. The prediction accuracy of these methods has increased by over 30% in the past decade. The accuracy of these methods is now on par with high-throughput methods for predicting localization, and they are beginning to play an important role in directing experimental research. In this chapter, we review some of the most important methods for the prediction of subcellular localization.
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Affiliation(s)
- Rajesh Nair
- CUBIC Department of Biochemistry and Molecular Biophysics and Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
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Sundaram S, Rathinasabapathi B, Ma LQ, Rosen BP. An arsenate-activated glutaredoxin from the arsenic hyperaccumulator fern Pteris vittata L. regulates intracellular arsenite. J Biol Chem 2007; 283:6095-101. [PMID: 18156657 DOI: 10.1074/jbc.m704149200] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To elucidate the mechanisms of arsenic resistance in the arsenic hyperaccumulator fern Pteris vittata L., a cDNA for a glutaredoxin (Grx) Pv5-6 was isolated from a frond expression cDNA library based on the ability of the cDNA to increase arsenic resistance in Escherichia coli. The deduced amino acid sequence of Pv5-6 showed high homology with an Arabidopsis chloroplastic Grx and contained two CXXS putative catalytic motifs. Purified recombinant Pv5-6 exhibited glutaredoxin activity that was increased 1.6-fold by 10 mm arsenate. Site-specific mutation of Cys(67) to Ala(67) resulted in the loss of both GRX activity and arsenic resistance. PvGrx5 was expressed in E. coli mutants in which the arsenic resistance genes of the ars operon were deleted (strain AW3110), a deletion of the gene for the ArsC arsenate reductase (strain WC3110), and a strain in which the ars operon was deleted and the gene for the GlpF aquaglyceroporin was disrupted (strain OSBR1). Expression of PvGrx5 increased arsenic tolerance in strains AW3110 and WC3110, but not in OSBR1, suggesting that PvGrx5 had a role in cellular arsenic resistance independent of the ars operon genes but dependent on GlpF. AW3110 cells expressing PvGrx5 had significantly lower levels of arsenite when compared with vector controls when cultured in medium containing 2.5 mm arsenate. Our results are consistent with PvGrx5 having a role in regulating intracellular arsenite levels, by either directly or indirectly modulating the aquaglyceroporin. To our knowledge, PvGrx5 is the first plant Grx implicated in arsenic metabolism.
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Affiliation(s)
- Sabarinath Sundaram
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, University of Florida, Gainesville, FL 32611-0690, USA
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Giorio G, Stigliani AL, D'Ambrosio C. Phytoene synthase genes in tomato (Solanumlycopersicum L.) - new data on the structures, the deduced amino acid sequences and the expression patterns. FEBS J 2007; 275:527-35. [PMID: 18167141 DOI: 10.1111/j.1742-4658.2007.06219.x] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fruit of tomato (Solanum lycopersicum L.) is a berry: red, fleshy and rich in seeds. Its colour is due to the high content of lycopene whose synthesis is activated by the phytoene synthase 1 (PSY1) enzyme, encoded by Psy1 which is distinct from Psy2. In the present study, we report on the genomic structures of the Psy1 and Psy2 genes and on their transcription patterns in different tomato tissues. Our results have completely clarified the structure of the Psy1 and Psy2 genes in the coding sequence region. The two genes were shown to have an highly conserved structure, with seven exons being almost identical and six introns being much more variable. For Psy1 and Psy2, respectively, the sequenced regions were 4527 and 3542 bp long, the coding sequences were 1239 bp and 1317 bp long, whereas the predicted protein sequences were 412 and 438 amino acids. The two proteins are almost identical in the central region, whereas most differences are present in the N-terminus and C-terminus. Quantitative real time PCR analysis showed that Psy2 transcript was present in all tested plant tissues, whereas Psy1 transcript could be detected in chromoplast-containing tissues, particularly in fruit where it activates and boosts lycopene accumulation. Interestingly, the organ with the highest relative content of Psy2 transcript is the petal and not the leaf. Psy1 is a Psy2 paralog derived through a gene duplication event that have involved other genes encoding rate controlling enzymes of the carotenoid pathway. Duplicate genes have been recruited to allow carotenoid synthesis in petals and fruits. However, recruitment of carotenoid metabolism for fruit pigmentation could have occurred later in the evolution, either because phytoene synthase gene duplication occurred later or because the fruit pigmentation process required a more sophisticated mechanism involving tight control of the transcription of other genes.
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Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 2007; 450:560-5. [PMID: 18033299 DOI: 10.1038/nature06269] [Citation(s) in RCA: 838] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2007] [Accepted: 09/18/2007] [Indexed: 11/08/2022]
Abstract
From the standpoints of both basic research and biotechnology, there is considerable interest in reaching a clearer understanding of the diversity of biological mechanisms employed during lignocellulose degradation. Globally, termites are an extremely successful group of wood-degrading organisms and are therefore important both for their roles in carbon turnover in the environment and as potential sources of biochemical catalysts for efforts aimed at converting wood into biofuels. Only recently have data supported any direct role for the symbiotic bacteria in the gut of the termite in cellulose and xylan hydrolysis. Here we use a metagenomic analysis of the bacterial community resident in the hindgut paunch of a wood-feeding 'higher' Nasutitermes species (which do not contain cellulose-fermenting protozoa) to show the presence of a large, diverse set of bacterial genes for cellulose and xylan hydrolysis. Many of these genes were expressed in vivo or had cellulase activity in vitro, and further analyses implicate spirochete and fibrobacter species in gut lignocellulose degradation. New insights into other important symbiotic functions including H2 metabolism, CO2-reductive acetogenesis and N2 fixation are also provided by this first system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation. Our results underscore how complex even a 1-microl environment can be.
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Badugu R, Garcia M, Bondada V, Joshi A, Geddes JW. N terminus of calpain 1 is a mitochondrial targeting sequence. J Biol Chem 2007; 283:3409-3417. [PMID: 18070881 DOI: 10.1074/jbc.m706851200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The ubiquitous m- and mu-calpains are thought to be localized in the cytosolic compartment, as is their endogenous inhibitor calpastatin. Previously, mu-calpain was found to be enriched in mitochondrial fractions isolated from rat cerebral cortex and SH-SY5Y neuroblastoma cells, but the submitochondrial localization of mu-calpain was not determined. In the present study, submitochondrial fractionation and digitonin permeabilization studies indicated that both calpain 1 and calpain small subunit 1, which together form mu-calpain, are present in the mitochondrial intermembrane space. The N terminus of calpain 1 contains an amphipathic alpha-helical domain, and is distinct from the N terminus of calpain 2. Calpain 1, but not calpain 2, was imported into mitochondria. Removal of the N-terminal 22 amino acids of calpain 1 blocked the mitochondrial calpain import, while addition of this N-terminal region to calpain 2 or green fluorescent protein enabled mitochondrial import. The N terminus of calpain 1 was not processed following mitochondrial import, but was removed by autolysis following calpain activation. Calpain small subunit 1 was not directly imported into mitochondria, but was imported in the presence of calpain 1. The presence of a mitochondrial targeting sequence in the N-terminal region of calpain 1 is consistent with the localization of mu-calpain to the mitochondrial intermembrane space and provides new insight into the possible functions of this cysteine protease.
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Affiliation(s)
- RamaKrishna Badugu
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky
| | - Matthew Garcia
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky; Department of Anatomy and Neurobiology, University of Kentucky, Lexington, Kentucky
| | - Vimala Bondada
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky
| | - Aashish Joshi
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky; Department of Anatomy and Neurobiology, University of Kentucky, Lexington, Kentucky
| | - James W Geddes
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky; Department of Anatomy and Neurobiology, University of Kentucky, Lexington, Kentucky.
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