The Plant Short-Chain Dehydrogenase (SDR) superfamily:genome-wide inventory and diversification patterns

Background Short-chain dehydrogenases/reductases (SDRs) form one of the largest and oldest NAD(P)(H) dependent oxidoreductase families. Despite a conserved 'Rossmann-fold' structure, members of the SDR superfamily exhibit low sequence similarities, which constituted a bottleneck in terms of identification. Recent classification methods, relying on hidden-Markov models (HMMs), improved identification and enabled the construction of a nomenclature. However, functional annotations of plant SDRs remain scarce. Results Wide-scale analyses were performed on ten plant genomes. The combination of hidden Markov model (HMM) based analyses and similarity searches led to the construction of an exhaustive inventory of plant SDR. With 68 to 315 members found in each analysed genome, the inventory confirmed the over-representation of SDRs in plants compared to animals, fungi and prokaryotes. The plant SDRs were first classified into three major types --- 'classical', 'extended' and 'divergent' --- but a minority (10 % of the predicted SDRs) could not be classified into these general types ('unknown' or 'atypical' types). In a second step, we could categorize the vast majority of land plant SDRs into a set of 49 families. Out of these 49 families, 35 appeared early during evolution since they are commonly found through all the Green Lineage. Yet, some SDR families --- tropinone reductase-like proteins (SDR65C), 'ABA2-like'-NAD dehydrogenase (SDR110C), 'salutaridine/menthone-reductase-like' proteins (SDR114C), 'dihydroflavonol 4-reductase'-like proteins (SDR108E) and 'isoflavone-reductase-like' (SDR460A) proteins --- have undergone significant functional diversification within vascular plants since they diverged from Bryophytes. Interestingly, these diversified families are either involved in the secondary metabolism routes (terpenoids, alkaloids, phenolics) or participate in developmental processes (hormone biosynthesis or catabolism, flower development), in opposition to SDR families involved in primary metabolism which are poorly diversified. Conclusion The application of HMMs to plant genomes enabled us to identify 49 families that encompass all Angiosperms ('higher plants') SDRs, each family being sufficiently conserved to enable simpler analyses based only on overall sequence similarity. The multiplicity of SDRs in plant kingdom is mainly explained by the diversification of large families involved in different secondary metabolism pathways, suggesting that the chemical diversification that accompanied the emergence of vascular plants acted as a driving force for SDR evolution

RSpred, a set of Hidden Markov Models to detect and classify the RIFIN and STEVOR proteins of Plasmodium falciparum

<p>Abstract</p> <p>Background</p> <p>Many parasites use multicopy protein families to avoid their host's immune system through a strategy called antigenic variation. RIFIN and STEVOR proteins are variable surface antigens uniquely found in the malaria parasites <it>Plasmodium falciparum </it>and <it>P. reichenowi</it>. Although these two protein families are different, they have more similarity to each other than to any other proteins described to date. As a result, they have been grouped together in one Pfam domain. However, a recent study has described the sub-division of the RIFIN protein family into several functionally distinct groups. These sub-groups require phylogenetic analysis to sort out, which is not practical for large-scale projects, such as the sequencing of patient isolates and meta-genomic analysis.</p> <p>Results</p> <p>We have manually curated the <it>rif </it>and <it>stevor </it>gene repertoires of two <it>Plasmodium falciparum </it>genomes, isolates DD2 and HB3. We have identified 25% of mis-annotated and ~30 missing <it>rif </it>and <it>stevor </it>genes. Using these data sets, as well as sequences from the well curated reference genome (isolate 3D7) and field isolate data from Uniprot, we have developed a tool named RSpred. The tool, based on a set of hidden Markov models and an evaluation program, automatically identifies STEVOR and RIFIN sequences as well as the sub-groups: A-RIFIN, B-RIFIN, B1-RIFIN and B2-RIFIN. In addition to these groups, we distinguish a small subset of STEVOR proteins that we named STEVOR-like, as they either differ remarkably from typical STEVOR proteins or are too fragmented to reach a high enough score. When compared to Pfam and TIGRFAMs, RSpred proves to be a more robust and more sensitive method. We have applied RSpred to the proteomes of several <it>P. falciparum </it>strains, <it>P. reichenowi, P. vivax</it>, <it>P. knowlesi </it>and the rodent malaria species. All groups were found in the <it>P. falciparum </it>strains, and also in the <it>P. reichenowi </it>parasite, whereas none were predicted in the other species.</p> <p>Conclusions</p> <p>We have generated a tool for the sorting of RIFIN and STEVOR proteins, large antigenic variant protein groups, into homogeneous sub-families. Assigning functions to such protein families requires their subdivision into meaningful groups such as we have shown for the RIFIN protein family. RSpred removes the need for complicated and time consuming phylogenetic analysis methods. It will benefit both research groups sequencing whole genomes as well as others working with field isolates. RSpred is freely accessible via <url>http://www.ifm.liu.se/bioinfo/</url>.</p

IL-17RA Is Required for CCL2 Expression, Macrophage Recruitment, and Emphysema in Response to Cigarette Smoke

Chronic Obstructive Pulmonary Disease (COPD) is characterized by airspace enlargement and peribronchial lymphoid follicles; however, the immunological mechanisms leading to these pathologic changes remain undefined. Here we show that cigarette smoke is a selective adjuvant that augments in vitro and in vivo Th17, but not Th1, cell differentiation via the aryl hydrocarbon receptor. Smoke exposed IL-17RA−/− mice failed to induce CCL2 and MMP12 compared to WT mice. Remarkably, in contrast to WT mice, IL-17RA−/− mice failed to develop emphysema after 6 months of cigarette smoke exposure. Taken together, these data demonstrate that cigarette smoke is a potent Th17 adjuvant and that IL-17RA signaling is required for chemokine expression necessary for MMP12 induction and tissue emphysema

Bioinformatic methods in protein characterization

Bioinformatics is an emerging interdisciplinary research field in which mathematics. computer science and biology meet. In this thesis. bioinformatic methods for analysis of functional and structural properties among proteins will be presented. I have developed and applied bioinformatic methods on the enzyme superfamily of short-chain dehydrogenases/reductases (SDRs), coenzyme-binding enzymes of the Rossmann fold type, and amyloid-forming proteins and peptides. The basis for bioinformatics is the availability of biological data, collected in different types of database. A non-redundant protein sequence database, KIND, has been compiled using a modification of the naïve algorithm. The database consists of the non- redundant union of the two protein sequence databases SWISSPROT and PIR, and the two databases derived from open reading frames TrEMBL and Genpept. By applying sequence comparison techniques in the form of multiple and pair-wise alignment methods, protein sequences from known complete genomes have been compared and SDR members have been identified. Inter-species comparisons reveal eight protein clusters in common to human, animal and plant genomes. The SDR superfamily, previously divided into only two families, is now found to consist of Five families. Using a combination of hidden Markov models and motifs, an extendable assignment scheme has been developed, including a subfamily division of the two largest families, based on coenzyme specificity. This scheme will be a valuable tool in functional and structural assignments of novel SDR members. Coenzyme specificity has also been addressed in a more general sense, where a coenzyme prediction method has been developed. The method is based on the existence of specific sequence motifs, characteristic of coenzyme binding. Given an amino acid sequence, identification of coenzyme-binding regions can be done with over 90% success rate, but prediction of coenzyme type still needs to be improved. A method to predict amyloid fibril-forming proteins has been developed, utilizing unsuccessful secondary structure predictions of regions with weak a-helical propensities. Experimentally determined a-helices were compared with their predicted secondary structures. in a large set of proteins. Among these, it was found that proteins with amyloid fibril-forming tendencies harbours a-helices that are falsely predicted to be beta-strands, suggesting that this type of proteins have segments with ail amino acid composition typical of beta-strands rather than a-helices. This phenomenon, now referred to as discordance, probably is one of the reasons why some proteins fail to fold properly. and instead form insoluble fibrils that, directly or indirectly, are the cause of severe diseases such as Alzheimer's disease and the prion diseases. In conclusion. this thesis shows that bioinformatic methods, applied to protein sequence data, are important tools to study and characterize structural and functional properties among proteins

Classification of the short-chain dehydrogenase/reductase superfamily using hidden Markov models

The short-chain dehydrogenase/reductase (SDR) superfamily now has over 47 000 members, most of which are distantly related, with typically 20-30% residue identity in pairwise comparisons, making it difficult to obtain an overview of this superfamily. We have therefore developed a family classification system, based upon hidden Markov models (HMMs). To this end, we have identified 314 SDR families, encompassing about 31,900 members. In addition, about 9700 SDR forms belong to families with too few members at present to establish valid HMMs. In the human genome, we find 47 SDR families, corresponding to 82 genes. Thirteen families are present in all three domains (Eukaryota, Bacteria, and Archaea), and are hence expected to catalyze fundamental metabolic processes. The majority of these enzymes are of the 'extended' type, in agreement with earlier findings. About half of the SDR families are only found among bacteria, where the 'classical' SDR type is most prominent. The HMM-based classification is used as a basis for a sustainable and expandable nomenclature system

Short-chain dehydrogenase/reductase (SDR) relationships: A large family with eight clusters common to human, animal, and plant genomes

The progress in genome characterizations has opened new routes for studying enzyme families. The availability of the human genome enabled us to delineate the large family of short-chain dehydrogenase/reductase (SDR) members. Although the human genome releases are not yet final, we have already found 63 members. We have also compared these SDR forms with those of three model organisms: Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana. We detect eight SDR ortholog clusters in a cross-genome comparison. Four of these clusters represent extended SDR forms, a subgroup found in all life forms. The other four are classical SDRs with activities involved in cellular differentiation and signalling. We also find 18 SDR genes that are present only in the human genome of the four genomes studied, reflecting enzyme forms specific to mammals. Close to half of these gene products represent steroid dehydrogenases, emphasizing the regulatory importance of these enzymes

Personnel Selection in the Public Sector: Case Study of Latvia and Estonia

Pēc Padomju Savienības sabrukuma un neatkarības atjaunošanas 1991.gadā, Igaunijā un Latvijā kā viens no uzdevumiem tika izvirzīts izveidot savas valsts civildienestu, kas būtu balstīts uz demokrātiskiem principiem, kur civildienests būtu neitrāls un bez jebkādas ideoloģiskas kontroles. Savukārt civildienesta personāla atlasei būtu jābalstās uz nopelnu principiem, lai panāktu to, ka ierēdņi spēj nodrošināt profesionālu un kompetentu civildienesta darbu un balstītos uz augstiem ētiskiem standartiem. Lai noskaidrotu, vai abām valstīm ir izdevies nodrošināt to, ka personāla atlase balstās uz nopelnu sistēmas pamatprincipiem par bakalaura darba mērķi ir izvirzīts izpētīt pastāvošās civildienesta rekrutācijas sistēmas Latvijas un Igaunijas civildienestos, kā arī noskaidrot, kura no šīm sistēmām dominē civildienestos. Galvenais jautājums ir noskaidrot, vai personāla atlase balstās uz nopelnu principiem. Savukārt jānoskaidro arī tas, vai ir vērojama politisko spēku ietekme uz personāla atlases procesiem Latvijā un Igaunijā, kas liecinātu par to, ka tiek izmantoti patronāžas sistēmas elementi civildienestā? Saistībā ar jautājumiem par to, kādas rekrutācijas sistēmas tiek izmantotas personāla atlasē, darbā tika izvirzīta hipotēze: Lai gan, vadoties no tiesību aktos atrunātajiem principiem, Latvijā un Igaunijā civildienesta personāla atlasē darbojas nopelnu sistēmas modelis, abu valstu civildienesta personāla izvēlē novērojami arī patronāžas sistēmas elementi. Darbā tika izdarīti galvenie secinājumi par to, ka gan Latvijas, gan Igaunijas civildienestā formāli tiek uzskatīts, ka personāla atlases procesā tiek izmantoti nopelnu sistēmas elementi, kur ierēdņa amata pretendenta zināšanas, atbilstoša izglītība, darba pieredze ir kā galvenie priekšnoteikumi atlases procesā, kas tādējādi var nodrošināt efektīvu un profesionālu civildienesta darbību, tomēr civildienesta likumi pieļauj to, ka tiek izmantoti un var tikt izmantoti arī patronāžas sistēmas elementi, kas nosaka politisko spēku ietekmi pār civildienesta ierēdņu personāla atlases procesiemAfter the breakdown of the Soviet Union and independence declaration on 1991, one of the most important challenge for Latvia and Estonia was the construction of the civil service where emphasis was put on legalistic aspects and democratic principles. In order to guarantee a neutrality from political control and providing effectiveness and productivity in the civil service work, the selection for personnel required to be uphold on the merit principles. The aim of this research is to find out what kind of recruitation principles are used in personnel selection and which principles are dominated. Whether the personnel recruitation in Latvia and Estonia is based on merit principles or patronage when politicians play great role in personnel selection process and made the civil service work too much politicized. The hypothesis of this research is: Despite that in legislation there is written that personnel selection is based on the merit principles in Latvia and Estonia, there exist also a patronage in both countries. The main conclusions are that the civil service laws in both countries allow to use patronage in personnel selection process in spite of the proposals that they are selecting their personnel on merit principles in order to form a effective and neutral civil service

Evolutionary Conservation of the Ribosomal Biogenesis Factor Rbm19/Mrd1 : Implications for Function

Ribosome biogenesis in eukaryotes requires coordinated folding and assembly of a pre-rRNA into sequential pre-rRNA-protein complexes in which chemical modifications and RNA cleavages occur. These processes require many small nucleolar RNAs (snoRNAs) and proteins. Rbm19/Mrd1 is one such protein that is built from multiple RNA-binding domains (RBDs). We find that Rbm19/Mrd1 with five RBDs is present in all branches of the eukaryotic phylogenetic tree, except in animals and Choanoflagellates, that instead have a version with six RBDs and Microsporidia which have a minimal Rbm19/Mrd1 protein with four RBDs. Rbm19/Mrd1 therefore evolved as a multi-RBD protein very early in eukaryotes. The linkers between the RBDs have conserved properties; they are disordered, except for linker 3, and position the RBDs at conserved relative distances from each other. All but one of the RBDs have conserved properties for RNA-binding and each RBD has a specific consensus sequence and a conserved position in the protein, suggesting a functionally important modular design. The patterns of evolutionary conservation provide information for experimental analyses of the function of Rbm19/Mrd1. In vivo mutational analysis confirmed that a highly conserved loop 5-β4-strand in RBD6 is essential for function.funding agencies|Swedish Research Council||Carl Tryggers Stiftelse||Linkoping University||</p

The Plant Short-Chain Dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns

Abstract Background Short-chain dehydrogenases/reductases (SDRs) form one of the largest and oldest NAD(P)(H) dependent oxidoreductase families. Despite a conserved ‘Rossmann-fold’ structure, members of the SDR superfamily exhibit low sequence similarities, which constituted a bottleneck in terms of identification. Recent classification methods, relying on hidden-Markov models (HMMs), improved identification and enabled the construction of a nomenclature. However, functional annotations of plant SDRs remain scarce. Results Wide-scale analyses were performed on ten plant genomes. The combination of hidden Markov model (HMM) based analyses and similarity searches led to the construction of an exhaustive inventory of plant SDR. With 68 to 315 members found in each analysed genome, the inventory confirmed the over-representation of SDRs in plants compared to animals, fungi and prokaryotes. The plant SDRs were first classified into three major types — ‘classical’, ‘extended’ and ‘divergent’ — but a minority (10% of the predicted SDRs) could not be classified into these general types (‘unknown’ or ‘atypical’ types). In a second step, we could categorize the vast majority of land plant SDRs into a set of 49 families. Out of these 49 families, 35 appeared early during evolution since they are commonly found through all the Green Lineage. Yet, some SDR families — tropinone reductase-like proteins (SDR65C), ‘ABA2-like’-NAD dehydrogenase (SDR110C), ‘salutaridine/menthone-reductase-like’ proteins (SDR114C), ‘dihydroflavonol 4-reductase’-like proteins (SDR108E) and ‘isoflavone-reductase-like’ (SDR460A) proteins — have undergone significant functional diversification within vascular plants since they diverged from Bryophytes. Interestingly, these diversified families are either involved in the secondary metabolism routes (terpenoids, alkaloids, phenolics) or participate in developmental processes (hormone biosynthesis or catabolism, flower development), in opposition to SDR families involved in primary metabolism which are poorly diversified. Conclusion The application of HMMs to plant genomes enabled us to identify 49 families that encompass all Angiosperms (‘higher plants’) SDRs, each family being sufficiently conserved to enable simpler analyses based only on overall sequence similarity. The multiplicity of SDRs in plant kingdom is mainly explained by the diversification of large families involved in different secondary metabolism pathways, suggesting that the chemical diversification that accompanied the emergence of vascular plants acted as a driving force for SDR evolution.</p