Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species

<p>Abstract</p> <p>Background</p> <p>The <it>Bacteroidetes </it>and <it>Chlorobi </it>species constitute two main groups of the <it>Bacteria </it>that are closely related in phylogenetic trees. The <it>Bacteroidetes </it>species are widely distributed and include many important periodontal pathogens. In contrast, all <it>Chlorobi </it>are anoxygenic obligate photoautotrophs. Very few (or no) biochemical or molecular characteristics are known that are distinctive characteristics of these bacteria, or are commonly shared by them.</p> <p>Results</p> <p>Systematic blast searches were performed on each open reading frame in the genomes of <it>Porphyromonas gingivalis </it>W83, <it>Bacteroides fragilis </it>YCH46, <it>B. thetaiotaomicron </it>VPI-5482, <it>Gramella forsetii KT0803, Chlorobium luteolum </it>(formerly <it>Pelodictyon luteolum</it>) DSM 273 and <it>Chlorobaculum tepidum </it>(formerly <it>Chlorobium tepidum</it>) TLS to search for proteins that are uniquely present in either all or certain subgroups of <it>Bacteroidetes </it>and <it>Chlorobi</it>. These studies have identified > 600 proteins for which homologues are not found in other organisms. This includes 27 and 51 proteins that are specific for most of the sequenced <it>Bacteroidetes </it>and <it>Chlorobi </it>genomes, respectively; 52 and 38 proteins that are limited to species from the <it>Bacteroidales </it>and <it>Flavobacteriales </it>orders, respectively, and 5 proteins that are common to species from these two orders; 185 proteins that are specific for the <it>Bacteroides </it>genus. Additionally, 6 proteins that are uniquely shared by species from the <it>Bacteroidetes </it>and <it>Chlorobi </it>phyla (one of them also present in the <it>Fibrobacteres</it>) have also been identified. This work also describes two large conserved inserts in DNA polymerase III (DnaE) and alanyl-tRNA synthetase that are distinctive characteristics of the <it>Chlorobi </it>species and a 3 aa deletion in ClpB chaperone that is mainly found in various <it>Bacteroidales, Flavobacteriales </it>and <it>Flexebacteraceae</it>, but generally not found in the homologs from other organisms. Phylogenetic analyses of the <it>Bacteroidetes </it>and <it>Chlorobi </it>species is also reported based on concatenated sequences for 12 conserved proteins by different methods including the character compatibility (or clique) approach. The placement of <it>Salinibacter ruber </it>with other <it>Bacteroidetes </it>species was not resolved by other phylogenetic methods, but this affiliation was strongly supported by the character compatibility approach.</p> <p>Conclusion</p> <p>The molecular signatures described here provide novel tools for identifying and circumscribing species from the <it>Bacteroidetes </it>and <it>Chlorobi </it>phyla as well as some of their main groups in clear terms. These results also provide strong evidence that species from these two phyla (and also possibly <it>Fibrobacteres</it>) are specifically related to each other and they form a single superphylum. Functional studies on these proteins and indels should aid in the discovery of novel biochemical and physiological characteristics that are unique to these groups of bacteria.</p

Proteomic and functional mapping of cardiac NaV1.5 channel phosphorylation sites

Phosphorylation of the voltage-gated Na+ (NaV) channel NaV1.5 regulates cardiac excitability, yet the phosphorylation sites regulating its function and the underlying mechanisms remain largely unknown. Using a systematic, quantitative phosphoproteomic approach, we analyzed NaV1.5 channel complexes purified from nonfailing and failing mouse left ventricles, and we identified 42 phosphorylation sites on NaV1.5. Most sites are clustered, and three of these clusters are highly phosphorylated. Analyses of phosphosilent and phosphomimetic NaV1.5 mutants revealed the roles of three phosphosites in regulating NaV1.5 channel expression and gating. The phosphorylated serines S664 and S667 regulate the voltage dependence of channel activation in a cumulative manner, whereas the nearby S671, the phosphorylation of which is increased in failing hearts, regulates cell surface NaV1.5 expression and peak Na+ current. No additional roles could be assigned to the other clusters of phosphosites. Taken together, our results demonstrate that ventricular NaV1.5 is highly phosphorylated and that the phosphorylation-dependent regulation of NaV1.5 channels is highly complex, site specific, and dynamic

Proteomic and functional mapping of cardiac NaV1.5 channel phosphorylation sites

Phosphorylation of the voltage-gated Na+ (NaV) channel NaV1.5 regulates cardiac excitability, yet the phosphorylation sites regulating its function and the underlying mechanisms remain largely unknown. Using a systematic, quantitative phosphoproteomic approach, we analyzed NaV1.5 channel complexes purified from nonfailing and failing mouse left ventricles, and we identified 42 phosphorylation sites on NaV1.5. Most sites are clustered, and three of these clusters are highly phosphorylated. Analyses of phosphosilent and phosphomimetic NaV1.5 mutants revealed the roles of three phosphosites in regulating NaV1.5 channel expression and gating. The phosphorylated serines S664 and S667 regulate the voltage dependence of channel activation in a cumulative manner, whereas the nearby S671, the phosphorylation of which is increased in failing hearts, regulates cell surface NaV1.5 expression and peak Na+ current. No additional roles could be assigned to the other clusters of phosphosites. Taken together, our results demonstrate that ventricular NaV1.5 is highly phosphorylated and that the phosphorylation-dependent regulation of NaV1.5 channels is highly complex, site specific, and dynamic

Perceived economic self‑sufficiency: a countryand generation‑comparative approach

We thank Michael Camasso and Radha Jagannathan as well as Asimina Christoforou, Gerbert Kraaykamp, Fay Makantasi, Tiziana Nazio, Kyriakos Pierrakakis, Jacqueline O’Reilly and Jan van Deth for their contribution to the CUPESSE project (Seventh Framework Programme; Grant Agreement No. 61325). CUPESSE received additional funding from the Mannheim Centre for European Social Research (MZES) and the Field of Focus 4 “Self-Regulation and Regulation: Individuals and Organisations” at Heidelberg University. We further acknowledge helpful comments on this article by two anonymous reviewers. Julian Rossello provided valuable research assistance.Electronic supplementary material The online version of this article (https ://doi.org/10.1057/ s4130 4-018-0186-3) contains supplementary material, which is available to authorized users.Existing datasets provided by statistical agencies (e.g. Eurostat) show that the economic and financial crisis that unfolded in 2008 significantly impacted the lives and livelihoods of young people across Europe. Taking these official statistics as a starting point, the collaborative research project “Cultural Pathways to Economic Self-Sufficiency and Entrepreneurship in Europe” (CUPESSE) generated new survey data on the economic and social situation of young Europeans (18–35 years). The CUPESSE dataset allows for country-comparative assessments of young people’s perceptions about their socio-economic situation. Furthermore, the dataset includes a variety of indicators examining the socio-economic situation of both young adults and their parents. In this data article, we introduce the CUPESSE dataset to political and social scientists in an attempt to spark a debate on the measurements, patterns and mechanisms of intergenerational transmission of economic self-sufficiency as well as its political implications.CUPESSE project (Seventh Framework Programme; Grant Agreement No. 61325

Partial sequence alignments of alanyl-tRNA synthetase showing a conserved insert of about 12–14 aa that is a distinctive characteristic of homologs and not found in other bacteria

<p><b>Copyright information:</b></p><p>Taken from "Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species"</p><p>http://www.biomedcentral.com/1471-2148/7/71</p><p>BMC Evolutionary Biology 2007;7():71-71.</p><p>Published online 8 May 2007</p><p>PMCID:PMC1887533.</p><p></p> The dashes (-) denote identity with the amino acid on the top line. Additional abbreviations:

Neighbour-joining tree based on concatenated sequences for 12 highly conserved proteins

<p><b>Copyright information:</b></p><p>Taken from "Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species"</p><p>http://www.biomedcentral.com/1471-2148/7/71</p><p>BMC Evolutionary Biology 2007;7():71-71.</p><p>Published online 8 May 2007</p><p>PMCID:PMC1887533.</p><p></p> The tree was rooted using sequences for species and numbers on the nodes indicate bootstrap scores in the NJ and maximum-likelihood analyses (NJ/MP). The branching position of , which became available after this analysis was completed, is not shown. However, our analysis of a smaller dataset indicates that it exhibits closest affinity for the flavobacteria (results not shown)

A summary diagram showing the evolutionary stages where different signature proteins and conserved indels that are specific for the and species have likely evolved or originated

<p><b>Copyright information:</b></p><p>Taken from "Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species"</p><p>http://www.biomedcentral.com/1471-2148/7/71</p><p>BMC Evolutionary Biology 2007;7():71-71.</p><p>Published online 8 May 2007</p><p>PMCID:PMC1887533.</p><p></p> Some of the conserved inserts that are specific for these groups or indicate their branching position relative to other bacterial phyla have been described in earlier work [30,43,69]

Character compatibility tree (or the largest clique of mutually compatible characters) based on two states sites in the concatenated sequence alignment for the 12 proteins

<p><b>Copyright information:</b></p><p>Taken from "Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species"</p><p>http://www.biomedcentral.com/1471-2148/7/71</p><p>BMC Evolutionary Biology 2007;7():71-71.</p><p>Published online 8 May 2007</p><p>PMCID:PMC1887533.</p><p></p> The clique consisted of 410 mutually compatible characters. The numbers of characters that distinguished different clades are indicated on the nodes. Rooting was done using the sequences for species

Structure and Protein-Protein Interaction Studies on Chlamydia trachomatis Protein CT670 (YscO Homolog)▿

Comparative genomic studies have identified many proteins that are found only in various Chlamydiae species and exhibit no significant sequence similarity to any protein in organisms that do not belong to this group. The CT670 protein of Chlamydia trachomatis is one of the proteins whose genes are in one of the type III secretion gene clusters but whose cellular functions are not known. CT670 shares several characteristics with the YscO protein of Yersinia pestis, including the neighboring genes, size, charge, and secondary structure, but the structures and/or functions of these proteins remain to be determined. Although a BLAST search with CT670 did not identify YscO as a related protein, our analysis indicated that these two proteins exhibit significant sequence similarity. In this paper, we report that the CT670 crystal, solved at a resolution of 2 Å, consists of a single coiled coil containing just two long helices. Gel filtration and analytical ultracentrifugation studies showed that in solution CT670 exists in both monomeric and dimeric forms and that the monomer predominates at lower protein concentrations. We examined the interaction of CT670 with many type III secretion system-related proteins (viz., CT091, CT665, CT666, CT667, CT668, CT669, CT671, CT672, and CT673) by performing bacterial two-hybrid assays. In these experiments, CT670 was found to interact only with the CT671 protein (YscP homolog), whose gene is immediately downstream of ct670. A specific interaction between CT670 and CT671 was also observed when affinity chromatography pull-down experiments were performed. These results suggest that CT670 and CT671 are putative homologs of the YcoO and YscP proteins, respectively, and that they likely form a chaperone-effector pair

Adar2 Mislocalization And Widespread Rna Editing Aberrations In C9Orf72-Mediated Als/Ftd

The hexanucleotide repeat expansion GGGGCC (G 4 C 2 ) n in the C9orf72 gene is the most common genetic abnormality associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Recent findings suggest that dysfunction of nuclear-cytoplasmic trafficking could affect the transport of RNA binding proteins in C9orf72 ALS/FTD. Here, we provide evidence that the RNA editing enzyme adenosine deaminase acting on RNA 2 (ADAR2) is mislocalized in C9orf72 repeat expansion mediated ALS/FTD. ADAR2 is responsible for adenosine (A) to inosine (I) editing of double-stranded RNA, and its function has been shown to be essential for survival. Here we show the mislocalization of ADAR2 in human induced pluripotent stem cell-derived motor neurons (hiPSC-MNs) from C9orf72 patients, in mice expressing (G 4 C 2 ) 149 , and in C9orf72 ALS/FTD patient postmortem tissue. As a consequence of this mislocalization we observe alterations in RNA editing in our model systems and across multiple brain regions. Analysis of editing at 408,580 known RNA editing sites indicates that there are vast RNA A to I editing aberrations in C9orf72-mediated ALS/FTD. These RNA editing aberrations are found in many cellular pathways, such as the ALS pathway and the crucial EIF2 signaling pathway. Our findings suggest that the mislocalization of ADAR2 in C9orf72 mediated ALS/FTD is responsible for the alteration of RNA processing events that may impact vast cellular functions, including the integrated stress response (ISR) and protein translation