Phylogenetic and functional analysis of the Cation Diffusion Facilitator (CDF) family: improved signature and prediction of substrate specificity-0

<p><b>Copyright information:</b></p><p>Taken from "Phylogenetic and functional analysis of the Cation Diffusion Facilitator (CDF) family: improved signature and prediction of substrate specificity"</p><p>http://www.biomedcentral.com/1471-2164/8/107</p><p>BMC Genomics 2007;8():107-107.</p><p>Published online 23 Apr 2007</p><p>PMCID:PMC1868760.</p><p></p>t. Amino acid position refers to PtdMTP1. The hypothetical secondary structure (TMDs II and III) is shown below

Phylogenetic and functional analysis of the Cation Diffusion Facilitator (CDF) family: improved signature and prediction of substrate specificity-1

<p><b>Copyright information:</b></p><p>Taken from "Phylogenetic and functional analysis of the Cation Diffusion Facilitator (CDF) family: improved signature and prediction of substrate specificity"</p><p>http://www.biomedcentral.com/1471-2164/8/107</p><p>BMC Genomics 2007;8():107-107.</p><p>Published online 23 Apr 2007</p><p>PMCID:PMC1868760.</p><p></p>SD) until O.D. = 1. Serial dilutions were spotted on SD or on SD + 15 mM ZnCl(15 mM Zn). Photographs were taken after 6 days of growth at 30°C. For each mutation different yeast transformants were used and gave the same results. The amino acid substitutions along with their topological positions are shown on the left. EV: empty vector; PtdMTP1: wild type protein

Phylogenetic and functional analysis of the Cation Diffusion Facilitator (CDF) family: improved signature and prediction of substrate specificity-3

<p><b>Copyright information:</b></p><p>Taken from "Phylogenetic and functional analysis of the Cation Diffusion Facilitator (CDF) family: improved signature and prediction of substrate specificity"</p><p>http://www.biomedcentral.com/1471-2164/8/107</p><p>BMC Genomics 2007;8():107-107.</p><p>Published online 23 Apr 2007</p><p>PMCID:PMC1868760.</p><p></p>) regions are indicated for each cluster. When more than one metal is transported, the metal preference is reflected by the written order within these metals. For each group and for Zrg17-like and ZnT9-like clusters logos showing the conserved residues in TMDs II and V are shown on the right. A simplified phylogenetic tree representation, expressed as a dendogram using Zrg17-like cluster as outgroup, is shown on the left. B. Montanini, D. Blaudez, M. Chalot, unpublished data; D. Blaudez, M. Chalot, unpublished data; assessed by heterologous complementation; deduced by mutant phenotype or over-expression in homologous system; measured in reconstituted proteoliposomes or in everted membrane vesicles; indirect evidence; measured in oocytes; by referring to the CDF domain

Phylogenetic and functional analysis of the Cation Diffusion Facilitator (CDF) family: improved signature and prediction of substrate specificity-2

<p><b>Copyright information:</b></p><p>Taken from "Phylogenetic and functional analysis of the Cation Diffusion Facilitator (CDF) family: improved signature and prediction of substrate specificity"</p><p>http://www.biomedcentral.com/1471-2164/8/107</p><p>BMC Genomics 2007;8():107-107.</p><p>Published online 23 Apr 2007</p><p>PMCID:PMC1868760.</p><p></p>ith respect to metal specificity: blue is for zinc, green for iron/zinc, violet for manganese and brown for unknown specificity. The three CDF groups are surrounded with coloured boxes with the same colour-code. Bootstrap values are indicated for each cluster. The scale bar indicates an evolutionary distance of 0.1 amino acid substitution per site

Primer pairs, PCR conditions, and peptide nucleic acid clamps affect fungal diversity assessment from plant root tissues

High-throughput sequencing has become a prominent tool to assess plant-associated microbial diversity. Still, some technical challenges remain in characterising these communities, notably due to plant and fungal DNA co-amplification. Fungal-specific primers, Peptide Nucleic Acid (PNA) clamps, or adjusting PCR conditions are approaches to limit plant DNA contamination. However, a systematic comparison of these factors and their interactions, which could limit plant DNA contamination in the study of plant mycobiota, is still lacking. Here, three primers targeting the ITS2 region were evaluated alone or in combination with PNA clamps both on nettle (Urtica dioica) root DNA and a mock community. PNA clamps did not improve the richness or diversity of the fungal communities but increased the number of fungal reads. Among the tested factors, the most significant was the primer pair. Specifically, the 5.8S-Fun/ITS4-Fun pair exhibited a higher OTU richness but fewer fungal reads. Our study demonstrates that the choice of primers is critical for limiting plant and fungal DNA co-amplification. PNA clamps increase the number of fungal reads when ITS2 is targeted but do not result in higher fungal diversity recovery at high sequencing depth. At lower read depths, PNA clamps might enhance microbial diversity quantification for primer pairs lacking fungal specificity.</p