MOESM1 of Molecular and catalytic properties of fungal extracellular cellobiose dehydrogenase produced in prokaryotic and eukaryotic expression systems

Additional file 1: Table S1. Purification schemes of recombinant CtDH/CtCDH. Table S2. Comparison of recombinant DH domain and intact CDHs from literatures. Figure S1. SDS-PAGE of recombinant CtDH expressed in E. coli. Figure S2. Thermostability of CtDH/CtCDHs measured by the tryptophan fluorescence (A-D) and the ThermoFAD method (E-H)

MOESM1 of Salt-responsive lytic polysaccharide monooxygenases from the mangrove fungus Pestalotiopsis sp. NCi6

Additional file 1. Production, purification and characterization of lytic polysaccharide monooxygenases secreted by Pestalotiopsis sp. NCi6

Overview of repeat contents of S. brevicaulis genome.

<p>*Some elements are fragmented hence; numbers are higher in some cases.</p><p>Overview of repeat contents of S. brevicaulis genome.</p

Summary of top 20 Pfam domains of <i>S</i>. <i>brevicaulis</i> genome encoded proteins.

<p>Full details of all Pfam domains are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140398#pone.0140398.s006" target="_blank">S3 Table</a>.</p

Summary of 18 identified gene clusters responsible for the production of different bioactive compounds in the assembled genome of <i>S</i>. <i>brevicaulis</i>.

<p>Gene clusters are numbered as C1-C18 followed by scaffold and positions on the scaffold and different colors are illustrating different types of clusters. Biosynthetic genes are key gene (like either nrps or pks and so on) and main supporting genes such as a cytochrome P450 gene as per antiSMASH [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140398#pone.0140398.ref048" target="_blank">48</a>] guidelines. Similarly, other genes are any other gene in the cluster, which are not key genes, regulatory (such as transcription factor or suppressor) and transporters (such as ABC transporter) and are marked in grey shade.</p

Summary of secondary metabolite encoding genes in the <i>S</i>. <i>brevicaulis</i> genome.

<p>*Only full length PKS genes are considered.</p><p>Summary of secondary metabolite encoding genes in the <i>S</i>. <i>brevicaulis</i> genome.</p

Top 10 expressed transporter genes.

<p>Top 10 expressed transporter genes.</p

Overview of de novo assembled genome assemblies of S. brevicaulis, produced using Roche 454, Illumina and Ion-torrent sequencing methods.

<p>*Length of the contig/scaffold until which sum of lengths of contigs/scaffolds are reached to 25%, 50% and 75% of total assembled genome size are called N25, N50 and N75 respectively.</p><p>#Sequence–Number of sequences (= contigs/scaffolds) in the assembled genome that constitute particular N25 or N50 or N75</p><p>Overview of de novo assembled genome assemblies of S. brevicaulis, produced using Roche 454, Illumina and Ion-torrent sequencing methods.</p

Summary of transporter genes of S. <i>brevicaulis</i> and their expression data.

<p><b>A.</b> Comparison of MFS type and sugar transporters from S. <i>brevicaulis</i> and <i>N</i>. <i>crassa</i>. This classification is based on TCDB [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140398#pone.0140398.ref040" target="_blank">40</a>] categories. <b>B.</b> Distribution of TCDB categories [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140398#pone.0140398.ref040" target="_blank">40</a>] according to the number of classified MFS type and sugar transporters of <i>S</i>. <i>brevicaulis</i>. <b>C.</b> Distribution of TCDB categories [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140398#pone.0140398.ref040" target="_blank">40</a>] according to the combined RPKMs of the assigned MFS type and sugar transporters. The size of each category is presented as percentage of the total number of RPKMs. All categories with less than two percent were grouped together (“other”). The respective values for these categories are presented enlarged in the bar to the right. SP Family (TCDB category: 2.A.1.1): The Sugar Porter Family; OFA Family (2.A.1.11): The Oxalate:Formate Antiporter Family; SHS Family (2.A.1.12): The Sialate:H⁺ Symporter Family; MCP Family (2.A.1.13): The Monocarboxylate Porter Family; ACS Family (2.A.1.14): The Anion:Cation Symporter Family; SIT Family (2.A.1.16): The Siderophore-Iron Transporter Family; OCT Family (2.A.1.19): The Organic Cation Transporter Family; DHA1 Family (2.A.1.2): The Drug:H⁺ Antiporter-1 (12 Spanner) Family; FLVCR Family (2.A.1.28): The Feline Leukemia Virus Subgroup C Receptor Family; DHA2 Family (2.A.1.3): The Drug:H⁺ Antiporter-2 (14 Spanner) Family; YnfM Family (2.A.1.36): The Acriflavin-sensitivity Family; LAT3 Family (2.A.1.44): The L-Amino Acid Transporter-3) Family; V-BAAT Family (2.A.1.48): The Vacuolar Basic Amino Acid Transporter Family; NAG-T Family (2.A.1.58): The N-Acetylglucosamine Transporter Family; UMF12 Family (2.A.1.63): The Unidentified Major Facilitator-12 Family; FHS Family (2.A.1.7): The Fucose: H⁺ Symporter Family; UMF23 Family (2.A.1.75): The Unidentified Major Facilitator-23 Family; NNP Family (2.A.1.8): The Nitrate/Nitrite Porter Family; PHS Family (2.A.1.9): The Phosphate: H⁺ Symporter Family; TDT Family (2.A.16): The Tellurite-resistance/Dicarboxylate Transporter Family; POT/PTR Family (2.A.17): The Proton-dependent Oligopeptide Transporter Family; GPH:Cation Symporter Family (2.A.2): The Glycoside-Pentoside-Hexuronide:Cation Symporter Family; CPA1 Family (2.A.36): The Monovalent Cation:Proton Antiporter-1 Family.</p

Overview of expressed genes in the RNA-Seq data of UV-mutant M26 of <i>S</i>. <i>brevicaulis</i>.

<p>¹ for details, see <b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140398#pone.0140398.s011" target="_blank">S8 Table</a></b></p><p>Expressed genes are classified into 10 tiers based on their RPKM value.</p