KEGG pathway analysis.

(DOCX)</p

Proteomic analysis of EVs from uninfected and baculovirus infected <i>Tnms42</i> cells.

(A) The volcano plot shows differentially abundant proteins in EVs from infected compared to uninfected cells. The horizontal dashed grey line represents the set significance threshold (> 15) and significantly differentially abundant proteins are highlighted in black. (B) The bar chart shows the KEGG pathway analysis and the number of matched objects for the top 15 categories with the most matched objects, including metabolic pathways, endocytosis and signalling pathways.</p

Schematic overview of the employed EV isolation protocol.

Tnms42 cells were grown uninfected and infected with baculovirus at MOI 5 in parallel. EVs were isolated from conditioned media 48 hpi. Several low-speed centrifugation steps eliminated cells, cell debris and large vesicles. A filtration step was applied to additionally clarify the conditioned media. Via ultracentrifugation EVs were first caught in a sucrose cushion, washed, and pelleted via another ultracentrifugation step.</p

Comparison proteins in EVs.

(XLSX)</p

Protein identification and quantification.

(XLSX)</p

Fermentation of <i>L</i>. <i>buchneri</i> CD034 grown under aerobic and anaerobic conditions.

<p>The fermentation was separated in three phases: phase 1 represents aerobic, phase 2 anaerobic and phase 3 again aerobic conditions with respect to the oxygen concentration of the gas inlet (O_2,in). (A) Gas phase composition during fermentation as described by oxygen and carbon dioxide concentrations in the gas inlet (O_2,in, CO_2,in) and in the gas outlet (O_2,out, CO_2,out). (B) pH, dissolved oxygen concentration in the medium (dO₂) and optical density (OD). (C) Concentration of carbohydrates glucose, xylose and arabinose and (D) concentration of organic acids lactate and acetate. Fermentations were performed in duplicates. Arrows indicate sampling time points for RNA-Seq. Parameters shown originate from fermenter 1. For fermenter 2 see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134149#pone.0134149.s001" target="_blank">S1 Fig</a>.</p

Genes of <i>L</i>. <i>buchneri</i> CD034 found to be highly¹ up-regulated under aerobic <i>vs</i>. anaerobic conditions.

<p>¹ fold change > 2</p><p>² genes related to bacteriophages are not shown.</p><p>³ Reads per kilobase of transcript per million mapped reads.</p><p>Genes of <i>L</i>. <i>buchneri</i> CD034 found to be highly<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134149#t003fn001" target="_blank">¹</a> up-regulated under aerobic <i>vs</i>. anaerobic conditions.</p

Volcano plot representing transcriptional levels for <i>L</i>. <i>buchneri</i> CD034 genes under aerobic <i>vs</i>. anaerobic conditions.

<p>For each protein encoding gene the −log₂(p-value) is plotted against its log₂(fold change). Genes up-regulated (p < 0.01) under aerobic conditions are colored blue while down-regulated genes are colored red. Genes found to be located between bacteriophagous attachment sites are colored in yellow (<i>ΦLbu-1</i>) and orange (<i>ΦLbu-2</i>) irrespective of their relative transcriptional levels. For genes with gene names that were found to be highly up- (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134149#pone.0134149.t003" target="_blank">Table 3</a>) or down- (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134149#pone.0134149.t004" target="_blank">Table 4</a>) regulated the gene name is given. Abbreviations represent gene names: <i>pox2</i>, <i>-3</i>: pyruvate oxidase; <i>lctO</i>: lactate oxidase; <i>hsp1</i>, <i>-2</i>: molecular chaperones; <i>oppA3</i>: oligopeptide transport system, substrate binding protein; <i>arcC3</i>: carbamate kinase; <i>aguA1</i>: agmatine deiminase; <i>pctA</i>: putrescine carbamoyltransferase; <i>gntP</i>: H+/gluconate symporter; <i>gntR</i>: gluconate operon transcriptional regulator; <i>gntK1</i>: gluconokinase; <i>pyrG</i>: CTP synthetase; <i>rihB</i>: ribosylpyrimidine nucleosidase; <i>pgd</i>: 6-phosphogluconate dehydrogenase; <i>adhA</i>: alcohol dehydrogenase; <i>hisD</i>: histidinol dehydrogenase; <i>tagG</i>: teichoic acid permease; <i>tagB</i>, teichoic acid biosynthesis protein; <i>argH</i>: argininosuccinate lyase; <i>nupC</i>: pyrimidine specific nucleoside symporter. For genes lacking gene names the index numbers of their respective locus tags (LBUCD034_XXXX) are given.</p