Data_Sheet_1.DOCX

<p>Cytophaga hutchinsonii is a gliding Gram-negative bacterium in the phylum Bacteroidetes with the capability to digest crystalline cellulose rapidly, but the mechanism is unclear. In this study, deletion of chu_0125, encoding a homolog of the peptidoglycan-associated lipoprotein (Pal), was determined to prevent degradation of the crystalline region of cellulose. We found that the chu_0125 deletion mutant grew normally in regenerated amorphous cellulose medium but displayed defective growth in crystalline cellulose medium and increased the degree of crystallinity of Avicel. The endoglucanase and β-glucosidase activities on the cell surface were reduced by 60 and 30% without chu_0125, respectively. Moreover, compared with the wild type, the chu_0125 deletion mutant was found to be more sensitive to some harmful compounds and to release sixfold more outer membrane vesicles (OMVs) whose protein varieties were dramatically increased. These results indicated that CHU_0125 played a critical role in maintaining the integrity of the outer membrane. Further study showed that the amounts of some outer membrane proteins were remarkably decreased in the chu_0125 deletion mutant. Western blotting revealed that CHU_3220, the only reported outer membrane protein that was necessary and specialized for degradation of the crystalline region of cellulose, was largely leaked from the outer membrane and packaged into OMVs. We concluded that the deletion of chu_0125 affected the integrity of outer membrane and thus influenced the localization of some outer membrane proteins including CHU_3220. This might be the reason why deletion of chu_0125 prevented degradation of the crystalline region of cellulose.</p

Additional file 5: of Direct measurement of pervasive weak repression by microRNAs and their role at the network level

Figure S3. Cumulative distribution of mRNA decay rates of with or without AU-rich, GU-rich and U-rich elements in 3’UTR, 5’UTR, Intron, Exon, and CDS simultaneously in (a) the WT and (b) KO line. AU-rich, GU-rich and U-rich element: ATTTA, AWTAAA, GTTTG, TTTGTTT, WTTTW, WWTTTWW, WWWTTTWWW, WWWWTTTWWWW, and WWWWWTTTWWWWW. W: A/U. P values are from Wilcoxon rank sum tests. (TIF 98 kb

Additional file 8: of Direct measurement of pervasive weak repression by microRNAs and their role at the network level

Figure S5. The relationship between the decay rate calculated by qRT-PCR and mRNA-seq. RP49 is used as the reference. (TIF 72 kb

Additional file 7: of Direct measurement of pervasive weak repression by microRNAs and their role at the network level

Figure S4. (a-c) Distribution of the equilibrium expression and degradation change of 3’UTR targets conserved between D. melanogaster and D. yakuba. Targets’ degradation rates were normalized by the mode of the background decay rate. The median of equilibrium expression value is 15.3 for WT and 16.4 for KO. The median of degradation rate is 1.19 for WT and 1.14 for KO. (a) The cumulative distribution of equilibrium expression change. (b) The cumulative distribution of degradation change. (c) The contour distribution of miR310s targets’ degradation between WT and KO. The red dot on the contour plot marks the densest point (1.04, 0.92). (TIF 212 kb

Additional file 9: of Direct measurement of pervasive weak repression by microRNAs and their role at the network level

Table S4. Real-time polymerase chain reaction primers used for mRNA quantification. (PDF 198 kb

Additional file 6: of Direct measurement of pervasive weak repression by microRNAs and their role at the network level

Table S3. The decay rates of three targets that belong to the RNA binding protein (RBP) family. (PDF 196 kb

Additional file 3: of Direct measurement of pervasive weak repression by microRNAs and their role at the network level

Table S1. Relating mRNA stability to gene function using a Gene Ontology (GO) analysis in the WT line (the 200 least stable genes). (PDF 133 kb

Additional file 4: of Direct measurement of pervasive weak repression by microRNAs and their role at the network level

Table S2. Relating mRNA stability to gene function using a Gene Ontology (GO) analysis in the WT line (the 200 most stable genes). (PDF 163 kb

Additional file 2: of Direct measurement of pervasive weak repression by microRNAs and their role at the network level

Figure S2. Half-lives of whole transcripts in D. melanogaster third instar larvae. (TIF 157 kb

Additional file 1: of Direct measurement of pervasive weak repression by microRNAs and their role at the network level

Figure S1. Correlation of all transcript and target expression (log2 transformed) between two biological replicates at 0 h, 2 h, 4 h, and 8 h. (a-d) results from the WT line, (e-h) results from the KO line. (TIF 368 kb