MOESM6 of A bacterial negative transcription regulator binding on an inverted repeat in the promoter for epothilone biosynthesis

Additional file 6: Table S4. Primers used in RT-qPCR

MOESM2 of A bacterial negative transcription regulator binding on an inverted repeat in the promoter for epothilone biosynthesis

Additional file 2: Table S1. Homologous amino acid sequences of Esi protein

MOESM4 of A bacterial negative transcription regulator binding on an inverted repeat in the promoter for epothilone biosynthesis

Additional file 4: Table S2. Strains and plasmids used in this study

MOESM1 of A bacterial negative transcription regulator binding on an inverted repeat in the promoter for epothilone biosynthesis

Additional file 1: Figure S1. The ramachandran plot of the Esi structure model, which showed 80.6% residues in favored region, 13.5% residues in allowed region, 5.9% residues in outlier region

MOESM5 of A bacterial negative transcription regulator binding on an inverted repeat in the promoter for epothilone biosynthesis

Additional file 5: Table S3. Primers used in construction of vectors and mutant strains

Mechanisms Involved in the Functional Divergence of Duplicated GroEL Chaperonins in <em>Myxococcus xanthus</em> DK1622

<div><p>The gene encoding the GroEL chaperonin is duplicated in nearly 30% of bacterial genomes; and although duplicated <i>groEL</i> genes have been comprehensively determined to have distinct physiological functions in different species, the mechanisms involved have not been characterized to date. <i>Myxococcus xanthus</i> DK1622 has two copies of the <i>groEL</i> gene, each of which can be deleted without affecting cell viability; however, the deletion of either gene does result in distinct defects in the cellular heat-shock response, predation, and development. In this study, we show that, from the expression levels of different <i>groELs</i>, the distinct functions of <i>groEL1</i> and <i>groEL2</i> in predation and development are probably the result of the substrate selectivity of the paralogous GroEL chaperonins, whereas the lethal effect of heat shock due to the deletion of <i>groEL1</i> is caused by a decrease in the total <i>groEL</i> expression level. Following a bioinformatics analysis of the composition characteristics of GroELs from different bacteria, we performed region-swapping assays in <i>M. xanthus</i>, demonstrating that the differences in the apical and the C-terminal equatorial regions determine the substrate specificity of the two GroELs. Site-directed mutagenesis experiments indicated that the GGM repeat sequence at the C-terminus of GroEL1 plays an important role in functional divergence. Divergent functions of duplicated GroELs, which have similar patterns of variation in different bacterial species, have thus evolved mainly via alteration of the apical and the C-terminal equatorial regions. We identified the specific substrates of strain DK1622's GroEL1 and GroEL2 using immunoprecipitation and mass spectrometry techniques. Although 68 proteins bound to both GroEL1 and GroEL2, 83 and 46 proteins bound exclusively to GroEL1 or GroEL2, respectively. The GroEL-specific substrates exhibited distinct molecular sizes and secondary structures, providing an encouraging indication for GroEL evolution for functional divergence.</p> </div

MOESM7 of Increasing on-target cleavage efficiency for CRISPR/Cas9-induced large fragment deletion in Myxococcus xanthus

Additional file 7: Table S2. Primers used in this study

Quantitative PCR analysis of the <i>groEL1</i> and <i>groEL2</i> expression levels and survival rates after heat shock at 42°C for 30 min.

<p>(A) Gene expression levels. (B) Survival rates after heat shock. The left panel is a schematic diagram of the <i>groELs</i> gene present in the different strains. The values for each <i>groEL</i> gene are shown as levels relative to the expression of <i>groEL1</i> in DK1622, which was defined as 100%. The survival rates of the different strains were calculated as a percentage of the survival rate of DK1622, which was 1.01×10⁻² after the heat shock treatment and was defined as 100%. The error bars show the standard deviation of three replicates. DK1622, wild-type strain; YL0301, <i>groEL1</i>-deletion mutant; YL0302, <i>groEL2</i>-deletion mutant; YL0901, YL0301 complemented with GroEL1; YL0902, YL0301 complemented with GroEL2; YL0906, YL0302 complemented with GroEL1; YL0907, YL0302 complemented with GroEL2. “c” denotes “complement.”</p

The predation of an <i>E. coli</i> mat by different strains.

<p>(A) The time for the different strains to reach the edge of the <i>E. coli</i> mat. (B) Zones of predation after 18 h and 36 h for the knockout and complemented mutants. DK1622, wild-type strain; YL0302, <i>groEL2</i>-deletion mutant; YL0906, YL0302 complemented with GroEL1; YL0907, YL0302 complemented with GroEL2; YL0908, YL0302 complemented with GroEL1-equatorial-N_GroEL2; YL0909, YL0302 complemented with GroEL1-apical_GroEL2; YL0910, YL0302 complemented with GroEL1-equatorial-C_GroEL2.</p

Optimal design through the sub-relaxation method: understanding the basic principles

This book provides a comprehensive guide to analyzing and solving optimal design problems in continuous media by means of the so-called sub-relaxation method. Though the underlying ideas are borrowed from other, more classical approaches, here they are used and organized in a novel way, yielding a distinct perspective on how to approach this kind of optimization problems. Starting with a discussion of the background motivation, the book broadly explains the sub-relaxation method in general terms, helping readers to grasp, from the very beginning, the driving idea and where the text is heading. In addition to the analytical content of the method, it examines practical issues like optimality and numerical approximation. Though the primary focus is on the development of the method for the conductivity context, the book’s final two chapters explore several extensions of the method to other problems, as well as formal proofs. The text can be used for a graduate course in optimal design, even if the method would require some familiarity with the main analytical issues associated with this type of problems. This can be addressed with the help of the provided bibliography