Mitochondrial genome evolution in the <i>Saccharomyces sensu stricto</i> complex - Fig 4

<p>(A) The nucleotide identities of all mitochondrial genes in the <i>Saccharomyces sensu stricto</i> group. The nucleotide identity was calculated based on the proportion of completely conserved nucleotides in multiple sequence alignments of five <i>SSS</i> yeasts conducted using ClustalOmega. The red bars represent protein-coding genes; the green bar is rRNA; the gray bar is tRNA and the yellow bar is <i>rpm1</i>. (B) Comparison of amino-acid identities among nuclear proteins, nuclear MT proteins and mitochondrial proteins. We identified 3,887 nuclear proteins which are present in all five <i>SSS</i> yeasts. Among them, 618 proteins were located in the mitochondria. The amino-acid identity for each protein was calculated based on the proportion of completely conserved amino-acid residues in the multiple sequences alignment (MSA) results. The dark blue, green and yellow bars represent the distribution of nuclear proteins, nuclear MT proteins and mitochondrial proteins, respectively. The table insert indicates the number of proteins which have identities greater than 90% in three protein sets. The <i>p</i>-values were calculated based on a hypergeometric test whether the number of MT proteins with high identity was significantly greater than those in the other two protein sets. (C) Box-plot comparisons of the dN/dS ratios estimated for the eight MT protein-coding genes between the genus <i>Lachancea</i> and the <i>Saccharomyces sensu stricto</i> linage.</p

The distribution of introns in mtDNAs.

<p><b>(A) <i>cox1</i> gene; (B) <i>cob</i> gene (C) <i>rnl</i> gene.</b> The X axis represents the gene length and the vertical lines indicate the position of introns. The numbers on top represent the relative location of each intron in different yeasts. The rectangular frames indicate Group II introns, which include introns 1, 2 and 10 in <i>cox1</i>, and intron 3 in <i>cob</i>. The triangular frames indicate the Group I introns. The filled frames indicate the introns with embedded ORFs, and the empty frames indicate introns without ORFs.</p

Evolution of gene order within the <i>Saccharomyces sensu stricto</i> group.

<p>Block1 includes <i>rnl</i>, <i>tRNAs</i> (T2,C,H,L,Q,K,R1,G,D,S1,R2,A,I,Y,N,M1) and <i>cox2</i>. Block2 includes <i>tRNAs</i> (F,T1,V), and <i>cox3</i>. Block3 includes <i>tRNA</i> (M2), <i>rpm1</i> and <i>tRNA</i> (P). Block4 includes <i>cox1</i>, <i>atp8</i> and <i>atp6</i>. Block5 includes <i>tRNA</i> (E) and <i>cob</i>. Block6 includes <i>rns</i> and <i>tRNA</i> (W). Block7 includes <i>atp9</i>, <i>tRNA</i> (S2) and <i>var1</i>. The downward and upward black arrows indicate the <i>ori</i> sequences in the positive and negative strands, respectively. The dashed arrows indicate that the <i>ori</i> sequences contain intervening GC clusters.</p

MOESM1 of Development of a modularized two-step (M2S) chromosome integration technique for integration of multiple transcription units in Saccharomyces cerevisiae

Additional file 1: Table S1. The sequence of various promoter. Table S2. The sequence of various terminators. Table S3. L sequence. Table S4. The integration locus of chromosome. Table S5. PCR primers used in this work. Table S6. The sequence of integration locus (site2). Figure S1. The diagrams of promoter plasmids (Circular Display). Figure S2. The diagrams of terminator plasmids (linear display). Figure S3. The diagrams of integration locus (site1) plasmids. Figure S4. The transformants of β-carotene on SC-Ura solid medium

The distribution and new functions of PKs.

(A) The distribution of PKs across the tree of life, as referenced in Jillian F. Banfield’s study [38]. The blue color in pie chart represents species with PKs present in all genome sequenced species. (B) The catalytic activity of PKs from different species on different substrates. The displayed 7 PKs not only exhibited activity on F6P or Xu5P, but also demonstrated the ability to convert short-chain ketoses into AcP. The corresponding table on the right represents the catalytic activity of these 7 candidate PKs on 6 classes of ketose or ketose phosphate. Each color represents to a specific enzyme activity (U/mg). Detailed catalytic activity data are shown in S1 Table. The raw data was listed in S1 Data. AcP, acetyl-phosphate; F6P, fructose-6-phosphate; PK, phosphoketolase; Xu5P, xylulose-5-phosphate.</p

High-throughput screening of BbPK for glycolaldehyde (GALD).

The x-axis labels represent the selected location in the BbPK. The y-axis labels represent the relative catalytic activities of the different mutants. Relative activity was defined as the ratio of the reduction of substrate for mutants to that of the wild type. The raw data was listed in S1 Data. (TIF)</p

The raw image for S19 Fig.

The canonical glycolysis pathway is responsible for converting glucose into 2 molecules of acetyl-coenzyme A (acetyl-CoA) through a cascade of 11 biochemical reactions. Here, we have designed and constructed an artificial phosphoketolase (APK) pathway, which consists of only 3 types of biochemical reactions. The core enzyme in this pathway is phosphoketolase, while phosphatase and isomerase act as auxiliary enzymes. The APK pathway has the potential to achieve a 100% carbon yield to acetyl-CoA from any monosaccharide by integrating a one-carbon condensation reaction. We tested the APK pathway in vitro, demonstrating that it could efficiently catabolize typical C1-C6 carbohydrates to acetyl-CoA with yields ranging from 83% to 95%. Furthermore, we engineered Escherichia coli stain capable of growth utilizing APK pathway when glycerol act as a carbon source. This novel catabolic pathway holds promising route for future biomanufacturing and offering a stoichiometric production platform using multiple carbon sources.</div

Calculated energy profiles for the forming process of 2-α, β-dihydroxyethylidene-ThDP (DHEThDP) from short-chain ketoses.

(A) The energy profiles for 1,3-dihydroxyacetone. (B) The energy profiles for D-erythrulose. (C) The energy profiles for L-erythrulose. Energies are given in kilocalories per mole. Note: After adding the large basis set, solvation, and zero-point energy corrections, the energies of TS2 for 1, 3-dihydroxyacetone and D-erythrulose were calculated to be lower than those of int1. Therefore, intramolecular proton transfer of 1,3-dihydroxyacetone and D-erythrulose can be assumed to be barrierless or to occur with very low barriers. (TIF)</p

Optimized structures of the transition states and intermediate involved in the forming process of DHEThDP from D-erythrulose.

The key bond distances change is shown in the figure. Selected distances are given in Å. The distances between C2 of ThDP and carbonyl C of substrate changes from 3.1 Å in Reactant (R) to 2.2 Å in transition state 1 (TS1). The distance between O and H changes from 1.6 Å in intermediate 1 (int1) to 1.2 Å in TS2. The distance of C2 and C3 of substrate changes from 2.1 Å in TS3 to 4.2 Å in int3. (TIF)</p

The docking results of different substrates in PK.

The PK was shown in cartoon and colored gray. The ThDP, ligands, and 2 key residues R442 and K605 were shown in stick. The C, N, O, P, and S atoms were colored green, blue, red, orange, and yellow, respectively. The distance between the substrates and ThDP and the distances between the phosphate moiety of substrates and the key basic residues were shown as dashed lines. Selected distances are given in Å. (TIF)</p