Summary of the characteristics, expression, the availability of mouse model, and association to cancers of B- and Y-family translesion synthesis polymerases.

<p>Summary of the characteristics, expression, the availability of mouse model, and association to cancers of B- and Y-family translesion synthesis polymerases.</p

DNA damage bypass process.

<p>(A) Mechanism of the 2-step DNA damage bypass process. To bypass DNA damage, REV1 inserts deoxycytidine triphosphates across the damage or orchestrates the recruitment of the other polymerases, POL ι, POL κ, POL η, to replicate across the damage. Thereafter, POL ζ complex can help extend beyond the damage to enable re-initiation of undamaged DNA replication. If an incorrect nucleotide gets incorporated across the damage, this misincorporated nucleotide will lead to a mutation in the next round of replication. (B) A schematic representing the protein domains of the Y-family translesion synthesis (TLS) polymerases, REV1, POL ι, POL κ, POL η.</p

Total Tn-seq read counts for all annotated S. meliloti genes

Table shows the total number of Illumina reads obtained for each S. meliloti gene for all tested conditions. The raw results are shown as observed and then the normalized read counts per gene are also included

All S. meliloti genes Tn-seq results highlighting all Tn insertions

The table shows all Tn insertions that have been observed by Illumina sequencing and their corresponding read counts for each condition. The dataset includes raw read counts for each Tn insertion as well as the normalized read counts. The dataset also includes the location of each transposon in each corresponding gene

NMR Structure and Dynamics of the C-Terminal Domain from Human Rev1 and Its Complex with Rev1 Interacting Region of DNA Polymerase η

Rev1 is a translesion synthesis (TLS) DNA polymerase essential for DNA damage tolerance in eukaryotes. In the process of TLS stalled high-fidelity replicative DNA polymerases are temporarily replaced by specialized TLS enzymes that can bypass sites of DNA damage (lesions), thus allowing replication to continue or postreplicational gaps to be filled. Despite its limited catalytic activity, human Rev1 plays a key role in TLS by serving as a scaffold that provides an access of Y-family TLS polymerases polη, ι, and κ to their cognate DNA lesions and facilitates their subsequent exchange to polζ that extends the distorted DNA primer–template. Rev1 interaction with the other major human TLS polymerases, polη, ι, κ, and the regulatory subunit Rev7 of polζ, is mediated by Rev1 C-terminal domain (Rev1-CT). We used NMR spectroscopy to determine the spatial structure of the Rev1-CT domain (residues 1157–1251) and its complex with Rev1 interacting region (RIR) from polη (residues 524–539). The domain forms a four-helix bundle with a well-structured N-terminal β-hairpin docking against helices 1 and 2, creating a binding pocket for the two conserved Phe residues of the RIR motif that upon binding folds into an α-helix. NMR spin-relaxation and NMR relaxation dispersion measurements suggest that free Rev1-CT and Rev1-CT/polη-RIR complex exhibit μs-ms conformational dynamics encompassing the RIR binding site, which might facilitate selection of the molecular configuration optimal for binding. These results offer new insights into the control of TLS in human cells by providing a structural basis for understanding the recognition of the Rev1-CT by Y-family DNA polymerases

Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium <i>Sinorhizobium meliloti</i>

<div><p>Bacterial genome evolution is characterized by gains, losses, and rearrangements of functional genetic segments. The extent to which large-scale genomic alterations influence genotype-phenotype relationships has not been investigated in a high-throughput manner. In the symbiotic soil bacterium <i>Sinorhizobium meliloti</i>, the genome is composed of a chromosome and two large extrachromosomal replicons (pSymA and pSymB, which together constitute 45% of the genome). Massively parallel transposon insertion sequencing (Tn-seq) was employed to evaluate the contributions of chromosomal genes to growth fitness in both the presence and absence of these extrachromosomal replicons. Ten percent of chromosomal genes from diverse functional categories are shown to genetically interact with pSymA and pSymB. These results demonstrate the pervasive robustness provided by the extrachromosomal replicons, which is further supported by constraint-based metabolic modeling. A comprehensive picture of core <i>S</i>. <i>meliloti</i> metabolism was generated through a Tn-seq-guided <i>in silico</i> metabolic network reconstruction, producing a core network encompassing 726 genes. This integrated approach facilitated functional assignments for previously uncharacterized genes, while also revealing that Tn-seq alone missed over a quarter of wild-type metabolism. This work highlights the many functional dependencies and epistatic relationships that may arise between bacterial replicons and across a genome, while also demonstrating how Tn-seq and metabolic modeling can be used together to yield insights not obtainable by either method alone.</p></div

Characteristics of the core genetic components of <i>S</i>. <i>meliloti</i>.

<p>(<b>A</b>) A circular plot of the <i>S</i>. <i>meliloti</i> chromosome is shown. From the outside to inside: positive strand coding regions, negative strand coding regions (for both positive and negative strands, red indicates the position of the core 489 growth promoting genes), total insertion density, and GC skew. The insertion density displays the total transposon insertions across all experiments over a 10,000-bp window. The GC skew was calculated over a 10,000-bp window, with green showing a positive skew and blue showing a negative skew. Tick marks are every 50,000 bp. (<b>B</b>) A comparison of the overlap between the growth promoting genome (Group I and II genes, shown first) and the essential genome (Group I genes, values in parentheses) of each Tn-seq dataset. Each dataset is labeled with the strain (wild-type or ΔpSymAB) and the growth medium (defined medium or rich medium). (<b>C</b>) Functional enrichment plots for the indicated gene sets. Name abbreviations: Fit–fitness; Dec–decrease; WT–wild-type; ΔAB—ΔpSymAB; Def–defined medium; Rich–rich medium. For example, ‘Fit. dec. WT def > rich' means the genes with a greater fitness decrease in wild-type grown in defined medium compared to rich medium. Legend abbreviations: AA–amino acid; Attach–attachment; Carb–carbohydrate; Cofact–cofactor; e-–electron; Met–metabolism; Misc–miscellaneous; Mot–motility; Nucl–nucleotide; Oxidoreduct–oxidoreductase activity; Prot–protein; Trans–transduction. (<b>D</b>-<b>F</b>) Scatter plots comparing the fitness phenotypes, shown as the log₁₀ of the GEI scores (Gene Essentiality Index scores; i.e., number of insertions within the gene divided by gene length in nucleotides) of (<b>D</b>) wild-type grown in rich medium versus wild-type grown in defined medium, (<b>E</b>) wild-type grown in rich medium versus ΔpSymAB grown in rich medium, and (<b>F</b>) wild-type grown in defined medium versus ΔpSymAB grown in defined medium.</p

Sample genes showing strain specific phenotypes.

<p>The top ten genes from each of the indicated groupings, as determined based on the ratio of GEI (Gene Essentiality Index) scores of the two strains, are shown. GEI scores are shown first for the wild-type (WT) followed by the scores for the ΔpSymAB (dAB) strain.</p

Gene essentiality index (GEI) changes for genes of selected biological pathways.

<p>Each data point represents an individual gene, and shows the log₁₀ of the ratio of the GEI for that gene in the ΔpSymAB background compared to the wild-type background. Lines indicate the median value of all genes included from the biological process. The underlying data is given in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007357#pgen.1007357.s012" target="_blank">S9 Table</a>. Genes included in each process are as follows: Cytochrome C oxidase related genes–<i>ctaB</i>, <i>ctaC</i>, <i>ctaD</i>, <i>ctaE</i>, <i>ctaG</i>, <i>ccsA</i>, <i>cycH</i>, <i>cycJ</i>, <i>cycK</i>, <i>cycL</i>, <i>ccmA</i>, <i>ccmB</i>, <i>ccmC</i>, <i>ccmD</i>, <i>ccmG</i>; Proline biosynthesis–<i>proA</i>, <i>proB1</i>, <i>proC</i>; Histidine biosynthesis–<i>hisB</i>, <i>hisD</i>, <i>smc04042</i>; Glycolysis and related genes–<i>glk</i>, <i>frk</i>, <i>pgi</i>, <i>zwf</i>, <i>pgl</i>, <i>edd</i>, <i>eda2</i>, <i>gap</i>, <i>pgk</i>, <i>gpmA</i>, <i>eno</i>, <i>pykA</i>, <i>pyc</i>; Periplamic cyclic β-glucan biosynthesis–<i>feuN</i>, <i>feuP</i>, <i>feuQ</i>, <i>ndvA</i>, <i>ndvB</i>; Arginine biosynthesis–<i>argB</i>, <i>argC</i>, <i>argD</i>, <i>argF1</i>, <i>argG</i>, <i>argH1</i>, <i>argJ</i>; AICAR biosynthesis–<i>purB</i>, <i>purC</i>, <i>purD</i>, <i>purE</i>, <i>purF</i>, <i>purH</i>, <i>purK</i>, <i>purL</i>, <i>purM</i>, <i>purN</i>, <i>purQ</i>, <i>smc00494</i>; UMP biosynthesis–<i>carA</i>, <i>carB</i>, <i>pyrB</i>, <i>pyrC</i>, <i>pyrD</i>, <i>pyrE</i>, <i>pyrF</i>, <i>smc01361</i>; LPS core oligosaccharide biosynthesis–<i>lpsC</i>, <i>lpsD</i>, <i>lpsE</i>.</p

Summary schematic of core <i>S</i>. <i>meliloti</i> metabolism.

<p>The iGD726 core metabolic model was visualized using the iPath v2.0 webserver [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007357#pgen.1007357.ref083" target="_blank">83</a>], which maps the reactions of the metabolic model to KEGG metabolic pathways; it therefore does not capture metabolism not present in the KEGG pathways included in iPath. Reactions and metabolites are color coded according to their biological role, as indicated. Reactions whose associated genes were not identified as growth promoting in this study are in dashed lines.</p