| Literature DB >> 25201548 |
Gamaliel López-Leal1, Maria Luisa Tabche, Santiago Castillo-Ramírez, Alfredo Mendoza-Vargas, Miguel A Ramírez-Romero, Guillermo Dávila.
Abstract
BACKGROUND: Regulation of transcription is essential for any organism and Rhizobium etli (a multi-replicon, nitrogen-fixing symbiotic bacterium) is no exception. This bacterium is commonly found in the rhizosphere (free-living) or inside of root-nodules of the common bean (Phaseolus vulgaris) in a symbiotic relationship. Abiotic stresses, such as high soil temperatures and salinity, compromise the genetic stability of R. etli and therefore its symbiotic interaction with P. vulgaris. However, it is still unclear which genes are up- or down-regulated to cope with these stress conditions. The aim of this study was to identify the genes and non-coding RNAs (ncRNAs) that are differentially expressed under heat and saline shock, as well as the promoter regions of the up-regulated loci.Entities:
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Year: 2014 PMID: 25201548 PMCID: PMC4167512 DOI: 10.1186/1471-2164-15-770
Source DB: PubMed Journal: BMC Genomics ISSN: 1471-2164 Impact factor: 3.969
Figure 1Stress responses following heat and saline shock in . Venn diagram showing how the over-expressed genes overlap for the heat shock and saline shock responses of R. etli. The arrows indicate the number of up-regulated and down-regulated genes in the conditions analysed. The intersection indicates the number of overlapping genes for both conditions.
Figure 2Chromosomal and plasmid genes are differentially expressed following heat and saline shock. Percentage of chromosomal and plasmid differentially expressed genes under A) heat shock and B) saline shock conditions.
Figure 3Replicon distribution of over-expressed genes following heat and saline shock. Proportions of the up-regulated gene contributions for each replicon. Axis labels correspond to: chromosome (Ch), plasmid pRet42a (pa), plasmid pRet42b (pb), plasmid pRet42c (pc), plasmid pRet42d (pd), plasmid pRet42e (pe), and plasmid pRet42f (pf). The proportions were obtained by normalising the number of up-regulated genes to the number of annotated genes for each replicon. *Indicates significant difference in the proportions of the up-regulated and down-regulated genes between the chromosome and plasmids (Two-sample for equality proportions with 99 percent confidence intervals).
Figure 4Differentially expressed genes grouped by COG functional classification. The fractions of the differentially expressed genes that fell within the various Clusters of Orthologous Gene (COG) categories. The columns are labelled as follows: C, energy production and conversion; D, cell division and chromosome partitioning; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme metabolism; I, lipid transport and metabolism; J, translation, ribosomal structure and biogenesis; K, transcription; L, DNA replication, recombination and repair; M, cell wall/membrane biogenesis; N, cell motility; O, posttranslational modification, protein turnover, chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolite biosynthesis, transport and catabolism; R, general function prediction only; S, function unknown; T, signal transduction mechanisms; U, intracellular trafficking and secretion; V, defence mechanisms; and Hy, hypothetical proteins. Each fraction was obtained by normalising the number of total of genes assigned to each COG group per condition. A) Up-regulated genes. B) Down-regulated genes.
Figure 5Promoter consensus motifs of . The sequence logos of three different sigma factors are shown. A) The logo shows the promoter consensus sequences for RpoH, as obtained from 107 putative promoters regions. B) The logo shows the promoter consensus sequences for RpoE, as obtained from 74 putative promoters regions. C) The logo shows the promoter consensus sequences for SigA, as obtained from 96 putative promoters regions (see Methods). The coloured sequence logos were generated using MEME. The scale of bits in each logo is represented by the height of each letter (nucleotide), showing the positional probability of that nucleotide multiplied by the information of the logo. The −35 box consensus motifs are displayed on the left side of the figure, and the −10 box consensus motifs are displayed on the right side of the figure. The 11 to 23-nt spacer region between the two boxes is not shown.
Novel ncRNAs detected by RNA-Seq plotted data
| Id | Start | Stop | Strand | Length | Prediction |
|---|---|---|---|---|---|
| ReC 101 | 672255 | 672116 | Minus | 140 bp | ncRNA |
| ReC 102 | 1331946 | 1331792 | Minus | 155 bp | ncRNA |
| ReC 103 | 1674693 | 1674827 | Plus | 135 bp | Protein |
| ReC 104 | 1747454 | 1747598 | Plus | 145 bp | ncRNA |
| ReC 105 | 1748816 | 1748663 | Minus | 154 bp | ncRNA |
| ReC 106 | 1749213 | 1748896 | Minus | 318 bp | Protein |
| ReC 107 | 1832463 | 1832580 | Plus | 118 bp | ncRNA |
| ReC 108 | 1839511 | 1839637 | Plus | 127 bp | ncRNA |
| ReC 109 | 1932797 | 1932959 | Plus | 163 bp | ncRNA |
| ReC 110 | 2475589 | 2475733 | Plus | 145 bp | Protein |
| ReC 111 | 2546193 | 2546004 | Minus | 190 bp | ncRNA |
| ReC 112 | 2763999 | 2764196 | Plus | 198 bp | ncRNA |
| ReC 113 | 2940023 | 2939896 | Minus | 128 bp | ncRNA |
| ReC 114 | 3416634 | 3416858 | Plus | 225 bp | Protein |
| ReC 115 | 3620823 | 3620581 | Minus | 243 bp | Protein |
| ReC 116 | 3634855 | 3634540 | Minus | 316 bp | Protein |
| ReC 117 | 3719937 | 3719559 | Minus | 379 bp | Protein |
| ReC 118 | 3776471 | 3776654 | Plus | 184 bp | ncRNA |
Table 1. Novel ncRNAs detected using the RNA-Seq plotted data. Eighteen transcribed regions were identified as novel ncRNAs or non-annotated proteins using Artemis (Graph, Add User Plot). The coordinates, strands and lengths of the ncRNAs and non-annotated proteins are shown (see the Methods section for more details).