Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen <i>Pectobacterium atrosepticum</i>

BACKGROUND: Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Enterobacteriaceae (SRE) group of pathogens. Although the main ecological niches for these pathogens are plants, a significant part of their life cycle is undertaken outside their host within adverse soil environment. However, the mechanisms of SRE adaptation to this harsh nutrient-deficient environment are poorly understood. RESULTS: In the study reported herein, by using strand-specific RNA-seq analysis and in silico sRNA predictions, we describe the sRNA pool of Pectobacterium atrosepticum and reveal numerous sRNA candidates, including those that are induced during starvation-activated stress responses. Consequently, strand-specific RNA-seq enabled detection of 137 sRNAs and sRNA candidates under starvation conditions; 25 of these sRNAs were predicted for this bacterium in silico. Functional annotations were computationally assigned to 68 sRNAs. The expression of sRNAs in P. atrosepticum was compared under growth-promoting and starvation conditions: 68 sRNAs were differentially expressed with 47 sRNAs up-regulated under nutrient-deficient conditions. Conservation analysis using BLAST showed that most of the identified sRNAs are conserved within the SRE. Subsequently, we identified 9 novel sRNAs within the P. atrosepticum genome. CONCLUSIONS: Since many of the identified sRNAs are starvation-induced, the results of our study suggests that sRNAs play key roles in bacterial adaptive response. Finally, this work provides a basis for future experimental characterization and validation of sRNAs in plant pathogens. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2376-0) contains supplementary material, which is available to authorized users

Rhizobium pongamiae sp. nov. from Root Nodules of Pongamia pinnata

Pongamia pinnata has an added advantage of N2-fixing ability and tolerance to stress conditions as compared with other biodiesel crops. It harbours “rhizobia” as an endophytic bacterial community on its root nodules. A gram-negative, nonmotile, fast-growing, rod-shaped, bacterial strain VKLR-01T was isolated from root nodules of Pongamia that grew optimal at 28°C, pH 7.0 in presence of 2% NaCl. Isolate VKLR-01 exhibits higher tolerance to the prevailing adverse conditions, for example, salt stress, elevated temperatures and alkalinity. Strain VKLR-01T has the major cellular fatty acid as C18:1  ω7c (65.92%). Strain VKLR-01T was found to be a nitrogen fixer using the acetylene reduction assay and PCR detection of a nifH gene. On the basis of phenotypic, phylogenetic distinctiveness and molecular data (16S rRNA, recA, and atpD gene sequences, G + C content, DNA-DNA hybridization etc.), strain VKLR-01T = (MTCC 10513T = MSCL 1015T) is considered to represent a novel species of the genus Rhizobium for which the name Rhizobium pongamiae sp. nov. is proposed. Rhizobium pongamiae may possess specific traits that can be transferred to other rhizobia through biotechnological tools and can be directly used as inoculants for reclamation of wasteland; hence, they are very important from both economic and environmental prospects

Identification of two genes encoding microsomal oleate desaturases (FAD2) from the biodiesel plant Pongamia pinnata L.

Key message: The current study dissect microsomal oleate desaturase genes having differential expression pattern with respect to temperature from the seeds ofPongamia pinnata,and are grouped with other legumes and biofuel plants. Abstract: Biofuel often is available as plant oil or products derived thereafter, such as biodiesel. In view of the anticipated fossil fuel shortage, the biochemical and genetic basis of vegetable oil biosynthesis is vital. We are focusing on the versatile oil-yielding legume tree Pongamia pinnata. Microsomal oleate desaturase (FAD2) is the key enzyme responsible for the production of linoleic acid in non-photosynthetic tissues. This work reports on the isolation of two full length cDNA clones, tissue expression and copy number detection of Pongamia FAD2 genes, and also on the transcriptional regulation at low and high temperatures. The deduced amino acid sequences of both PpFAD2 proteins share 83\ua0% identity and display three typical histidine boxes that are characteristics of all membrane-bound microsomal oleate desaturases. Both sequences possess aromatic amino acid containing sequence motifs at the C-terminal end necessary for maintaining endoplasmic reticulum (ER) localization. Southern blot analysis is consistent with the presence of at least two copies of FAD2 in the pongamia genome. Quantitative real-time PCR analysis showed that PpFAD2-1 is expressed strongly in developing seeds and, showing very low levels of expression in vegetative tissues, whereas PpFAD2-2 is constitutively expressed in both vegetative tissues and the developing seeds, with higher transcript levels in roots, stems and leaves. In response to low temperature stress PpFAD2-1 and PpFAD2-2 were differentially expressed in various tissues. The PpFAD2-2 transcript dramatically decreased in roots, stems and leaves under low temperatures, whereas PpFAD2-1 showed a significant increase in these tissues