Abstract
The genus Herbaspirillum includes several strains isolated from different grasses. The identification of non-coding RNAs (ncRNAs) in the genus Herbaspirillum is an important stage studying the interaction of these molecules and the way they modulate physiological responses of different mechanisms, through RNA–RNA interaction or RNA–protein interaction. This interaction with their target occurs through the perfect pairing of short sequences (cis-encoded ncRNAs) or by the partial pairing of short sequences (trans-encoded ncRNAs). However, the companion Hfq can stabilize interactions in the trans-acting class. In addition, there are Riboswitches, located at the 5′ end of mRNA and less often at the 3′ end, which respond to environmental signals, high temperatures, or small binder molecules. Recently, CRISPR (clustered regularly interspaced palindromic repeats), in prokaryotes, have been described that consist of serial repeats of base sequences (spacer DNA) resulting from a previous exposure to exogenous plasmids or bacteriophages. We identified 285 ncRNAs in Herbaspirillum seropedicae (H. seropedicae) SmR1, expressed in different experimental conditions of RNA-seq material, classified as cis-encoded ncRNAs or trans-encoded ncRNAs and detected RNA riboswitch domains and CRISPR sequences. The results provide a better understanding of the participation of this type of RNA in the regulation of the metabolism of bacteria of the genus Herbaspirillum spp.
Highlights
The genus Herbaspirillum was described by Baldani et al [1] and includes the Herbaspirillum seropedicae (H. seropedicae) species with several strains isolated from different grasses [1]
The computational tool Infernal 1.1.1 was employed for this study and the multiple covariance detection and sequence analysis had as its input the RNA family database (Rfam, available link http://rfam.xfam.org/; accessed on 18 February 2016), while the prediction of the 16 species of non-coding sRNAs (ncRNAs) made up the genus Herbaspirillum spp., as shown in Supplementary Material S1
The genomes of H. seropedicae SmR1, H. seropedicae Z67, H. lusitanum P6-12, H. hiltneri, H. frisingense GSF30 N3, Herbaspirillum spp. strain B65, H. rubrisubalbicans M1, H. autotrophicum IAM 14942, H. huttiense subsp. putei, Herbaspirillum spp. strain B501, Herbaspirillum spp. strain GW103, Herbaspirillum spp. strain RV1423, H. rhizosphaerae UMS-37, H. rubrisubalbicans spp. strain Os34, H. rubrisubalbicans spp. strain Os45, and Herbaspirillum AU14040 were obtained from the database of the National Center for Biotechnology Information (NCBI) search
Summary
The genus Herbaspirillum was described by Baldani et al [1] and includes the Herbaspirillum seropedicae (H. seropedicae) species with several strains isolated from different grasses [1]. Herbaspirillum seropedicae is characterized by fixing nitrogen (diazotrophic) and colonizing plants. A second diazotrophic species, Pseudomonas rubrisubalbicans, was reclassified under the name of Herbaspirillum rubrisubalbicans and has the ability to colonize plants [2]. From the 1990s, new species were included in the genus Herbaspirillum: H. autotrophicum Pseudomonas huttiense) [3] H. frisingense [4], H. lusitanum [5], H. cholorophenolicum [6], H. hiltneri [7], H. rhizosphaerae [8], H. aquaticum [9], H. massiliense [10], H. canariense, H. aurantiacum, and H. soli [11], and H. seropedicae AU14040 [12]. The H. putei species was reclassified as H. huttiense subspecies putei [9]
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