Transcriptome analysis of cyst formation in Rhodospirillum centenum reveals large global changes in expression during cyst development.

Qian Dong,Carl E Bauer

doi:10.1186/s12864-015-1250-9

Abstract

BackgroundRhodospirillum centenum is a photosynthetic member of the Gram-negative Azospirillum clade members of which exhibit a complex developmental life-cycle featuring morphologically distinct cell types. Under periods of nutrient deprivation, replicative vegetative cells differentiate into metabolically dormant cysts that survive harsh environmental stresses such as desiccation. Encystment involves a multi-stage developmental process that includes the rounding of cells, production of large intracellular storage granules of poly-hydroxybutyrate (PHB) and the excretion of a protective exopolysaccharide coating that envelops dormant cysts.ResultsTo study the process of cyst development, we performed RNA-seq studies on cells that were induced to undergo cyst development. To assay for temporal changes in gene expression, RNA was extracted at 4, 24, 48, 72, 96 hours during development and subjected to deep sequence analysis. These results show that 812 genes exhibit log2 ≥ 1.5-fold changes in expression over a 96 hour cyst induction period demonstrating large global changes in gene expression during cyst development.ConclusionsNotable changes in expression occurred in numerous genes involved in cell wall and lipid biosynthesis, metabolic enzymes, and numerous regulatory genes such as histidine kinases and transcription factors. Many genes involved in protein synthesis and DNA replication were also significantly reduced during late stages of cyst development. Genes previously identified by genetic screens as being critical for cyst development also exhibited changes of expression during cyst induction. This study provides the first transcriptome profile of global changes in gene expression that occur during development of cysts in a Gram-negative species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1250-9) contains supplementary material, which is available to authorized users.

Highlights

Rhodospirillum centenum is a photosynthetic member of the Gram-negative Azospirillum clade members of which exhibit a complex developmental life-cycle featuring morphologically distinct cell types
Overview of the transcriptional profile and identification of differentially expressed genes by RNA-Seq As previously reported, R. centenum undergoes induction of cyst development when shifted from a complex nutrient rich growth medium (CENS) to a nutrient poor defined medium that uses butyrate as a sole carbon source (CENBA) [16]
Regarding R. centenum, the observed temporal changes in expression pattern of several sigma factor genes as identified in this study highly suggests that the cyst development process involves the use of sigma factors to control global changes in developmental gene expression

Summary

Introduction

Rhodospirillum centenum is a photosynthetic member of the Gram-negative Azospirillum clade members of which exhibit a complex developmental life-cycle featuring morphologically distinct cell types. Many bacteria survive unfavorable conditions by differentiating into metabolically quiescent resting stages, commonly referred to as cysts or spores [1]. Gram-positive spores display exceptional resistance to physical and chemical stresses such as desiccation, high temperatures (>100°C), radiation, oxidizing agents and pressure [3,6,7]. These spores arise from asymmetric cell division, which produces a prespore that becomes engulfed, matured, and released by lysis of the mother cell. Resting cysts produced by this group do not survive high temperatures and pressure but do provide resistance to desiccation and to moderate heat stress. As is typical of cysts produced by other Gram-negative genera, Dong and Bauer BMC Genomics (2015) 16:68 myxospores are only moderately resistant to heat (up to 60°C), as well as resistant to desiccation, sonication, UV-irradiation, detergents and enzymatic digestion [8]

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