Comparative transcriptomics across the prokaryotic tree of life

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Recent whole-transcriptome sequencing reveals significant complexity in bacterial and archaeal transcriptomes.
• Abundant non-coding RNAs, cis-antisense transcripts, and regulatory untranslated regions (UTRs) present challenges in understanding microbial gene regulation.
• Distinguishing functional RNAs from 'transcriptional noise' is a key challenge in microbial genomics.

Purpose of the Study:

• To develop a searchable, comparative transcriptome resource for exploring conserved genetic elements across the microbial tree of life.
• To facilitate the identification and functional characterization of non-coding RNAs and regulatory regions in bacteria and archaea.
• To establish a standardized reference transcriptome for major microbial phyla.

Main Methods:

• Generation of comparative transcriptome maps for 18 model organisms spanning 10 bacterial and archaeal phyla/subphyla.
• Standardized RNA-sequencing (RNA-seq) methods were employed for all organisms.
• Development of a web server enabling BLAST-searchable comparisons of gene families and transcriptomic elements.

Main Results:

• The comparative transcriptome maps revealed conserved transcriptomic elements, including genes with exceptionally long 5' UTRs across multiple species.
• Identification of numerous known riboswitches and suggestion of novel putative regulatory elements associated with these long 5' UTRs.
• The resource provides a searchable collection of standardized reference transcriptomes for clinically and environmentally relevant microbial phyla.

Conclusions:

• Comparative transcriptome analysis is a powerful approach for uncovering conserved regulatory elements in microbial genomes.
• The developed web server and transcriptome collection provide a valuable framework for future studies of the microbial non-coding genome.
• This resource aids in understanding the functional significance of non-coding RNAs and regulatory UTRs in bacteria and archaea.