Insights from the architecture of the bacterial transcription apparatus

Abstract

We provide a portrait of the bacterial transcription apparatus in light of the data emerging from structural studies, sequence analysis and comparative genomics to bring out important but underappreciated features. We first describe the key structural highlights and evolutionary implications emerging from comparison of the cellular RNA polymerase subunits with the RNA-dependent RNA polymerase involved in RNAi in eukaryotes and their homologs from newly identified bacterial selfish elements. We describe some previously unnoticed domains and the possible evolutionary stages leading to the RNA polymerases of extant life forms. We then present the case for the ancient orthology of the basal transcription factors, the sigma factor and TFIIB, in the bacterial and the archaeo-eukaryotic lineages. We also present a synopsis of the structural and architectural taxonomy of specific transcription factors and their genome-scale demography. In this context, we present certain notable deviations from the otherwise invariant proteome-wide trends in transcription factor distribution and use it to predict the presence of an unusual lineage-specifically expanded signaling system in certain firmicutes like Paenibacillus. We then discuss the intersection between functional properties of transcription factors and the organization of transcriptional networks. Finally, we present some of the interesting evolutionary conundrums posed by our newly gained understanding of the bacterial transcription apparatus and potential areas for future explorations.

Fig. 1

Structure of the bacterial transcription initiation complex. The cartoon representation was derived from an EM structure of the initiation complex (PDB: 3iyd) in association with DNA that contains the α, β, β′, ω, σ⁷⁰ and the wHTH domains of CRP (CAP) transcription factor. For increased clarity, only the key globular domains of these proteins are shown and labeled. The remaining parts of the structure are shown as coils.

Fig. 2

Structures of key conserved domains of the β, β′ and α subunits. Strands are colored green, whereas helices are colored red or blue. Only the core conserved regions of the domains are shown. Inserts in domains are mostly suppressed or excised as depicted. The C-terminal domain of the ribosomal L25 protein is also depicted to illustrate its structural relationship with the conserved domain inserted into the ASCR domain of the α subunit (L25C–like domain). Structural elements in the L25C–like domain of the α subunit that are not present in the ribosomal L25 protein are colored orange.

Fig. 3

Domain architectures of the RNA polymerase β and β′ subunits, yeast killer plasmid RNA polymerase, NCgl1702-like RNA polymerases and the prokaryotic RdRP-like RNA polymerases. For the β and β′ subunits, the domain architecture reconstructed to the last universal common ancestor is shown in the center and inserts in various lineages are shown around this core. Archaeo-eukaryotic domain inserts are indicated with a red arrow and bacterial inserts are marked with a black arrow. Lineages in which the inserts are observed are indicated near the arrows or architecture. Red asterisks indicate new domains discovered in this study. Bacterial inserts, on occasions, differ within members of a closely related bacterial lineage. For a more detailed discussion of these variations, refer to Lane and Darst (2010a). A similar representation is used for the prokaryotic RdRP-like proteins, where lineage-specific inserts are marked with a representative gene and species name around a core conserved architecture. Genes in operons are shown as box-arrows with the arrow head pointing from the 5′ to the 3′ direction of the coding sequence. Operons are labeled with the gene name of the polymerase gene and species name. Refer to the supplement for more detailed domain architectures and gene neighborhoods. Standard abbreviations are used for domain and lineage names. The DCL domain is an RNA binding domain which is also found in a stand-alone form in bacteria and in several eukaryotic rRNA biogenesis proteins. Other abbreviations: A, E: archaea and eukaryotes, ASCR: alpha subunit core related, ATL: AT-Hook like motifs, PPI: peptidyl prolyl isomerase, ZnR: zinc ribbon.

Fig. 4

Higher order evolutionary relationships of bacterial specific transcription factors containing a HTH domain. The horizontal lines represent temporal epochs corresponding to major transitions in evolution of bacteria, namely the last universal common ancestor and the diversification of archaea and bacteria. Solid lines reflect the maximum depth of time to which a particular family can be traced. Broken lines indicate an uncertainty with respect to the exact point of origin of a lineage. The ellipses encompass groups of lineages from which a new lineage with relatively limited distribution could have potentially emerged. Lineages of archaeal origin are colored blue, those of bacterial origin are colored orange and those present in archaea and bacteria are colored black. The phyletic distribution of the lineages are also shown in brackets, where A: Archaea; B: bacteria and E: eukaryotes. The “>” reflects lateral transfer with the arrow head pointing to the potential direction of transfer. Also shown to the right are cartoon representations of the major structural types of HTH domains found in bacterial transcription factors. The TFIIB lineage of archaeo-eukaryotic HTHs is shown to illustrate its relationship with the sigma factor.

Fig. 5

Examples of domain architectures of bacterial transcription factors described in the text. Proteins are labeled with their gene and species names. The domains are not drawn to scale. Standard nomenclatures were mostly used to depict the various domains. Some additional abbreviations include: TM: transmembrane, σ-54 N: globular domain found at the N-terminus of σ⁵⁴, Sigma-N2 and SigmaN: Conserved N-terminal domains found in σ⁷⁰, BTAD: conserved domain found in bacterial signaling proteins, ZnRib: Zinc ribbon, FER: classical Ferredoxin domain of the RRM fold.

Fig. 6

Scaling of bacterial transcription factors with proteome size. All graphs show a scatter plot of number of transcription factors in a given proteome (Y-axis) versus the number of protein-coding genes in that organism (X-axis). In (A) and (B), the Y-axis is the overall number of transcription factors across bacteria and in individual lineages respectively. In (C) The Y-axis is the number of predicted two-component system proteins. Note that anomalous numbers in Geobacillus and Paenibacillus that are shown as red points. (D) The Y-axis is number of one-component system and other phospho-relay system proteins.