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Evolution of the extracytoplasmic function ? factor protein family.

ABSTRACT: Understanding transcription has been a central goal of the scientific community for decades. However, much is still unknown, especially concerning how it is regulated. In bacteria, a single DNA-directed RNA-polymerase performs the whole of transcription. It contains multiple subunits, among which the ? factor that confers promoter specificity. Besides the housekeeping ? factor, bacteria encode several alternative ? factors. The most abundant and diverse family of alternative ? factors, the extracytoplasmic function (ECF) family, regulates transcription of genes associated with stressful scenarios, making them key elements of adaptation to specific environmental changes. Despite this, the evolutionary history of ECF ? factors has never been investigated. Here, we report on our analysis of thousands of members of this family. We show that single events are in the origin of alternative modes of regulation of ECF ? factor activity that require partner proteins, but that multiple events resulted in acquisition of regulatory extensions. Moreover, in Bacteroidetes there is a recent duplication of an ecologically relevant gene cluster that includes an ECF ? factor, whereas in Planctomycetes duplication generates distinct C-terminal extensions after fortuitous insertion of the duplicated ? factor. At last, we also demonstrate horizontal transfer of ECF ? factors between soil bacteria.

SUBMITTER: Pinto D

PROVIDER: S-EPMC7671368 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Evolution of the extracytoplasmic function σ factor protein family.

Pinto Daniela D da Fonseca Rute R RR

NAR genomics and bioinformatics 20200113 1

Understanding transcription has been a central goal of the scientific community for decades. However, much is still unknown, especially concerning how it is regulated. In bacteria, a single DNA-directed RNA-polymerase performs the whole of transcription. It contains multiple subunits, among which the σ factor that confers promoter specificity. Besides the housekeeping σ factor, bacteria encode several alternative σ factors. The most abundant and diverse family of alternative σ factors, the extra ...[more]

PMID: 33575573

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Project description:A-factor (2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone) at an extremely low concentration triggers streptomycin production and aerial mycelium formation in Streptomyces griseus. A-factor induces the expression of an A-factor-dependent transcriptional activator, AdpA, essential for both morphological and physiological differentiation by binding to the A-factor receptor protein ArpA, which has bound and repressed the adpA promoter, and dissociating it from the promoter. Nine DNA fragments that were specifically recognized and bound by histidine-tagged AdpA were isolated by cycles of a gel mobility shift-PCR method. One of them was located in front of a gene encoding an extracytoplasmic function sigma factor belonging to a subgroup of the primary sigma(70) family. The cloned gene was named AdpA-dependent sigma factor gene (adsA), and the gene product was named sigma(AdsA). Transcription of adsA depended on A-factor and AdpA, since adsA was transcribed at a very low and constant level in an A-factor-deficient mutant strain or in an adpA-disrupted strain. Consistent with this, transcription of adsA was greatly enhanced at or near the timing of aerial hyphae formation, as determined by low-resolution S1 nuclease mapping. High-resolution S1 mapping determined the transcriptional start point 82 nucleotides upstream of the translational start codon. DNase I footprinting showed that AdpA bound both strands symmetrically between the transcriptional start point and the translational start codon; AdpA protected the antisense strand from positions +7 to +41 with respect to the transcriptional start point and the sense strand from positions +12 to +46. A weak palindrome was found in the AdpA-binding site. The unusual position bound by AdpA as a transcriptional activator, in relation to the promoter, suggested the presence of a mechanism by which AdpA activates transcription of adsA in some unknown way. Disruption of the chromosomal adsA gene resulted in loss of aerial hyphae formation but not streptomycin or yellow pigment production, indicating that sigma(AdsA) is involved only in morphological development and not in secondary metabolic function. The presence of a single copy in each of the Streptomyces species examined by Southern hybridization suggests a common role in morphogenesis in this genus.

Dataset Information

Evolution of the extracytoplasmic function ? factor protein family.

Publications

Evolution of the extracytoplasmic function σ factor protein family.

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