Biology subjects

Sweredoski, M.

Publications and source records attributed to Sweredoski, M..

4 recordsLinked to original sources

bioRxiv2024

The Molecular Evolution of the SARS-COV-2 Spike Protein: Study of Amino Acid Substitutions and Types

The molecular evolution of SARS-COV-2 has been challenging to predict. Emergence of the Omicron Variant of Concern (VOC) and its sublineages indicated that SARS-COV-2 could evolve more rapidly than previously thought. We analyzed the mutation and amino acid substitution patterns in the spike (S) protein of SARS-COV-2 VOCs to assess how they evolved in response to the selective pressure exerted by both natural immunity and vaccination. Our results indicate less evolutionary constraint on the first part of the S protein, allowing more amino acid substitutions, especially in the NTD, RBD, and subdomain 1. Omicron lineages introduced mutations in the FP and HR1 domains for the first time. The NTD, subdomain 1, and FP domains allowed more radical amino acid substitutions, followed by RBD and HR1, possibly due to their function. There were up to nine conservative and one radical substitutions in the amino acids interacting with the Human ACE2 receptor in the RBM of the Omicron sublineages only, a remarkable departure from the previous VOCs. We show that the molecular evolution of SARS-COV-2 S protein was relatively limited up to the Omicron lineage. The selective pressure from previous VOCs and global vaccination potentially accelerated the emergence of the highly transmissible Omicron lineage. This antigenic drift in Omicron is fueled by a high rate of radical amino acid substitutions in the S1 domains, resulting in positive selection with a high potential to change due to adaptive evolution. However, the conservative nature of changes in the RBM may signal a relative stabilization.

molecular biology↗

bioRxiv2018

Bud13 Promotes a Type I Interferon Response By Countering Intron Retention in Irf7

Intron retention (IR) has emerged as an important mechanism of gene expression control. Despite this, the factors that control IR events remain poorly understood. We observed consistent IR in one intron of the Irf7 gene and identified Bud13 as an RNA-binding protein that acts at this intron to increase the amount of successful splicing. Deficiency in Bud13 led to increased IR, decreased mature Irf7 transcript and protein levels, and consequently to a dampened type I interferon response. This impairment of Irf7 production in Bud13-deficient cells compromised their ability to withstand VSV infection. Global analysis of Bud13 knockdown and BUD13 cross-linking to RNA revealed a subset of introns that share many characteristics with the one found in Irf7 and are spliced in a Bud13-dependent manner. Deficiency of Bud13 led to decreased mature transcript from genes containing such introns. Thus, by acting as an antagonist to IR, Bud13 facilitates the expression of genes at which IR occurs.

molecular biology↗

bioRxiv2018

The dormancy specific regulator, SutA, is an intrinsically-disordered protein that modulates transcription initiation in Pseudomonas aeruginosa

Though bacteria in nature are often nutritionally limited and growing slowly, most of our understanding of core cellular processes such as transcription comes from studies in a handful of model organisms doubling rapidly under nutrient-replete conditions. We previously identified a small protein of unknown function, called SutA, in a global screen of proteins synthesized in Pseudomonas aeruginosa under growth arrest (Babin BM, et al. (2016) SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa. PNAS 113(5):E597-605). SutA binds RNA polymerase (RNAP), causing widespread changes in gene expression, including upregulation of the ribosomal RNA (rRNA) genes. Here, using biochemical and structural methods, we examine how SutA interacts with RNAP and the functional consequences of these interactions. We show that SutA consists of a central -helix with unstructured N- and C-terminal tails, and binds to the {beta}1 domain of RNAP. It activates transcription from the P. aeruginosa rrn promoter by both the housekeeping sigma factor holoenzyme (E{sigma}70) and the general stress response sigma factor holoenzyme (E{sigma}S) in vitro, and its N-terminal tail is required for activation in both holoenzyme contexts. However, we find that the interaction between SutA and each holoenzyme is distinct, with the SutA C-terminal tail and an acidic loop unique to {sigma}70 playing the determining roles in these differences. Our results add SutA to a growing list of transcription regulators that use their intrinsically disordered regions to remodel transcription complexes.\n\nSIGNIFICANCELittle is known about how bacteria regulate their activities during periods of dormancy, yet growth arrest dominates bacterial existence in most environments and is directly relevant to the problem of physiological antibiotic tolerance. Though much is known about transcription in the model organism, Escherichia coli, even there, our understanding of gene expression during dormancy is incomplete. Here we explore how transcription under growth arrest is modulated in Pseudomonas aeruginosa by the small acidic protein, SutA. We show that SutA binds to RNA polymerase and controls transcription by a mechanism that is distinct from other known regulators. Our work underscores the potential for fundamental, mechanistic discovery in this important and understudied realm of bacterial physiology.

molecular biology↗

bioRxiv2017

A systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria

Gene regulation is one of the most ubiquitous processes in biology. But while the catalog of bacterial genomes continues to expand rapidly, we remain ignorant about how almost all of the genes in these genomes are regulated. At present, characterizing the molecular mechanisms by which individual regulatory sequences operate requires focused efforts using low-throughput methods. Here we show how a combination of massively parallel reporter assays, mass spectrometry, and information-theoretic modeling can be used to dissect bacterial promoters in a systematic and scalable way. We demonstrate this method on both well-studied and previously uncharacterized promoters in the enteric bacterium Escherichia coli. In all cases we recover nucleotide-resolution models of promoter mechanism. For some promoters, including previously unannotated ones, the approach allowed us to further extract quantitative biophysical models describing input-output relationships. This method opens up the possibility of exhaustively dissecting the mechanisms of promoter function in E. coli and a wide range of other bacteria.

biophysics↗