Biology subjects

Freedman, Z.

Publications and source records attributed to Freedman, Z..

4 recordsLinked to original sources

bioRxiv2026

S. cerevisiae Cwc15p Tunes the Spliceosome Active Site for 5' Splice Site Cleavage

Pre-mRNA splicing is an essential step in eukaryotic gene expression during which spliceosomes remove introns from nascent RNAs while ligating the adjacent exons. Spliceosomes are cellular nanomachines composed of five small nuclear (snRNA) components and dozens of proteins, most of which are highly conserved. Despite the high conservation of many splicing factors between S. cerevisiae and H. sapiens, several protein components of the S. cerevisiae spliceosome are not essential for growth under normal laboratory conditions. This is particularly surprising for nonessential factors whose conserved domains contact the spliceosomes catalytic core. Uncovering a function for these splicing factors can be challenging since they are not required for viability, may engage in functionally redundant interactions, and may display only weak phenotypes in the absence of secondary mutations in other spliceosome components. One such nonessential factor is the Cwc15 protein. Cwc15s highly conserved N-terminus directly contacts the U2/U6 di-snRNA within the spliceosome catalytic core; yet its precise role in splicing has not been defined in any organism. In this work, we use molecular genetics in S. cerevisiae combined with splicing reporter assays to study Cwc15p function. We propose that Cwc15p not only promotes the stability of the active site but also its structural transitions. These functions may be critical for splicing in S. cerevisiae under nonoptimal conditions, facilitating use of weak or alternate splice sites, and could have implications for proofreading of spliceosome active site formation.

molecular biology↗

bioRxiv2025

Patterns of Microbial Succession and Niche Differentiation Across Depth and Age in a Landfill Have Implications for Management Strategies

Despite microorganisms being primarily responsible for landfill material decomposition, limited characterization has been performed across both landfill depth and age. Here, we investigated the microbial communities and physicochemical parameters in two active and two closed landfill wells from surface to bottom, as well as fill dirt and leachate at a sanitary landfill near Madison, Wisconsin, USA. Amplicon community sequencing fungi, bacteria and archaea revealed distinct microbial community structures across landfill sites. The observed patterns of microbial community succession by depth and age mirror the known phases of the landfill life cycle. Younger surface samples were dominated by aerobic fungi, which transitioned to fermentative bacteria and methanogenic archaea in older, deeper, layers. Simultaneously, high species richness was preserved across landfill ages, while reduced evenness at specific depths support spatial niche differentiation. In conjunction with the lack of trends found for physicochemical parameters by depth, this supports niche differentiation driven by the highly heterogenous waste inputs. This study provides the first comprehensive vertical profile of bacterial, fungal, and archaeal communities across landfill depths and ages, highlighting the influence of these parameters on physicochemical factors and microbial distribution within landfills. These results have implications for improving landfill management, including renewable gas energy production, minimizing emissions, and increasing degradation rates.

microbiology↗

bioRxiv2025

Anthropogenic nitrogen deposition decouples relationships with decomposing microbes, altering SOM molecular composition, but not molecular complexity or diversity

Soil organic matter (SOM) consists of diverse biochemical constituents, spanning a spectrum of chemical complexity, and the relative abundance of these substrates influences microbial metabolism and soil carbon persistence. However, mechanistic controls governing these processes and how they may be affected by environmental change remains incomplete. This study aims to assess (1) the molecular-level changes that occur across stages of root decomposition, from undecayed plant root litter to 1-year decomposed root litter, to mineral SOM and (2) how these changes are altered by anthropogenic nitrogen (N) deposition by using SOM biochemical and microbiome datasets and a long-term field experiment. N deposition did not significantly alter undecomposed or 1-year decomposed root litter, but did alter decomposing microbial communities and mineral SOM biochemical composition, specifically in lignin- and lipid-derived compounds. Taken together, this restructuring of microbial communities and alteration of SOM biochemistry likely contributed to the previously observed reduction in SOM decomposition.

ecology↗

bioRxiv2024

Root exudation and rhizosphere microbial recruitment are influenced by novel plant trait diversity in carrot genotypes

Root exudate composition can influence rhizosphere microbial recruitment and is tightly controlled by plant genetics. However, little research has profiled root exudate in vegetable crops or determined their role in rhizosphere microbial community and metabolite composition. It is also not well understood how root exudates and resulting rhizosphere dynamics shift across plant trait diversity and with the development of novel crop genotypes. To address these knowledge gaps, this study paired metabolomics and microbiome analyses to evaluate associations between the composition of exudates, soil bacterial and fungal communities, and soil metabolites across four genotypes of organically produced carrot of differential breeding histories, including two experimental genotypes. Plant genotypes modified soil microbial diversity and composition, and differentially recruited bacterial taxa with demonstrated potential for plant-growth related functions including ammonia oxidation, nitrogen fixation, and phytohormone production. Bacterial rhizosphere recruitment from bulk soil was genotype and root exudate-mediated, while fungal recruitment was not. Moreover, root exudate composition was distinct in an heirloom genotype and a novel nematode resistant genotype, compared to other genotypes tested. Root exudate and rhizosphere metabolite composition was decoupled, and soil metabolites strongly associated with fungal, but not bacterial communities. Taken together, the results of this study suggest that novel crop trait diversity and breeding histories hold consequences for the functional potential of soils through the diversification of root exudate mediated plant-microbe interactions.

microbiology↗