Biology subjects

Mower, J. P.

Publications and source records attributed to Mower, J. P..

3 recordsLinked to original sources

bioRxiv2025

Origin and rapid evolution of minicircular and highly heteroplasmic mitogenome in the holoparasitic plant genus Rhopalocnemis

The holoparasitic plant Rhopalocnemis phalloides displays unique features in mitogenome organization, sequence heteroplasmy, DNA replication and gene transcription. To understand the origin and evolution of these unique features, we compared the mitogenomes of three R. phalloides individuals and one individual of a newly discovered congeneric species. These mitogenomes comprise dozens of minicircular chromosomes ([~]2-8 kb), with fairly small mitogenome sizes between 121.1 and 147.5 kb. Each R. phalloides individual contains extremely conserved regions (CRs) on all chromosomes, yet these CRs vary significantly among individuals, suggesting rapid divergence in a concerted manner. In contrast, the congeneric species lacks such CRs. Although nearly identical gene and intron content, there is significant sequence divergence between the two species. Extremely high mitogenome heteroplasmy was observed in all three individuals of R. phalloides and all the variants of protein coding genes are transcribed, but few heteroplasmic variants are shared among the three individuals. No sequence heteroplasmy was detected in the congeneric species. PacBio sequencing revealed concatenated mitochondrial chromosomes in the two species, suggesting rolling circle replication of mitochondrial DNA. We infer that the origins of the CR and sequence heteroplasmy are later than the origin of all-minicircular chromosomes in Rhopalocnemis, and propose a plasmid incorporation model to explain the origin of the CR. The rapid intraspecific variation in mitogenome structure, sequence and heteroplasmy in R. phalloides may result from relaxed selective constraint. The striking heteroplasmy in the R. phalloides mitogenome can not be explained by mitochondrion-targeted DNA-RRR gene loss characterized in this study.

evolutionary biology↗

bioRxiv2025

Aromatic Patch in WhiB-Like Transcription Factors Facilitates Primary Sigma Factor Interaction in Mycobacterium tuberculosis

WhiB-like (Wbl) family proteins are a unique family of iron-sulfur ([4Fe-4S]) cluster-bound transcription factors found exclusively in Actinobacteria and actinobacteriophages, including the notoriously persistent pathogen Mycobacterium tuberculosis (Mtb). Despite their critical roles in cell development, stress response and antibiotic resistance, the mechanisms of gene regulation by the Wbl family proteins are not fully understood due to the lack of a canonical DNA-binding motif in most Wbl proteins. Here, we present structural and biochemical evidence demonstrating that all Mtb Wbl proteins bind to the same site in the conserved region 4 of the primary sigma 70 factor facilitated by a previously unrecognized structural motif, the aromatic patch, in the Wbl family. Our phylogenetic findings provide compelling evidence for a complex evolutionary relationship of Wbls between actinobacteria and the associated phages. Together, this work fills a critical gap in our understanding of the function, mechanism and evolutionary origin of Wbls.

biochemistry↗

bioRxiv2023

Chromosome-level genomes of multicellular algal sisters to land plants illuminate signaling network evolution

The filamentous and unicellular algae of the class Zygnematophyceae are the closest algal relatives of land plants. Inferring the properties of the last common ancestor shared by these algae and land plants allows us to identify decisive traits that enabled the conquest of land by plants. We sequenced four genomes of filamentous Zygnematophyceae (three strains of Zygnema circumcarinatum and one strain of Z. cylindricum) and generated chromosome-scale assemblies for all strains of the emerging model system Z. circumcarinatum. Comparative genomic analyses reveal expanded genes for signaling cascades, environmental response, and intracellular trafficking that we associate with multicellularity. Gene family analyses suggest that Zygnematophyceae share all the major enzymes with land plants for cell wall polysaccharide synthesis, degradation, and modifications; most of the enzymes for cell wall innovations, especially for polysaccharide backbone synthesis, were gained more than 700 million years ago. In Zygnematophyceae, these enzyme families expanded, forming co-expressed modules. Transcriptomic profiling of over 19 growth conditions combined with co-expression network analyses uncover cohorts of genes that unite environmental signaling with multicellular developmental programs. Our data shed light on a molecular chassis that balances environmental response and growth modulation across more than 600 million years of streptophyte evolution. HIGHLIGHTSO_LIGenomes of four filamentous algae (Zygnema) sisters to land plants C_LIO_LIZygnema are rich in genes for multicellular growth and environmental acclimation: signaling, lipid modification, and transport C_LIO_LICell wall innovations: diversification of hexameric rosette cellulose synthase in Zygnematophyceae C_LIO_LICo-expression networks reveal conserved modules for balancing growth and acclimation C_LI

evolutionary biology↗