Biology subjects

Aliaga Goltsman, D. S.

Publications and source records attributed to Aliaga Goltsman, D. S..

3 recordsLinked to original sources

bioRxiv2026

Genetic exchange drives relatedness of large linear and circular extrachromosomal elements of archaea

Archaeal extra-chromosomal elements (ECEs) play key roles in archaeal host biology and evolution, yet little is known about their diversity and interactions with each other. Here, we report 42 complete 66 - 165 kbp genomes: 23 "Klingons", 8 "Romulans" and "Romulan-like elements", and 11 "Ferengi", three new families of archaeal ECEs from diverse terrestrial environments. Methylation patterns, phylogenetics and gene sharing analyses suggest that Klingons and Romulans associate with Candidatus Methanoperedens and Ferengi are likely hosted by Candidatus Bathyarchaeaota. Like known archaeal viruses and plasmids, these ECEs both have circular genomes and replicate bi-directionally, unlike the linear Borg and mini-Borg ECEs that also replicate in Methanoperedens. The new ECE genomes all encode genes for methylation, glycosylation, protein degradation, and novel TnpB-like enzymes, which may interact with novel CRISPR-like arrays. All genomes also encode proteins with strong structural similarity to archaeal viral capsid proteins, and some are predicted to multimerize into pentameric or hexameric subunit capsid-like arrays and thus may encapsulate themselves. The three new ECE families share gene content with each other and with Borgs and mini-Borgs, often concentrated in specific genomic regions. Discordance among single gene and genomic phylogenies suggests that apparent relatedness of the five distinct ECE types stems from extensive horizontal gene transfer, rather than evolution from a common ancestor. The three new families of ECEs broaden our understanding of the diversity of archaeal ECEs and highlight the role of horizontal gene transfer in modulating the archaeal and archaeal ECE gene pools.

genomics↗

bioRxiv2025

Comparative characterization of Cas12f orthologs reveals mechanistic features underlying enhanced genome editing efficiency

Miniature CRISPR-Cas12f nucleases are attractive candidates for therapeutic genome editing owing to their compact size and compatibility with adeno-associated virus (AAV) delivery. However, editing efficiencies in mammalian cells are lower than those of larger systems such as Cas12a and SpCas9. The extensive phylogenetic diversity of Cas12f suggests unexplored mechanistic variation with the potential for optimization. Here, we characterize a naturally occurring Cas12f ortholog discovered through metagenomics, Cas12f-MG119-28, which supports robust genome editing in human cells. Through structural, biochemical, and kinetic analyses, we compare Cas12f-MG119-28 with two recently described orthologs, Oscillibacter sp. Cas12f (OsCas12f) and Ruminiclostridium herbifermentans Cas12f (RhCas12f). These orthologs present divergent architectures and regulatory features governing PAM recognition, gRNA binding, dimerization, and DNA cleavage. Notably, Cas12f-MG119-28 achieves efficient R-loop formation via a stable dimer interface and a naturally optimized guide RNA. These discoveries elucidate key mechanistic determinants of Cas12f activity and may offer a framework for engineering compact genome editors with therapeutic potential.

biochemistry↗

bioRxiv2019

Differential gene expression and the importance of regulatory ncRNAs in acidophilic microorganisms

Gene expression profiles provide insight into how microorganisms respond to changing environmental conditions. However, few studies have integrated expression profile analyses of both coding genes and non-coding RNAs (ncRNAs) to characterize the functional activity of microbial community members. Here, we defined gene expression profiles from environmental and laboratory-grown acidophilic biofilms using RNASeq. In total, 15.8 million Illumina reads were mapped to the genomes of 26 acidophilic microorganisms and nine viruses reconstructed from the Richmond Mine at Iron Mountain, California. More than 99% of the genome was transcribed in three Leptospirillum species, and > 80% in the archaea G-plasma and Ferroplasma Type II. High gene expression by G-plasma and the Leptospirillum Group II UBA strain correlated with extremely acidic conditions, whereas high transcriptional expression of Leptospirillum Group III and Leptospirillum Group II 5way-CG strain occurred under higher pH and lower temperature. While expression of CRISPR Cas genes occurs on the sense strand, expression of the CRISPR loci occurs on the antisense strand in the Leptospirilli. A novel riboswitch associated with the biosynthetic pathway for the osmolyte ectoine was upregulated when each specific Leptospirillum Group II strain was growing under the conditions most favorable for it. Newly described ncRNAs associated with CO dehydrogenase (CODH) suggest regulation of expression of CODH as a CO sensor in mature biofilms in the Leptospirilli. Results reveal the ways in which environmental conditions shape transcriptional profiles of organisms growing in acidophilic microbial communities and highlight the significance of ncRNAs in regulating gene expression. IMPORTANCEMicroorganisms play important roles in environmental acidification and in metal-recovery based bioleaching processes. Therefore, characterizing how actively growing microbial communities respond to different environments is key to understanding their role in those processes. Microorganisms express their genes, both coding and non-coding, differently depending on environmental factors, thus evaluating community expression profiles inform about the ecology of actively growing microorganisms. Here we used community transcriptomic analyses to characterize gene expression profiles from biofilm communities growing under extremely acidic conditions. Results expand our knowledge of how acidophilic microorganisms respond to changes in their environment and provide insight into possible gene regulation mechanisms.

microbiology↗