Biology subjects

Malavin, S.

Publications and source records attributed to Malavin, S..

3 recordsLinked to original sources

bioRxiv2026

Cysteine-rich repeats trace past horizontal gene transfers in eukaryotes

Movement of genetic material between non-parental organisms, called horizontal gene transfer (HGT), is well recognized in prokaryotes but represents an underestimated force for the acquisition of novel traits in eukaryotes. The mechanisms of cross-domain HGT remain poorly understood despite numerous reports of its occurrence. Thus, progress in the field remains limited by the lack of targeted approaches for detecting HGT events. Using BLASTp search and sequence identity, we describe an HGT-derived protein from the chytridiomycete fungus Neocallimastix californiae. This protein has two cysteine-rich repeats (CysRReps) and other functional domains that are highly similar to those of prokaryotes. Based on the alignment of several CysRReps, we identified 859 additional eukaryotic proteins spanning 43 protein families, each with at least one match to bacterial, archaeal, or viral proteins. HGT-derived proteins with CysRReps belong to multiple eukaryotic taxa, some of which are well-known HGT models. Bacterial, archaeal, and viral proteins comprise the prokaryotic counterparts. Bacteria belong to 15 phyla, spanning a diverse array of physiologies, habitats, and lifestyles. Viral diversity is largely restricted to Caudoviricetes, suggesting a virus-mediated mechanism of DNA integration underlying these transfers. Although the function of CysRReps remains unclear, their association with HGT events across diverse eukaryotic and prokaryotic taxa suggests the existence of a universal molecular mechanism that facilitates gene transfer across phylogenetic boundaries.

evolutionary biology↗

bioRxiv2024

Metabolically-versatile Ca. Thiodiazotropha symbionts of the deep-sea lucinid clam Lucinoma kazani have the genetic potential to fix nitrogen

Lucinid clams are one of the most diverse and widespread symbiont-bearing animal groups in both shallow and deep-sea chemosynthetic habitats. Lucicnids harbor Ca. Thiodiazotropha symbionts that can oxidize inorganic and organic substrates such as hydrogen sulfide and formate to gain energy. The interplay between these key metabolic functions, nutrient uptake and biotic interactions in Ca. Thiodiazotropha is not fully understood. We collected Lucinoma kazani individuals from next to a deep-sea brine pool in the eastern Mediterranean Sea, at a depth of 1150 m and used Oxford Nanopore and Illumina sequencing to obtain high-quality genomes of their Ca. Thiodiazotropha gloverae symbiont. The genomes served as the basis for transcriptomic and proteomic analyses to characterize the in situ gene expression, metabolism and physiology of the symbionts. We found genes needed for N2 fixation in the deep-sea symbionts genome, which, to date, were only found in shallow-water Ca. Thiodiazotropha. However, we did not detect the expression of these genes and thus the potential role of nitrogen fixation in this symbiosis remains to be determined. We also found the high expression of carbon fixation and sulfur oxidation genes, which indicates chemolithoautotrophy as the key physiology of Ca. Thiodiazotropha. However, we also detected the expression of pathways for using methanol and formate as energy sources. Our findings highlight the key traits these microbes maintain to support the nutrition of their hosts and interact with them.

microbiology↗

bioRxiv2023

Collaborative metabolic curation of an emerging model marine bacterium, Alteromonas macleodii ATCC 27126

Inferring the metabolic capabilities of an organism from its genome is a challenging process, relying on computationally-derived or manually curated metabolic networks. Manual curation can correct mistakes in the draft network and add missing reactions based on the literature, but requires significant expertise and is often the bottleneck for high-quality metabolic reconstructions. Here, we present a synopsis of a community curation workshop for the emerging model marine bacterium Alteromonas macleodii ATCC 27126 and its genome database in BioCyc, focusing on pathways for utilizing organic carbon and nitrogen sources. Due to the scarcity of biochemical information or gene knock-outs, the curation process relied primarily on published growth phenotypes and bioinformatic analyses, including comparisons with related Alteromonas strains. We report full pathways for the utilization of the algal polysaccharides alginate and pectin in contrast to inconclusive evidence for one carbon metabolism and mixed acid fermentation, in accordance with the lack of growth on methanol and formate. Pathways for amino acid degradation are ubiquitous across Alteromonas macleodii strains, yet enzymes in the pathways for the degradation of threonine, tryptophan and tyrosine were not identified. Nucleotide degradation pathways are also partial in ATCC 27126. We postulate that demonstrated growth on nitrate as sole N source proceeds via a nitrate reductase pathway that is a hybrid of known pathways. Our evidence highlights the value of joint and interactive curation efforts, but also shows major knowledge gaps regarding Alteromonas metabolism. The manually-curated metabolic reconstruction is available as a "Tier-2" database on BioCyc. ImportanceMetabolic reconstructions are vital for the systemic understanding of an organisms ecology. Here, we report the outcome of a collaborative, interactive curation workshop to build a curated "metabolic encyclopedia" for Alteromonas macleodii ATCC 27126, a marine heterotrophic bacterium with widespread occurrence. Curating pathways for polysaccharide degradation, one-carbon metabolism, and others closed major knowledge gaps, and identified further avenues of research. Our study highlights how the combination of bioinformatic, genomic and physiological evidence can be harvested into a detailed metabolic model, but also identifies challenges if little experimental data is available for support. Overall, we show how an interactive get-together by a diverse group of scientists can advance the ecological understanding of emerging model bacteria, with relevance for the entire scientific community.

microbiology↗