Biology subjects

Garber, A.

Publications and source records attributed to Garber, A..

6 recordsLinked to original sources

bioRxiv2026

MagicLamp: a web server and software toolkit for targeted gene annotation of microbial functions

Genome and metagenome annotation tools designed for large databases are ill-suited to the discovery of specialized, ecologically relevant microbial functions. MagicLamp (https://github.com/Arkadiy-Garber/MagicLamp) is a modular command-line software toolkit that performs targeted functional gene annotation searches using curated collections of hidden Markov models (HMMs), each representing discrete microbial metabolic processes. MagicLamp is also available as a web server: https://midauthorbio.com/#magiclamp. This targeted approach enables sensitive and specific annotation of genes involved in defined microbial processes, allowing MagicLamp to serve as a dedicated repository for the annotation of specialized microbial functions currently overlooked in other databases and software. The server accepts unannotated genome assemblies or GenBank-formatted annotations to perform HMM-based searches against curated model sets with reproducible, model-specific bit-score thresholds. Automated results are returned as tabular summaries and interactive HTML reports containing cross-genome/metagenome comparisons.

bioinformatics↗

bioRxiv2026

The transcriptional and translational outcomes for pseudogenes in bacterial endosymbionts

Intracellular bacteria in the early stages of host adaptation often show extraordinarily disrupted genomes, where up to half of their ancestral genes are found in a pseudogenized state. The mealybug Pseudococcus longispinus hosts two bacterial endosymbionts with high pseudogene loads, Symbiopectobacterium endolongispinus and Sodalis endolongispinus. Here, we measure transcript abundance, ribosome-associated RNA, and protein abundance in these bacterial symbionts to understand how bacteria avoid (or fail to avoid) accumulating large amounts of non-functional RNAs and proteins from these pseudogenes. Consistent with previous work, we show that pseudogene transcripts remain detectable, but at lower levels compared to those from intact and functional genes, and that relatively few pseudogenes yield detectable proteins in proteomic data. However, we find that many pseudogene transcripts still bind to Symbiopectobacterium ribosomes, and uncover a possible role for the tmRNA ribosome rescue system in the targeting of pseudogene proteins for degradation. Our results suggest a possible mechanism by which bacterial endosymbionts remove aberrant pseudogene-derived proteins during the critical time when many pseudogenes have formed but not enough time has passed for sequence evolution to erode ribosome binding sites from pseudogene transcripts. SignificanceBacteria transitioning from free-living to host-dependent lifestyles often go through a transitory period where large numbers of genes are broken but not yet deleted. How cells navigate this period without producing useless or toxic gene products remains poorly understood. By combining transcriptomic, proteomic, and ribosomal profiling data from two bacterial endosymbionts, we uncover a possible mechanism that cells use to mitigate the presence of thousands of newly formed pseudogenes. We show that pseudogenes are still widely represented in the transcriptome and are often associated with ribosomes, but rarely yield measurable protein products. RNA sequencing from purified ribosomes suggests that the tmRNA ribosome rescue system may act as a short-term quality control mechanism during early stages of genome reduction. These findings provide a mechanistic glimpse into how endosymbionts survive the unstable phase between gene inactivation and gene deletion, a fleeting but critical window in the evolution of endosymbiosis.

evolutionary biology↗

bioRxiv2025

Evolutionary Variation of Poxvirus Genome Architecture

Poxviruses (PXV) are large double-stranded DNA viruses (dsDNA) that infect and cause disease in a wide variety of hosts, including humans.. They are studied as models to understand host-specific disease and they have a wide variety of applications in biotechnology, including vaccines, oncolytic virotherapy, and immunotherapy. Despite a nearly fourfold variation in genome sizes across the Poxviridae family, the basic genome architectural features driving their evolution remain poorly understood. In this study of the summated poxvirus genome sequence database, we report that while only a weak negative correlation exist between viral coding densities and genome sizes, we detected a strong positive correlation between the number of assigned open reading frames (ORF) and genome sizes. We observe an inflection point at a genome size of 229 kb, above or below with the percentage of genes encoding secreted proteins increasing with genome size, and the percentage of predicted cytoplasmic proteins decreasing with genome size. Additionally, we observed a weak positive correlation between the potential of transcript overlap that would be expected to generate dsRNA and genome size. Unexpectedly, we observed a significant positive correlation between coding density and GC-content in mpox virus isolates (R2 = 0.799). Further analysis illustrated a rise in both GC-content and coding density of mpox isolates between 2022 and 2024. Codon usage bias was observed to be clustered by virus families, with tryptophan being the least utilized amino acid across all poxviruses. Protein distribution analysis revealed a right-skewed distribution of poxviral predicted ORFs, with the 150 - 250 amino acid cohort containing the highest number of viral proteins. Finally, we observe a significant positive correlation between ITR sizes and duplicate gene clusters (R2 = 0.679). Together, these architectural findings outline the constraints and adaptive pathways governing poxviral evolution and biology. ImportanceThis study establishes a family genome design rulebook for poxviruses and illustrates how these rules might be linked with their biology and evolution. We demonstrate that genome growth is accompanied by a modest increase in noncoding DNA and an increase in extracellular proteome investment. We further demonstrate that ITR expansions correlate with duplicate gene clusters, rather than genome size, indicating that ITRs serve as hubs of innovation. Our results provide a standard for generating hypotheses and experiments with poxviruses. This work also introduces matrices for within-family viral comparisons.

microbiology↗

bioRxiv2024

Retention of an endosymbiont for the production of a single molecule

Sap-feeding insects often maintain multiple nutritional endosymbionts, which act in concert to produce compounds essential for insect survival. Many mealybugs have endosymbionts in a nested configuration: one or two bacterial species reside within the cytoplasm of another bacterium, and to-gether these bacteria have genomes which encode interdependent but complete sets of genes needed to produce key nutritional molecules. Here we show that the mealybug Pseudococcus viburni has three endosymbionts, one of which contributes only two genes that produce a single host nutrition-related molecule. All three bacterial endosymbionts have tiny genomes, suggesting that they have been co-evolving inside their insect host for millions of years. SignificanceNutritional endosymbionts synthesize (or contribute to the synthesis of) key metabolites such as essential amino acids and vitamins for their host organism. These nutrients are required by hosts because of their restricted diets, which in the case of mealybugs consists solely of plant phloem sap. Genome sequencing of insect endosymbionts has shown that their genomes can be very small, encoding few genes outside of core bacterial processes and nutrient provisioning. Here we highlight an example that has taken this reductive process to the extreme: a mealybug endosymbiont contributes only a single essential compound, chorismate, to the symbiosis.

evolutionary biology↗

bioRxiv2023

Evidence for a core set of microbial lichen symbionts from a global survey of metagenomes

Lichens are the archetypal symbiosis and the one for which the term was coined. Although application of shotgun sequencing techniques has shown that many lichen symbioses can harbour more symbionts than the canonically recognized fungus and photobiont, no global census of lichen organismal composition has been undertaken. Here, we analyze the genome content of 437 lichen metagenomes from six continents, and show that four bacterial lineages occur in the majority of lichen symbioses, at a frequency on par with algal photobionts. A single bacterial genus, Lichenihabitans, occurs in nearly one-third of all lichens sampled. Genome annotations from the most common lichen bacterial symbionts suggest they are aerobic anoxygenic photoheterotrophs and produce essential vitamins, but do not fix nitrogen. We also detected secondary basidiomycete symbionts in about two-thirds of analyzed metagenomes. Our survey suggests a core set of four to seven microbial symbionts are involved in forming and maintaining lichen symbioses.

microbiology↗

bioRxiv2018

Fe oxidation by a fused cytochrome-porin common to diverse Fe-oxidizing bacteria

Iron (Fe) oxidation is one of Earths major biogeochemical processes, key to weathering, soil formation, water quality, and corrosion. However, our understanding of microbial contribution is limited by incomplete knowledge of microbial iron oxidation mechanisms, particularly in neutrophilic iron-oxidizers. The genomes of many, diverse iron-oxidizers encode a homolog to an outer-membrane cytochrome (Cyc2) shown to oxidize iron in two acidophiles. Phylogenetic analyses show Cyc2 sequences from neutrophiles cluster together, suggesting a common function, though this function has not been verified in these organisms. Therefore, we investigated the iron oxidase function of heterologously expressed Cyc2 from a neutrophilic iron-oxidizer Mariprofundus ferrooxydans PV-1. Cyc2PV-1 is capable of oxidizing iron, and its redox potential is 208 {+/-} 20 mV, consistent with the ability to accept electrons from Fe2+ at neutral pH. These results support the hypothesis that Cyc2 functions as an iron oxidase in neutrophilic iron-oxidizing organisms. Sequence analysis and modeling reveal the entire Cyc2 family share a unique fused cytochrome-porin structure, with a defining consensus motif in the cytochrome region. Based on structural analyses, we predict that the monoheme cytochrome Cyc2 specifically oxidizes dissolved Fe2+, in contrast to multiheme iron oxidases, which may oxidize solid Fe(II). With our results, there is now functional validation for diverse representatives of Cyc2 sequences. We present a comprehensive Cyc2 phylogenetic tree and offer a roadmap for identifying cyc2/Cyc2 homologs and interpreting their function. The occurrence of cyc2 in many genomes beyond known iron-oxidizers presents the possibility that microbial iron oxidation may be a widespread metabolism. ImportanceIron is practically ubiquitous across Earths environments, central to both life and geochemical processes, which depend heavily on the redox state of iron. Although iron oxidation, or "rusting," can occur abiotically at near neutral pH, we find neutrophilic iron-oxidizing bacteria (FeOB) are widespread, including in aquifers, sediments, hydrothermal vents, pipes, and water treatment systems. FeOB produce highly reactive Fe(III) oxyhydroxides that bind a variety of nutrients and toxins, thus these microbes are likely a controlling force in iron and other biogeochemical cycles. There has been mounting evidence that Cyc2 functions as an iron oxidase in neutrophiles, but definitive proof of its function has long eluded us. This work provides conclusive biochemical evidence of iron oxidation by Cyc2 from neutrophiles. Cyc2 is common to a wide variety of iron-oxidizers, including acidophilic and phototrophic iron-oxidizers, suggesting that this fused cytochrome-porin structure is especially well-adapted for iron oxidation.

microbiology↗