Biology subjects

Jerlström-Hultqvist, J.

Publications and source records attributed to Jerlström-Hultqvist, J..

7 recordsLinked to original sources

bioRxiv2025

Anaerobic protist survival in microcosms is dependent on microbiome metabolic function.

Anaerobic environments serve as habitats for diverse microorganisms, including unicellular eukaryotes (protists) and prokaryotes. To thrive in low-oxygen environments, protists and prokaryotes often establish specialized metabolic cross-feeding associations, such as syntrophy, with other microorganisms. Previous studies show that the breviate protist Lenisia limosa engages in a mutualistic association with a denitrifying Arcobacter bacterium based on hydrogen exchange. Here, we investigate if the ability to form metabolic interactions is conserved in other breviates by studying five diverse breviate microcosms and their associated bacteria We show that five laboratory microcosms of marine breviates live with multiple hydrogen-consuming prokaryotes that are predicted to have different preferences for terminal electron acceptors using genome-resolved metagenomics. Growth of the prokaryotes and protists within the microcosms respond differently to electron acceptors depending on the make-up of the prokaryotic community. We find that the metabolic capabilities of the bacteria and not their taxonomic affiliations determine protist growth and survival and present new potential protist-interacting bacteria from the Arcobacteraceae, Desulfovibrioaceae and Terasakiella lineages. This investigation uncovers potential nitrogen and sulfur cycling pathways within these bacterial populations, hinting at their roles in syntrophic interactions with the protists via hydrogen exchange.

microbiology↗

bioRxiv2023

Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora.

Kingdom-level branches are being added to the tree of eukaryotes at a rate approaching one per year, with no signs of slowing down1-4. Some are completely new discoveries, while others are morphologically unusual protists that were previously described but lacked molecular data. For example, Hemimastigophora are predatory protists with two rows of flagella that were known since the 19th century, but proved to represent a new deep-branching eukaryote lineage when phylogenomic analyses were conducted2. Meteora sporadica Hausmann et al. 20025 is a protist with a unique morphology and motility; cells glide over substrates along a long axis of anterior and posterior projections, and have a pair of lateral arms that swing back and forth. Originally, Meteora was described by light microscopy only, from a short-term enrichment of deep-sea sediment. A small subunit ribosomal RNA (SSU rRNA) sequence was reported recently, but the phylogenetic placement of Meteora remained unresolved6. Here, we investigated two cultivated Meteora sporadica isolates in detail. Transmission electron microscopy showed that the anterior-posterior projections are supported by microtubules originating from a cluster of subnuclear MTOCs. Likewise, the arms are supported by microtubules, and neither have a flagellar axoneme-like structure. Sequencing the mitochondrial genome showed this to be amongst the most gene-rich known, outside jakobids. Remarkably, phylogenomic analyses of 254 nuclear protein-coding genes robustly support a close relationship with Hemimastigophora. Our study suggests that Meteora and Hemimastigophora together represent a morphologically diverse supergroup, and thus are important for resolving the tree of eukaryote life and early eukaryote evolution.

evolutionary biology↗

bioRxiv2023

A unique symbiosome in an anaerobic single-celled eukaryote

Symbiotic relationships drive evolutionary change and are important sources of novelty. Here we demonstrate a highly structured syntrophic symbiosis between species of the anaerobic protist Anaeramoeba (Anaeramoebae, Metamonada) and bacterial ectosymbionts. We dissected this symbiosis with long-read metagenomics, transcriptomics of host and symbiont cells coupled with fluorescent in situ hybridization (FISH), and microscopy. Genome sequencing, phylogenomic analyses and FISH show that the symbionts belong to the Desulfobacteraceae and were acquired independently in two different Anaeramoeba species. We show that ectosymbionts likely reside deep within cell surface invaginations in a symbiosomal membrane network that is tightly associated with cytoplasmic hydrogenosomes. Metabolic reconstructions based on the genomes and transcriptomes of the symbionts suggest a highly evolved syntrophic interaction. Host hydrogenosomes likely produce hydrogen, acetate, and propionate that are consumed by the symbionts dissimilatory sulfate reduction, Wood-Ljungdahl and methylmalonyl pathways, respectively. Because the host genome sequences encode several vitamin B12-dependent enzymes but appear to lack the ability to biosynthesize this vitamin, we hypothesize that the symbionts supply their hosts with B12. We detected numerous lateral gene transfers from diverse bacteria to Anaeramoeba, including genes involved in oxygen defense and anaerobic metabolism. Gene families encoding membrane-trafficking components that regulate the phagosomal maturation machinery are notably expanded in Anaeramoeba spp. and may be involved in organizing and/or stabilizing the symbiosomal membrane system. Overall, the Anaeramoebae have evolved a dynamic symbiosome comprised of a vacuolar system that facilitates positioning and maintenance of sulfate-reducing bacterial ectosymbionts.

evolutionary biology↗

bioRxiv2022

Rescue of Escherichia coli auxotrophy by de novo small proteins

Increasing numbers of small proteins with diverse physiological roles are being identified and characterized in both prokaryotic and eukaryotic systems, but the origins and evolution of these proteins remain unclear. Recent genomic sequence analyses in several organisms suggest that new functions encoded by small open reading frames (sORFs) may emerge de novo from noncoding sequences. However, experimental data demonstrating if and how randomly generated sORFs can confer beneficial effects to cells are limited. Here we show that by up-regulating hisB expression, de novo small proteins ([≤] 50 amino acids in length) selected from random sequence libraries can rescue Escherichia coli cells that lack the conditionally essential SerB enzyme. The recovered small proteins are hydrophobic and confer their rescue effect by binding to the 5 end regulatory region of the his operon mRNA, suggesting that protein binding promotes structural rearrangements of the RNA that allow increased hisB expression. This study adds RNA regulatory elements as another interacting partner for de novo proteins isolated from random sequence libraries, and provides further experimental evidence that small proteins with selective benefits can originate from the expression of nonfunctional sequences.

evolutionary biology↗

bioRxiv2022

Characterization of Cysteine-rich protein families of Giardia lamblia and their role during antigenic variation.

Giardia lamblia encode several families of cysteine-rich proteins. Among these families are the Variant-specific Surface Proteins (VSPs), which are involved in the process of antigenic variation. In addition to VSPs, other Cys-rich proteins have been described, such as High Cysteine Membrane Proteins (HCMPs), High Cysteine Proteins (HCPs) and Tenascin-like Proteins (TLPs). However, these proteins are less characterized and there is no consensus on their subcellular localization, function, expression, and relationship with the VSPs. Although numerous efforts have been made to determine the distinctive characteristics of VSPs and the number of VSP genes present in the genome of Giardia, a clear profile of the VSP repertoire is still lacking. Here, we performed an exhaustive analysis of the Cys-rich families in the recently updated version of the Giardia genome, including their organization, characteristic features, evolution and levels of expression, by combining simple pattern searches and predictions with massive sequencing techniques, integrating and reanalyzing as much omics data as possible. We propose a new classification for the Cys-rich protein-encoding genes and pseudogenes that better describes their involvement in the parasite biology and define unique characteristics of the VSPs that include, besides their known features, an Initiator element/Kozak-like sequence, an extended polyadenylation signal and a unique pattern of mutually exclusive transcript accumulation. Our findings also imply that the HCMPs (now named Cys-Rich Membrane Proteins, CRMPs) are upregulated under stress conditions and might protect the parasite during VSP switching. These results contribute to a better understanding of the process of antigenic variation in this pathogen. Author SummaryThe most common cause of parasite-induced diarrhea is Giardia lamblia. This intestinal parasite causes 180 million cases of symptomatic disease (giardiasis) yearly but also many asymptomatic infections, resulting in that more than 0.5 billion people are currently colonized by the parasite. One key virulence mechanism of G. lamblia, resulting in long-term infections and frequent re-infections, is antigenic variation of Variant-specific Surface Proteins (VSPs). The cysteine-rich VSP proteins are encoded by a multi-gene family but until now the number of genes and how they are regulated has been unclear. Here a recently assembled Giardia reference genome was analyzed using different bioinformatic analyses and this revealed that there are 136 VSP genes in the Giardia genome. The analyses revealed that there are additional cysteine rich proteins in gene families with fewer members that are related to VSPs but with other roles than antigenic variation. A large number of incomplete VSP genes were also identified and they can function as a sequence reservoir for generation of VSP variability. The VSP genes have unique regulatory elements in the upstream and downstream regions, suggesting a role in regulation. Several gene expression data sets were re-analyzed and it showed that one major VSP is expressed per cell. This study is the first to reveal the organization of VSPs in Giardia and it will be the basis for further studies of the mechanism of antigenic variation in this important intestinal parasite.

microbiology↗

bioRxiv2020

Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family

The first SAM degrading enzyme (SAMase) was discovered in bacteriophage T3, as a counter-defense against the bacterial restriction-modification system, and annotated as an S-adenosyl-L-methionine (SAM) hydrolase forming 5-methyl-thioadenosine (MTA) and L-homoserine. From environmental phages, we recently discovered three SAMases with barely detectable sequence similarity to T3 SAMase and without homology to proteins of known structure. Here, we present the very first phage SAMase structures, in complex with a substrate analogue and the product MTA. The structure shows a trimer of alpha-beta sandwiches similar to the GlnB-like superfamily, with active sites formed at the trimer interfaces. Quantum-mechanical calculations, thin-layer chromatography and NMR spectroscopy demonstrate that this family of enzymes are not hydrolases but lyases forming MTA and L-homoserine lactone in a unimolecular reaction mechanism. Sequence analysis, in vitro and in vivo mutagenesis support that T3 SAMase belongs to the same structural family and utilizes the same reaction mechanism.

biochemistry↗

bioRxiv2019

The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites

Diplomonad parasites of the genus Giardia have adapted to colonizing different hosts, most notably the intestinal tract of mammals. The human-pathogenic Giardia species, Giardia intestinalis, has been extensively studied at the genome and gene expression level, but no such information is available for other Giardia species. Comparative data would be particularly valuable for Giardia muris, which colonizes mice and is commonly used as a prototypic in vivo model for investigating host responses to intestinal parasitic infection. Here we report the draft-genome of G. muris. We discovered a highly streamlined genome, amongst the most densely encoded ever described for a nuclear eukaryotic genome. G. muris and G. intestinalis share many known or predicted virulence factors, including cysteine proteases and a large repertoire of cysteine-rich surface proteins involved in antigenic variation. Different to G. intestinalis, G. muris maintains tandem arrays of pseudogenized surface antigens at the telomeres, whereas intact surface antigens are present centrally in the chromosomes. The two classes of surface antigens engage in genetic exchange. Reconstruction of metabolic pathways from the G. muris genome suggest significant metabolic differences to G. intestinalis. Additionally, G. muris encodes proteins that might be used to modulate the prokaryotic microbiota. The responsible genes have been introduced in the Giardia genus via lateral gene transfer from prokaryotic sources. Our findings point to important evolutionary steps in the Giardia genus as it adapted to different hosts and it provides a powerful foundation for mechanistic exploration of host-pathogen interaction in the G. muris - mouse pathosystem.

evolutionary biology↗