Biology subjects

Rosselli, R.

Publications and source records attributed to Rosselli, R..

6 recordsLinked to original sources

bioRxiv2026

Redundancy relocated: the distributed metaparalog pool of an Arctic Pelagibacterales population

The presence of metaparalogs (related genes diverging in function) has been proven to be extensive in the pangenomes of streamlined Pelagibacterales genomes. Here by leveraging a large number of complete genomes from an Arctic population we have been able to establish their universality and mechanistic origins. The diversity of some metaparalog families was as high within a single population than comparing with another (Mediterranean) population/species, which points to an ancient diversification of metaparalog families predating genomospecies separation. Metaparalog families provided diversity for transport and envelope diversity which would provide vast capacities to degrade substrates within DOM and interact with other cells or viruses or other subcellular entities (like EVs). The pool does not saturate at fifteen genomes. Our results highlight the immense importance of the pangenome in understanding the biology of bacteria in natural environments and how critical is the study of population genomics for the future of microbiology.

microbiology↗

bioRxiv2024

Bridging Viruses and Prokaryotic Host through Miniature Inverted-repeat Transposable Elements (MITEs)

Transposable elements (TEs) have a pivotal role in the evolution of genomes across all life domains. "Miniature Inverted-repeat Transposable-Elements" (MITEs) are non-autonomous TEs mainly located in intergenic regions, relying on external transposases for mobilization. The boundaries of MITEs mobilome were explored across nearly 1700 prokaryotic genera, 183232 genomes, revealing a widespread distribution. MITEs were identified in 56.5% of genomes, totaling over 1.4 million cMITEs (cellular). Cluster analysis revealed that a significant 97.4% of cMITEs were conserved within genera boundaries, with up to 23% being species-specific. Subsequently, this genus-specificity was evaluated as a tool to link microbial host to their viruses. A total of 51655 cMITEs had counterparts in viral sequences, termed vMITE (viral), resulting in the identification of 2798 viral sequences with vMITEs. Among these, 1501 sequences were positively assigned to a previously known host (41.8% were isolated virus, and 12.3% were assigned through CRISPR data), while 379 new host-virus associations were predicted. Deeper analysis in Neisseria and Bacteroidetes groups allowed the association of 242 and 530 new additional viral sequences, respectively. Given the abundance of non-culturable virus sequences accumulated in databases lacking affiliations with their microbial targets, MITEs are proposed as a novel approach to establishing valid virus-host relationships. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/576219v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@f30826org.highwire.dtl.DTLVardef@19bff7borg.highwire.dtl.DTLVardef@a206eaorg.highwire.dtl.DTLVardef@17408ab_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

A host recognition module shared among distant Alteromonas bacteriophage families features tail fibers with transient chaperone caps

The host recognition modules encoding the injection machinery and receptor binding proteins (RBPs) of bacteriophages are variable genomic units predisposed to mutation and recombination to maintain infectivity toward co-evolving bacterial hosts. In this study, we reveal how Alteromonas mediterranea schitovirus A5 shares its host recognition module, including tail fiber (TF) and cognate chaperone, with phages from distantly related families including Alteromonas myovirus, V22. While the chaperone of V22 is essential for producing active TFs, here we demonstrate production of functional A5 TFs regardless of chaperone co-expression. AlphaFold-generated models of TF and chaperone pairs from phages A5, V22, and other Alteromonas phages reveal how amino acid insertions within both A5-like proteins results in a knob domain duplication in the TF and a {beta}-hairpin "tentacle" extension of the chaperone. These structural modifications are linked to chaperone dependency differences between the A5 and V22 TFs. Structural similarity between the chaperones and intramolecular chaperone domains of other phage RBPs suggests an additional function of these chaperones as transient TF "caps". Finally, our identification of homologous host recognition modules used by morphologically distinct phages implies that HGT and recombination events between unrelated phages may be a more common process than previously thought among Caudoviricetes phages.

microbiology↗

bioRxiv2020

New Viral Biogeochemical Roles Revealed Through Metagenomic Analysis of Lake Baikal

Lake Baikal is the largest body of liquid freshwater on Earth. Previous studies have described the microbial composition of this habitat but the viral communities from this ecosystem have not been characterized in detail. Here we describe the viral diversity of this habitat across depth and seasonal gradients. We discovered 19,475 bona fide viral sequences, which are derived from viruses predicted to infect abundant and ecologically important taxa that reside in Lake Baikal, such as Nitrospirota, Methylophilaceae and Crenarchaeota. Diversity analysis revealed significant changes in viral community composition between epipelagic and bathypelagic zones. Analysis of the gene content of individual viral populations allowed us to describe one of the first bacteriophages that infect Nitrospirota, and their extensive repertoire of auxiliary metabolic genes that might enhance carbon fixation through the reductive TCA cycle. We also described bacteriophages of methylotrophic bacteria with the potential to enhance methanol oxidation and the S-adenosyl-L-methionine cycle. These findings unraveled new ways by which viruses influence the carbon cycle in freshwater ecosystems, namely by using auxiliary metabolic genes that act upon metabolisms of dark carbon fixation and methylotrophy. Therefore, our results shed light on the processes through which viruses can impact biogeochemical cycles of major ecological relevance.

microbiology↗

bioRxiv2020

Viral channelrhodopsins: calcium-dependent Na+/K+ selective light-gated channels

Phytoplankton is the base of the marine food chain, oxygen, carbon cycle playing a global role in climate and ecology. Nucleocytoplasmic Large DNA Viruses regulating the dynamics of phytoplankton comprise genes of rhodopsins of two distinct families. We present a function-structure characterization of two homologous proteins representatives of family 1 of viral rhodopsins, OLPVR1 and VirChR1. VirChR1 is a highly selective, Ca2+-dependent, Na+/K+- conducting channel and, in contrast to known cation channelrhodopsins (ChRs), is impermeable to Ca2+ ions. In human neuroblastoma cells, upon illumination, VirChR1 depolarizes the cell membrane to a level sufficient to fire neurons. It suggests its unique optogenetic potential. 1.4 [A] resolution structure of OLPVR1 reveals their remarkable difference from the known channelrhodopsins and a unique ion-conducting pathway. The data suggest that viral channelrhodopsins mediate phototaxis of algae enhancing the host anabolic processes to support virus reproduction, and therefore, their key role in global phytoplankton dynamics.

biophysics↗

bioRxiv2019

Associations between depth and micro-diversity within marine viral communities revealed through metagenomics

Viruses are extremely abundant and diverse biological entities that contribute to the functioning of marine ecosystems. Despite their recognized importance no studies have addressed trends of micro-diversity in marine viral communities across depth gradients. To fill this gap we obtained metagenomes from both the cellular and viral fractions of Mediterranean seawater samples spanning the epipelagic to the bathypelagic zone at 15, 45, 60 and 2000 meters deep. The majority of viral genomic sequences obtained were derived from bacteriophages of the order Caudovirales, and putative host assignments suggested that they infect some of the most abundant bacteria in marine ecosystems such as Pelagibacter, Puniceispirillum and Prochlorococcus. We evaluated micro-diversity patterns by measuring the accumulation of synonymous and non-synonymous mutations in viral genes. Our results demonstrated that the degree of micro-diversity differs among genes encoding metabolic, structural, and replication proteins and that the degree of micro-diversity increased with depth. These trends of micro-diversity were linked to the changes in environmental conditions observed throughout the depth gradient, such as energy availability, host densities and proportion of actively replicating viruses. These observations allowed us to generate hypotheses regarding the selective pressures acting upon marine viruses from the epipelagic to the bathypelagic zones.

microbiology↗