Biology subjects

Giacomelli, G.

Publications and source records attributed to Giacomelli, G..

9 recordsLinked to original sources

bioRxiv2025

Equipositioning of Chromosomes in the Polyploid Archaeon Haloferax volcanii by HpaAB

Proper genome segregation is essential for all life forms, but in archaea, this process is less characterized as compared to bacteria, or eukarya. Archaea show considerable variability in chromosome and plasmid copy number, and organization. Stable maintenance of chromosomes and low-copy plasmids in organisms requires an active segregation system. Haloferax volcanii DS2 is a polyploid archaeon that contains a fragmented genome composed of a main chromosome, three secondary chromosomes, pHV1, pHV3 and pHV4, as well as a plasmid pHV2. Due to the high copy number of all replicons, genomic segregation in H. volcanii is typically considered random. However, we identified four two-gene operons encoding a ParA-like homologue and an uncharacterized protein. Here we characterized one of these systems, termed here HpaA (ParA-homolog) and HpaB, that is encoded on the secondary chromosome pHV3. HpaA, showing conserved ATPase walker motifs, is a ParA protein with a bacterial origin acquired via horizontal gene transfer. Mutation of key residues in HpaA alters its localization, and HpaA is necessary for proper spatial distribution of HpaB. HpaB, an archaeal protein capable of forming foci in the cytosol, is shown to function as a centromere-binding protein, thereby acting as a functional ParB homologue. qPCR data confirm that HpaB is crucial for maintaining the plasmid-to-chromosome ratio, as deletion of hpaB reduces pHV3 copy number. Single particle tracking suggests that absence of HpaB leads to an altered population distribution of HpaA, based on protein dynamics. Deletion of the genes hpaA and hpaB results in severe growth defects when cells are grown on xylose as a sole carbon source, in line with the location of the genes for the xylose degradation pathway on chromosome pHV3. We propose that H. volcanii has an active chromosome segregation system, essential for the "two-dimensional" segregation and equipositioning of its replicons. This function is crucial for ensuring stable replicon maintenance across the distinct cell morphologies of H. volcanii, which transition between rod-shaped and disc-shaped forms at different stages of growth.

microbiology↗

bioRxiv2025

The ParA-like ATPase PldP influences the TatA dynamics in Corynebacterium glutamicum

In bacterial cells, precise localization of protein complexes is achieved by unique positioning systems. One of the examples of such positioning systems is the ParAB-parS which is responsible for plasmid and chromosome segregation. In Corynebacterium glutamicum, a parAB deletion results in cell division and growth defects, while deletion of an orphan ParA-like protein pldP results only in a moderate cell division phenotype. Having confirmed a basal ATPase activity of PldP, we aimed to explore if the {Delta}pldP-related phenotype could be a consequence of the mislocalized secreted proteins, as the loss of extracellular proteins involved in cell wall metabolism results in a similar phenotype characterized by disrupted separation of daughter cells. Putative peptidoglycan hydrolase Rv2525c from Mycobacterium tuberculosis and Rv2525c-like glycoside hydrolase-like domain-containing protein Cg0955 from C. glutamicum were previously shown to be transported outside of the cell by twin-arginine protein translocation machinery (Tat). Here, we found that although the deletion of pldP did not lead to the altered secretion of the putative hydrolase Cg0955 by the Tat system, it resulted in the reduction of the Tat dynamics. Our findings highlight the interplay between the ParA-like ATPase PldP and the Tat translocon and contribute to the studies of ParA-like proteins being essential in positioning various cargos in the bacterial cells. ImportancePrecise spatio-temporal localization of protein complexes within a bacterial cell is essential for the survival and proliferation of bacteria. ParA-like ATPases play a crucial role in protein positioning, as well as chromosome and plasmid segregation. Here, we characterize a novel ParA-like ATPase PldP in Corynebacterium glutamicum, a model organism for the cell biology of Mycobacteriales and a biotechnological workhorse. Deletion of pldP results in the cell division phenotypes and impacts the intracellular dynamics of TatA, a component of the twin-arginine protein transport. We suggest that the mislocalization of the Tat-secreted putative peptidoglycan hydrolase caused by the indirect influence of pldP deletion might account for the observed cell separation defect.

microbiology↗

bioRxiv2024

Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold-standard

DNA methylation is a widely studied epigenetic mark and a powerful biomarker of cell type, age, environmental exposures, and disease. Whole-genome sequencing following selective conversion of unmethylated cytosines into thymines via bisulfite treatment or enzymatic methods remains the reference method for DNA methylation profiling genome-wide. While numerous software tools facilitate processing of DNA methylation sequencing reads, a comprehensive benchmarking study has been lacking thus far. In this study, we systematically compared complete computational workflows for processing DNA methylation sequencing data using a dedicated benchmarking dataset generated with five genome-wide profiling protocols. As an evaluation reference, we employed highly quantitative locus-specific measurements from our preceding benchmark of targeted DNA methylation assays. Based on this experimental gold-standard assessment and several comprehensive metrics, we identified workflows that consistently demonstrated superior performance and revealed major workflow development trends. To facilitate the sustainability of our benchmark, we implemented an interactive workflow execution and data presentation platform, adaptable to user-defined criteria and seamlessly expandable to future software.

bioinformatics↗

bioRxiv2023

Deletion of SMC renders FtsK essential in Corynebacterium glutamicum

Structural maintenance of chromosomes (SMC) are ubiquitously distributed proteins involved in chromosome organization. Deletion of smc causes severe growth phenotypes in many organisms. Surprisingly, smc can be deleted in Corynebacterium glutamicum, a member of the Actinomycetota phylum, without any apparent growth phenotype. Earlier work has shown that SMC in C. glutamicum is loaded in a ParB-dependent fashion to the chromosome and functions in replichore cohesion. The unexpected absence of a growth phenotype in the smc mutant prompted us to screen for unknown synthetic interactions within C. glutamicum. Therefore, we generated a high-density Tn-5 library based on wild-type and smc-deleted C. glutamicum strains. The transposon sequencing (Tn-seq) data revealed that the DNA-translocase FtsK is essential in a smc deletion strain. FtsK localized to the septa and cell poles in wild type cells, however deletion of smc resulted in a decreased polar FtsK localization. Single-particle tracking analysis further suggests that prolonged FtsK complex activity is both required and sufficient to make up for the absence of SMC, thus achieving efficient chromosome segregation in C. glutamicum. Further, single molecule dynamics of FtsK is influenced, albeit indirectly, by DNA-loaded SMC. Deletion of ParB results in an increased of both SMC and FtsK mobility. While the first change agrees with previous data that show how ParB is essential for SMC loading on DNA, the latter suggests that FtsK mobility is affected in cells with defects in chromosome organization. Based on our data we propose a simple, yet efficient mechanism for efficient DNA segregation in C. glutamicum, even in absence of SMC proteins. ImportanceFaithful DNA segregation is of fundamental importance for life. Bacteria have efficient systems to coordinate chromosome compaction, DNA segregation and cell division. A key factor in DNA compaction is the SMC-complex that is found to be essential in many bacteria. In members of the Actinomycetota smc is dispensable, but the reason for this was unclear. We show here that the divisome associated DNA-pump FtsK can compensate SMC loss and the subsequent loss in correct chromosome organization. In cells with distorted chromosomes, FtsK functions for an extended period of time at the septum, until chromosomes are segregated.

microbiology↗

bioRxiv2022

A novel nuclease is the executing part of a bacterial plasmid defense system

Cells are continuously facing the risk of taking up foreign DNA that can compromise genomic and cellular integrity. Therefore, bacteria are in a constant arms race with mobile genetic elements such as phages, transposons and plasmids. They have developed several active strategies against invading DNA molecules that can be seen as a bacterial innate immune system. Anti-phage systems are usually organized in defense islands and can consist of restriction-modification (R-M) systems, CRISPR-Cas, and abortive infection (Abi) systems. Despite recent advances in the field, much less is known about plasmid defense systems. We have recently identified the MksBEFG system in Corynebacterium glutamicum as a novel plasmid defense system which comprises homologues of the condensin system MukFEB. Here, we investigated the molecular arrangement of the MksBEFG complex. Importantly, we identified MksG as a novel nuclease that degrades plasmid DNA and is, thus, the executing part of the system. The crystal structure of MksG revealed a dimeric assembly through its DUF2220 C-terminal domains. This domain is homologous to the TOPRIM domain of the topoisomerase II family of enzymes and contains the corresponding divalent ion binding site that is essential for DNA cleavage in topoisomerases, explaining the in vitro nuclease activity of MksG. We further show that the MksBEF subunits exhibit an ATPase cycle similar to MukBEF in vitro and we reason that this reaction cycle, in combination with the nuclease activity provided by MksG, allows for processive degradation of invading plasmids. Super-resolution localization microscopy revealed that the Mks system is spatially regulated via to the polar scaffold protein DivIVA. Introduction of plasmids increases the diffusion rate and alters the localization of MksG, indicating an activation of the system in vivo.

microbiology↗

bioRxiv2021

The CTPase activity of ParB acts as a timing mechanism to control the dynamics and function of prokaryotic DNA partition complexes

DNA partitioning CTPases of the ParB family mediate the segregation of bacterial chromosomes and low-copy number plasmids. They act as DNA-sliding clamps that are loaded at parS motifs in the centromeric region of target DNA molecules and then spread laterally to form large nucleoprotein complexes that serve as docking points for the DNA segregation machinery. Here, we identify conformational changes that underlie the CTP- and parS-dependent closure of ParB clamps. Moreover, we solve crystal structures of ParB in the pre- and post-hydrolysis state and provide insights into the catalytic mechanism underlying nucleotide hydrolysis. The characterization of CTPase-deficient ParB variants reveals that CTP hydrolysis serves as a timing mechanism to control the sliding time of ParB. Hyperstable clamps are trapped on the DNA, leading to excessing spreading and severe chromosome segregation defects in vivo. These findings clarify the role of the ParB CTPase cycle in partition complex dynamics and function and thus complete our understanding of this prototypic CTP-dependent molecular switch.

microbiology↗

bioRxiv2020

Lsr2 is a nucleoid-associated protein that exerts pleiotropic effects on mycobacterial cellular processes

Lsr2 is involved in maintaining chromosome structure in asymmetrically dividing mycobacteria and is essential in the tubercle bacillus (M. tuberculosis) during infection. Here, we report that a lack of Lsr2 profoundly impacts the mycobacterial cell morphology and the properties of the cell envelope resulting in the formation of smooth, short and antibiotics sensitive cells. Lsr2 forms large and dynamic nucleoprotein complexes in vivo and deletion of lsr2 gene exerts a profound effect on the replication time and replisome dynamics. We suggest that the Lsr2 nucleoprotein complexes may contribute to maintaining the proper organization of the newly synthesized DNA. Moreover, we demonstrate that the N-terminal oligomerization domain of Lsr2 is indispensable for the formation of nucleoprotein complexes in vivo. Collectively, our results indicate that Lsr2 exerts a pleiotropic effect on cellular processes and appears to be an attractive target for the development of a novel antitubercular drugs.

microbiology↗

bioRxiv2019

Chromosome organization by a conserved condensin-ParB system in the actinobacterium Corynebacterium glutamicum

Higher-order chromosome folding and segregation is tightly regulated in all domains of life. In bacteria, details on nucleoid organization regulatory mechanisms and function remains poorly characterized, especially in non-model species. Here, we investigate the role of DNA partitioning protein ParB and condensin complexes, two key players in bacterial chromosome structuring, in the actinobacterium Corynebacterium glutamicum. Chromosome conformation capture reveals SMC-mediated long-range interactions around ten centromere-like parS sites clustered at the replication origin (oriC). At least one oriC-proximal parS site is necessary for a reliable chromosome segregation. Using a combination of chromatin immunoprecipitation and photoactivated single molecule localization microscopy evidences the formation of distinct ParB-nucleoprotein subclusters in dependence of parS numbers. We further identified and functionally characterized two condensin paralogs. Whereas SMC/ScpAB complexes are loaded via ParB at parS sites mediating chromosomal inter-arm contacts like in Bacillus subtilis, the MukBEF-like SMC complex MksBEFG does not contribute to chromosomal DNA-folding. Rather, the MksBEFG complex is involved in plasmid maintenance and interacts with the polar oriC-tethering factor DivIVA. These data complement current models of ParB-SMC/ScpAB crosstalk, while showing that some condensin complexes evolved functions uncoupled from chromosome folding.

microbiology↗

bioRxiv2018

Substrate-dependent cluster density dynamics in bacterial phosphotransferase system permeases

Bacteria take up carbohydrates by membrane-integral sugar specific phosphoenolpyruvate-dependent carbohydrate:phosphotransferase systems (PTS). Although PTS is at the heart of bacterial carbon uptake and centrally involved in regulation of carbon metabolism, little is known about localization and putative oligomerization of the permease subunits (EII) of PTS. Here, we analyzed localization of the fructose specific PtsF and the glucose specific PtsG transporters from C. glutamicum using widefield and single molecule localization microscopy. PtsG and PtsF form membrane embedded clusters that localize in a punctate pattern within the cell membrane. The size, number and fluorescence of the observed clusters changes upon presence or absence of the transported substrate. In presence of the transport substrate clusters significantly increased in size. Photo-activated localization microscopy (PALM) data revealed that, in presence of different carbon sources, the number of EII protein events per cluster remain the same, however the density of PTS molecules within a cluster reduces. Our work reveals a simple mechanism for efficient membrane occupancy regulation. Clusters of PTS EII transporters are densely packed in absence of a suitable substrate. In presence of a transport substrate the EII proteins in individual clusters occupy larger membrane areas, thereby decreasing protein density in individual clusters. This mechanism allows for efficient use of the limited membrane space under varying growth conditions without need of protein removal and re-synthesis.\n\nImportanceThe carbohydrate transport system PTS is centrally involved in the regulation of sugar metabolism. Although much is known about the regulatory interaction, the genetic control and the structure/function relationship of the individual PTS components, we know almost nothing about the spatio-temporal organization of the PTS proteins within the cell. We find dynamic clustering of PTS permeases in Corynebacterium glutamicum. Using single molecule resolution photo-activated localization microscopy we could show that PTS EII protein cluster are dynamically changing protein density upon substrate availability. Our findings imply a novel strategy of regulating limited membrane space efficiently. Furthermore, these data will provide important insights in modelling carbohydrate fluxes in cells, since current models assume a homogeneous distribution of PTS permeases within the membrane.

microbiology↗