Biology subjects

Baruch-Torres, N.

Publications and source records attributed to Baruch-Torres, N..

4 recordsLinked to original sources

bioRxiv2026

Plant MutS Homolog 1 is a mismatch-directed nuclease required for organelle genome maintenance

The exceptionally low mutation rates of plant organellar genomes imply the existence of DNA surveillance mechanisms that counteract replication errors and DNA damage. Genetic evidence implicates MutS HOMOLOG 1 (MSH1) as a central component of this pathway, as loss of MSH1 results in the accumulation of point mutations. MSH1 is a unique protein that combines an N-terminal MutS-like mismatch-recognition module with a Cterminal GIYYIG nuclease domain. Here, we show that Arabidopsis thaliana MSH1 (AtMsh1) recognizes mismatches, insertion/deletion loops, and damaged bases within double-stranded DNA and introduces staggered DNA breaks at positions flanking the mismatch or lesion. Given the presence of an active homologous recombination machinery in plant organelles, we hypothesize that these DNA ends may be processed by exonucleases to remove the mismatched or damaged DNA while generating 3' single-stranded DNA substrates suitable for homologous recombination-mediated repair and gene conversion. Together, our findings support a model in which AtMsh1 functions as a minimal mismatch repair system that couples mismatch recognition to DNA incision, providing a potential mechanism for suppressing mutation accumulation and maintaining the remarkable stability of plant organellar genomes

biochemistry↗

bioRxiv2026

Translesion DNA synthesis on pyrimidine dimers by Plant organellar DNA polymerases is metal-dependent

Ultraviolet (UV) radiation generates crosslinked DNA lesions--primarily cyclobutane pyrimidine dimers (CPDs) and [6-4] photoproducts ([6-4] PPs)--that block the progression of replicative DNA polymerases. In plants, these lesions are efficiently removed from nuclear DNA by dedicated repair pathways; however, comparable repair mechanisms are absent in plastids and mitochondria. Consequently, how plant organellar DNA polymerases (POPs) tolerate or bypass UV-induced damage has remained unclear. Here, we show that the two Arabidopsis thaliana organellar polymerases, AtPolIs, possess robust translesion synthesis (TLS) activity across CPDs. Although wild-type enzymes display only limited extension across [6-4] PPs, removal of their exonuclease function dramatically enhances bypass, yielding an efficiency of replication across the [6-4] PP that closely resembles that observed on an undamaged template. This establishes AtPolI as the first known replicative DNA polymerase capable of efficiently bypassing a [6-4] PP. We further demonstrate that TLS across UV photoproducts relies on three unique amino acid insertions within the AtPolI polymerase domain, as deletion of any single insertion abolishes TLS. Notably, Mn{superscript 2} can restore TLS activity in these variants, but only for CPD lesions. Together, these findings identify AtPolIs as the first plant organellar replicases with intrinsic [6-4] PP bypass capability and define the structural features that enable this function. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/701875v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@f497bcorg.highwire.dtl.DTLVardef@15ba2eorg.highwire.dtl.DTLVardef@724e29org.highwire.dtl.DTLVardef@697c8b_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Pol γ possesses separate metal binding sites for polymerase and strand displacement functions

Accurate replication of mitochondrial genome (mtDNA) integrity, which is essential for cellular metabolism and energy supply, relies primarily on DNA polymerase gamma (Pol {gamma}), Twinkle helicase, and mitochondrial single-stranded DNA binding protein (mtSSB). Twinkle alone exhibits little helicase activity while reports indicate that Pol {gamma} displays from modest to limited unwinding activity. This led us to dissect Pol {gamma} strand displacement activity using structural, biochemical and in silico approaches. Here, we show that human Pol {gamma} carries out robust strand displacement synthesis at physiological concentrations of divalent metal ions which reveals that distinct metal-binding sites can independently regulate DNA synthesis and unwinding activities. We further showed that Pol {gamma} can displace RNA/DNA hybrid with comparable efficiency as DNA/DNA duplex, representing a key implication on RNA primer removal to preserve mtDNA integrity. Our cryo-electron microscopy structures of Pol {gamma} complexed with a template containing downstream dsDNA and an incoming nucleotide revealed the structural mechanism for the strand displacement activity. We identified four conformational states that represent successive stages of DNA unwinding, accompanied by coordinated rearrangement of the downstream DNA and Pol {gamma} elements that mediate strand displacement. This work establishes biochemical and structural mechanisms of Pol {gamma} strand displacement activity, providing fundamental insight into human mitochondrial DNA replication and integrity. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=185 SRC="FIGDIR/small/701366v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1be1dborg.highwire.dtl.DTLVardef@8912c5org.highwire.dtl.DTLVardef@12f5e75org.highwire.dtl.DTLVardef@e25d2a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Decoration of Burkholderia Hcp1 protein to virus-like particles as a vaccine delivery platform.

Virus-like particles (VLPs) are protein-based nanoparticles frequently used as carrier in conjugate vaccine platforms. VLPs have been used to display foreign antigens for vaccination and to deliver immunotherapeutic against diseases. Hemolysin-coregulated proteins 1 (Hcp1) is a protein component of the Burkholderia type 6 secretion system which participates in intracellular invasion and dissemination. This protein has been reported as a protective antigen and is used in multiple vaccine candidates with various platforms against melioidosis, a severe infectious disease caused by the intracellular pathogen B. pseudomallei. In this study, we used P22 VLPs as a surface platform for decoration with Hcp1 using chemical conjugation. C57BL/6 mice were intranasally immunized with three doses of either PBS, VLPs or conjugated Hcp1-VLPs. Immunization with Hcp1-VLPs formulation induced Hcp1-specific-IgG, IgG1, IgG2c and IgA antibody responses. Furthermore, the serum from Hcp1-VLPs immunized mice enhanced the bacterial uptake and opsonophagocytosis by macrophages in the presence of complement. This study demonstrated an alternative strategy to develop a VLPs-based vaccine platform against Burkholderia species.

microbiology↗