Biology subjects

Santiago, E.

Publications and source records attributed to Santiago, E..

4 recordsLinked to original sources

bioRxiv2026

Structural characterization the LlaI anti-phage defense system reveals insights into the evolution of nucleotide specificity and the organization of DNA binding in McrBC restriction complexes

Canonical McrBC enzymes are nucleotide-powered, motor-driven endonucleases that bind and cleave modified bacteriophage DNA. Non-canonical McrBC homologs like LlaI and BsuMI are distinguished by a unique three-gene organization and the ability to target DNA site-specifically. Here, we report the atomic-resolution crystal structures of the DNA-binding module LlaI.R1 and AAA+ motor LlaI.R2 from the Lactococcus lactis LlaI anti-phage defense system. The crystallized LlaI.R2 hexamer traps two distinct active site conformations that correlate to different states of the nucleotide hydrolysis cycle and reveal that the organization of the critical catalytic machinery present in canonical McrB homologs is also conserved in non-canonical R2 proteins. Although canonical McrB homologs are strictly GTP-specific, we find that the R2 proteins from LlaI and BsuMI do not discriminate between different nucleotides, even when in complex with their respective R1 partners. Using mutagenesis, we define surfaces on the LlaI.R1 structure that are critical for DNA-binding and interaction with LlaI.R2. These observations support computational modelling of the assembled LlaI restriction system bound to DNA. Together, our data provide new insights into the evolution of nucleotide specificity in McrBC restriction complexes and the molecular mechanisms governing McrBC-catalyzed DNA translocation and cleavage.

biochemistry↗

bioRxiv2026

Estimation of effective size of large continuously distributed populations

Estimation of the effective size (Ne) of large populations with a continuous distribution across wide geographic areas and limited dispersal of individuals has been elusive so far. Estimates of the contemporary Ne from genetic markers for such large, structured populations, typically of plant and marine species, tend to be strongly biased downwards, which has led to question their relevance. Here we show that a recently proposed estimation method of Ne from linkage disequilibrium between markers, which accounts for population structure, yields estimates of metapopulation Ne when the sampling area is sufficiently large. The method is applied to empirical data of maritime pine (Pinus pinaster Aiton). While previous estimates of Ne in pine populations were of the order of a few hundred individuals, we show that estimates of the metapopulation Ne can reach values of the order of tens of thousands of individuals. This result is especially relevant from a conservation point of view, as populations with Ne lower than 500 individuals are considered to be under the risk of extinction.

genetics↗

bioRxiv2021

Natural selection does not affect the estimates of effective population size based on linkage disequilibrium

The effective population size (Ne) is a key parameter to quantify the magnitude of genetic drift and inbreeding, with important implications in human evolution. The increasing availability of high-density genetic markers allows the estimation of historical changes in Ne across time using measures of genome diversity or linkage disequilibrium between markers. Selection is expected to reduce diversity and Ne, and this reduction is modulated by the heterogeneity of the genome in terms of recombination rate. Here we investigate by computer simulations the consequences of selection (both positive and negative) and of recombination rate heterogeneity in the estimation of historical Ne. We also investigate the relationship between diversity parameters and Ne across the different regions of the genome using human marker data. We show that the estimates of historical Ne obtained from linkage disequilibrium between markers (NeLD) are virtually unaffected by selection. In contrast, those estimates obtained by coalescence mutation-recombination-based methods can be strongly affected by it, what could have important consequences for the estimation of human demography. The simulation results are supported by the analysis of human data. The estimates of NeLD obtained for particular genomic regions do not correlate with recombination rate, nucleotide diversity, polymorphism, background selection statistic, minor allele frequency of SNPs, loss of function and missense variants and gene density. This suggests that NeLD measures are merely indicative of demographic changes in population size across generations. Author summaryThe inference of the demographic history of populations is of great relevance in evolutionary biology. This inference can be made from genomic data using coalescence methods or linkage disequilibrium methods. However, the assessment of these methods is usually made assuming neutrality (absence of selection). Here we show by computer simulations and analyses of human data that the estimates of historical effective population size obtained from linkage disequilibrium between markers are unaffected by natural selection, either positive or negative. In contrast, estimates obtained by coalescence mutation-recombination-based methods can be strongly affected by it, which could have important consequences for recent estimations of human demography. Thus, only linkage disequilibrium methods appear to provide unbiased estimates of the population census size.

genetics↗

bioRxiv2019

Cyclin N-Terminal Domain-Containing 1 (CNTD1) coordinates meiotic crossover formation with cell cycle progression in a cyclin-independent manner

During meiotic prophase I, programmed DNA double-strand breaks repair as non-crossover or crossover events, the latter predominantly occurring via the Class I crossover pathway and requiring the cyclin family member CNTD1. Using an epitope-tagged Cntd1 allele, we show that mouse CNTD1 exists in vivo as a short isoform that lacks the predicted N-terminal cyclin domain and does not bind cyclin-dependent kinases. Instead, we find that CNTD1 associates with Replication Factor C to drive crossover formation and the Skp1-Cullin1-F-Box complex to regulate ubiquitination and subsequent degradation of the WEE1 kinase, thereby indirectly modulating cell cycle progression. We propose that these interactions enable CNTD1 to orchestrate the steps of prophase I and coordinate crossover formation with cellular division.

cell biology↗