Biology subjects

de la Cruz, J.

Publications and source records attributed to de la Cruz, J..

4 recordsLinked to original sources

bioRxiv2026

Ribosomal protein eL22 contributes to the assembly of 60S ribosomal subunits in Saccharomyces cerevisiae

Ribosome biogenesis is a highly coordinated pathway that involves the assembly of ribosomal RNAs (rRNAs) with ribosomal proteins (r-proteins) to generate functional ribosomal subunits (r-subunits). The Saccharomyces cerevisiae (yeast) large 60S r-subunit consists of three rRNA molecules and 46 r-proteins. The contributions of nearly all r-proteins of the yeast large r-subunit have been characterized; however, a few non-essential proteins remain poorly understood. Although non-essential, human eL22 has been identified as a key player in p53 regulation during ribosomal stress and as a highly mutated target in cancers. Despite this function, the role of eL22 in ribosome maturation is still ill-defined. In this study, we characterized yeast eL22 r-protein. Our results show that eL22 assembles into intermediate nucleolar pre-60S ribosomal particles. Loss of eL22 impairs cell growth and reduces 60S r-subunit accumulation, phenotypes that are exacerbated at low temperatures. Analysis of pre-rRNA processing by pulse-chase labeling, northern blot hybridization, and primer extension reveals a defect in 27S pre-rRNA maturation, specifically at the level of 27SB pre-rRNA processing. Consequently, nuclear export of eL22-deficient pre-60S particles is mildly impaired. Furthermore, we identify genetic interactions between eL22 and neighboring r-proteins, eL38 and eL31. We conclude that eL22 assembly is required for optimal pre-60S maturation during middle nucleolar stages, particularly at low temperatures, a function likely supported by the cooperative action of other r-proteins associated with common elements of 25S rRNA. HighlightsO_LIWe have studied the role of r-protein eL22 in yeast ribosome assembly. C_LIO_LIeL22 is required for 60S ribosomal subunit production. C_LIO_LIThe absence of eL22 is critical at low temperatures. C_LIO_LIeL22 is important for 27SB pre-rRNA processing and nuclear export of pre-ribosomes. C_LIO_LIeL22 functionally interacts with r-proteins eL38 and eL31 in domain III of 25S rRNA. C_LI

genetics↗

bioRxiv2026

BABYBOOM-like expression in the cowpea egg and central cellenables parthenogenesis, endosperm development, and viable haploid seed formation

Introductory Paragraph (Nature Plants format)Parthenogenesis or fertilization-independent embryogenesis occurs at low frequency in sexual plants. Expression of BABYBOOM-like (BBML) and PARTHENOGENESIS (PAR) genes in the egg cell of several diploid dicot crops induce parthenogenesis at varying frequency; however, recovery of viable haploid seeds has rarely been reported, perhaps due to a lack of viable endosperm formation. In the legume cowpea (Vigna unguiculata L. Walp), ectopic egg cell expression of the endogenous BBML homolog (VuBBML1) and PAR from Taraxacum officinale induces parthenogenesis; however, seeds abort as endosperm formation is blocked following self-pollination. Expression of VuBBML1 in both the egg cell and central cell, together with central cell fertilization following self-pollination, results in viable seeds that germinate and give rise to haploid plants. VuBBML1 has a functional role in the formation of cowpea embryo and endosperm seed compartments. This finding opens possibilities for establishing double haploid production during homozygous parental breeding, and asexual seed induction for fixing hybrid vigor in cowpea.

plant biology↗

bioRxiv2025

Ubiquitylome Rewiring by Bacterial E3 Ligases Reveals Multifaceted Host Subversion

Salmonella enterica has evolved an arsenal of effector proteins secreted via type III secretion systems (T3SS) to manipulate host cell functions. Among these, the NEL family E3 ubiquitin ligases (SlrP, SspH1, and SspH2) are known to modulate immune signaling, but the breadth of their impact on the host ubiquitylome remains unexplored. In this study, we have performed a global proteomic analysis to identify host proteins ubiquitylated in response to expression of these three effectors in human cells. Using enrichment strategies combined with mass spectrometry under conditions where the proteasome is active or not, we identified 214 putative substrates of ubiquitylation. Gene ontology and KEGG pathway analysis revealed enrichment in pathways related to RNA processing, ribosome biogenesis, cytoskeleton organization, chromatin remodeling, and vesicular trafficking. In vitro ubiquitylation assays validated five novel substrates and revealed differential substrate specificity and patterns of ubiquitin chain topology among the effectors. Notably, expression of SspH1 in Saccharomyces cerevisiae disrupted polysome profiles in a ligase activity dependent manner, indicating a direct impact of the bacterial effector on translation of eukaryotic cells. Comparison with previously published global interactomes and ubiquitylomes supports a model in which Salmonella NEL effectors subvert a broader range of host pathways through targeted ubiquitylation. Our findings uncover new roles for NEL ubiquitin ligases in host manipulation and provide a holistic analysis of their effects on the ubiquitylome of the host cell, constituting a valuable resource for the study of bacterial pathogenesis and infection biology.

microbiology↗

bioRxiv2025

Regulation of transcription elongation anticipates alternative gene expression strategies across the cell cycle

A growing body of evidence supports the idea that RNA polymerase II (RNAP II) activity during transcription elongation can be regulated to control transcription rates. Using genomic run-on and RNAP II chromatin immunoprecipitation, we measured both active and total RNAP II across the bodies of genes at three different stages of the mitotic cell cycle in Saccharomyces cerevisiae: G1, S, and G2/M. Comparison of active and total RNAP II levels at these stages revealed distinct patterns of transcription elongation control throughout the cell cycle. Previously characterized cycling genes were associated with some of these elongation patterns. A cluster of genes with highly divergent genomic run-on and RNAP II chromatin immunoprecipitation patterns was notably enriched in genes related to ribosome biogenesis and the structural components of the ribosome. We confirmed that the expression of ribosome biogenesis mRNAs increases after G1 but decreases following mitosis. Finally, we analyzed the contribution of mRNA stability to each cluster and found that a coordinated regulation of RNAP II activity and mRNA decay is necessary to fully understand the alternative strategies of gene expression across the cell cycle.

molecular biology↗