Biology subjects

de Carvalho, L.

Publications and source records attributed to de Carvalho, L..

6 recordsLinked to original sources

bioRxiv2026

Time-resolved cryo-EM reveals conformational trajectory of allosteric activation in isocitrate lyase

Isocitrate lyase 2 (ICL2) from Mycobacterium tuberculosis undergoes dramatic conformational rearrangements upon binding to the allosteric effector acetyl-CoA. Time-resolved cryo-EM captured conformational states along the ICL2 activation trajectory, revealing how acetyl-CoA binding at the allosteric sites leads to asymmetric, half-of-site activity at the catalytic centres. These findings support a conformational selection model of allostery, whereby acetyl-CoA binding shifts the pre-existing equilibrium towards an active state of the enzyme.

biochemistry↗

bioRxiv2025

Architecture of an asymmetric mycobacterial short chain/long chain acyl-CoA carboxylase

Endogenous extraction has revealed a mycobacterial hybrid acyl-CoA carboxylase (ACCase) complex exhibiting distinct long-chain (LC) and short-chain (LC) acyl-CoA carboxyl transferase (CT) activities. The presence of two different CT subunits (AccD4, AccD5) is triggered by a unique AccE5 dimer. AccE5 also generates a flexible biotin carboxylase (BC) / CT arrangement through a 9-stranded {beta}-barrel, which rotates the entire BC assembly by [~]90{degrees} in the presence of acyl-CoA substrates. These data demonstrate that asymmetric, multi-substrate ACCases differ fundamentally from symmetric, single-substrate ACCases.

microbiology↗

bioRxiv2025

mRNA interactions promote cotranslational association of heteromeric membrane proteins

Heteromeric membrane proteins play crucial physiological roles, yet how they are formed remains poorly understood. Heteromeric hERG1a/1b ion channels, essential for maintaining normal cardiac rhythm, assemble via cotranslational association of their encoding mRNAs. We hypothesized that direct hERG1a and 1b mRNA interactions facilitate this process. Using fluorescence colocalization and free energy of binding predictions, we found that hERG1a and 1b mRNAs form specific heterotypic condensates in vitro, suggesting direct interactions. When hERG1a mRNA was altered by synonymous mutations predicted to reduce its structural diversity and ability to interact with other mRNAs, overlap with hERG1b was dramatically diminished both in vitro and in cells, indicating weakened interactions. Reducing hERG1a structural diversity also influenced its translational complexes, defined by overlapping between fluorescently labeled mRNA and encoded protein (centroids within 400 nm). Whereas most of the wild-type hERG1a mRNA translates within heterotypic complexes, likely reflecting the biogenesis of hERG1a/1b heteromeric assemblies, reducing hERG1a structural diversity yielded more homotypic translational condensates and fewer hERG1a/1b heterotypic ones. This result suggests that the strength of mRNA interactions impact ion channel biogenesis. Further analysis of the heterotypic translational complexes revealed two distinct classes: a) simultaneous translation of both subunits and b) sequential association of fully translated hERG1b with translating hERG1a. Notably, reducing hERG1a structural diversity and interactions with 1b shifted translation toward the sequential mode. These findings identify a new role of mRNA sequence, structure, and interactions in orchestrating the cotranslational association of important heteromeric membrane proteins. SIGNIFICANCEThe physiological diversity of membrane protein complexes arises in part from the mixing of related yet functionally distinct subunits such as those forming "heteromeric" ion channels. How this mixing is achieved is not well understood. Here, we show that subunits composing heteromeric hERG1a/1b ion channels, crucial for normal cardiac function, predominantly associate in complexes where both subunits are simultaneously translated. This cotranslation is promoted by the association of the encoding mRNAs. Silent mutations disrupting hERG1a and 1b mRNA association, without altering the encoded protein, diminish simultaneous translation in favor of hERG1a translational complexes alone or in association with fully synthesized hERG1b. This study highlights the significant impact of RNA sequence, structure, and association on the formation of heteromeric membrane proteins.

biophysics↗

bioRxiv2024

Phylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species

Species belonging to the Mycobacterium kansasii complex (MKC) are frequently isolated from humans and the environment and can cause serious diseases. The most common MKC infections are caused by the species M. kansasii (stricto sensu), leading to tuberculosis-like disease. However, a broad spectrum of virulence, antimicrobial resistance and pathogenicity of these non-tuberculous mycobacteria (NTM) are observed across the MKC. Many genomic aspects of the MKC that relate to these broad phenotypes are not well elucidated. Here, we performed genomic analyses from a collection of 665 MKC strains, isolated from environmental, animal and human sources. We inferred the MKC pangenome, mobilome, resistome, virulome and defense systems and show that the MKC species harbors unique and shared genomic signatures. High frequency of presence of prophages and different types of defense systems was observed. We found that the M. kansasii species splits into four lineages, of which three are lowly represented and mainly in Brazil, while one lineage is dominant and globally spread. Moreover, we show that four sub-lineages of this most distributed M. kansasii lineage emerged during the 20th century. Further analysis of the M. kansasii genomes revealed almost 300 regions of difference contributing to genomic diversity, as well as fixed mutations that may explain the M. kansasiis increased virulence and drug resistance. RepositoriesBioProject PRJNA1048499. Impact statementMycobacterium kansasii complex (MKC) is a group of closely related non-tuberculous mycobacteria species, recognized as a significant source of human infection. Species belonging to the MKC may present a broad spectrum of virulence, antimicrobial resistance and pathogenicity and there is a lack of knowledge about their genomic content related to these broad phenotypes. We have provided whole genomic sequencing DNA for 342 MKC isolates and, together with public data, investigated the MKC pangenome, mobilome, resistome, virulome and defense systems and show unique and shared genetic signatures within MKC species. Furthermore, with phylogenomic and bayesian population analysis, we inferred the distribution and emergence of the Mycobacterium kansasii species lineages and sub-lineages. This study has considerably expanded the MKC available data, by providing genomic sequences of isolates from countries and global regions with unknown or poorly MKC data until now. Data summaryNGS data generated in the study are available in the NCBI Sequence Read Archive (SRA) repository under the accession number PRJNA1048499 and the accession numbers for all data sets used are provided in Supplementary Table 1.

evolutionary biology↗

bioRxiv2023

Divergent downstream biosynthetic pathways are supported by L-cysteine synthases of Mycobacterium tuberculosis

Mycobacterium tuberculosiss (Mtb) autarkic lifestyle within the host involves rewiring its transcriptional networks to combat host-induced stresses. With the help of RNA-seq performed under various stress conditions, we identified that genes belonging to Mtb sulfur metabolism pathways are significantly upregulated during oxidative stress. Using an integrated approach of microbial genetics, transcriptomics, metabolomics, animal experiments, chemical inhibition, and rescue studies, we investigated the biological role of non-canonical L-cysteine synthases, CysM and CysK2. While transcriptome signatures of Rv{Delta}cysM and Rv{Delta}cysK2 appear similar under regular growth conditions, we observed unique transcriptional signatures when subjected to oxidative stress. We followed pool size and labelling (34S) of key downstream metabolites, viz. mycothiol and ergothioneine, to monitor L-cysteine biosynthesis and utilization. This revealed the significant role of distinct L-cysteine biosynthetic routes on redox stress and homeostasis. CysM and CysK2 independently facilitate Mtb survival by alleviating host-induced redox stress, suggesting they are not fully redundant during infection. With the help of genetic mutants and chemical inhibitors, we show that CysM and CysK2 serve as unique, attractive targets for adjunct therapy to combat mycobacterial infection.

microbiology↗

bioRxiv2018

A role for a conserved kinase in the transcriptional control of methionine biosynthesis in Escherichia coli experiencing sustained nitrogen starvation

The initial adaptive transcriptional response to nitrogen (N) starvation in Escherichia coli involves large-scale alterations to the transcriptome mediated by the transcription activator, NtrC. One of the NtrC-activated genes is yeaG, which encodes a conserved bacterial kinase. Although it is known that YeaG is required for optimal survival under sustained N starvation, the molecular basis by which YeaG benefits N starved E. coli remains elusive. By combining transcriptomics with targeted metabolomics analyses, we demonstrate that the methionine biosynthesis pathway becomes transcriptionally dysregulated in{Delta} yeaG bacteria experiencing sustained N starvation. This results in the aberrant and energetically costly biosynthesis of methionine and associated metabolites under sustained N starvation with detrimental consequences to cell viability. It appears the activity of the master transcriptional repressor of methionine biosynthesis genes, MetJ, is compromised in{Delta} yeaG bacteria under sustained N starvation, resulting in transcriptional derepression of MetJ-regulated genes. The results suggest that YeaG is a novel regulatory factor and functions as a molecular brake in the transcriptional control of both the NtrC-regulon and methionine biosynthesis genes in E. coli experiencing sustained N starvation.

microbiology↗