Biology subjects

Batista, M.

Publications and source records attributed to Batista, M..

6 recordsLinked to original sources

bioRxiv2025

Structure and substrate recognition by the Twin-arginine translocation (Tat) pathway core complex

The twin-arginine translocation (Tat) system is a mechanistically unique protein transport pathway moving folded proteins across membranes (1-4). It is found in all domains of life and is essential for plant photosynthesis and bacterial virulence(2, 5-7). A core complex composed of membrane proteins TatA, TatB, and TatC binds substrate proteins and then recruits additional TatA protomers to form the transport site(8-10). Here we present structures of resting and substrate-bound states of the Tat core complex together with biochemical and functional analysis. Substrate proteins associate with the core complex solely through their N-terminal signal peptides with their Tat targeting sequences making specific contacts with TatC and the peptide body clamped by TatB. The core complex contains highly tilted transmembrane helices that drive extreme local membrane thinning. Based on our results we propose a model for the early steps in Tat transport.

biochemistry↗

bioRxiv2024

LC-MS/MS characterization of SOBERANA(R)02, a receptor binding domain-tetanus toxoid conjugate vaccine against SARS-CoV-2

SOBERANA(R)02 is a safe and effective conjugate vaccine against SARS-CoV-2, produced using the maleimide-thiol chemistry. In this vaccine, the Cys538 in the recombinant receptor binding domain (RBD) of SARS-CoV-2 is linked, through a thiosuccinimide linker, to lysine residues of tetanus toxoid (TT) preparation. LC-MS/MS analysis revealed that TT is a complex mixture of proteins, similar to other TTs where the detoxified tetanus neurotoxin (d-TeNT) has been shown to be the most abundant protein (30-56%), regardless the quantification method used. The fifteen most abundant proteins account for approximately 78% of the total proteins. LC-MS/MS analysis of the activation process showed that 102 out of 107 lysine residues in the d-TeNT incorporated a maleimide group. In contrast, when tryptic peptides isolated by Ni2+-NTA affinity chromatography, were analyzed by LC-MS/MS, only 22 Lys residues in the d-TeNT were cross-linked to the RBD C-terminal tryptic peptide (538CVNF541-HHHHHH), probably due to steric hindrance. Twelve and eighteen conjugation sites were assigned based on the identification of linear peptides carrying a conjugated lysine residues ({Delta}m = +1454.58 Da or {Delta}m = +1472.59 Da) and cross-linked peptides with stabilized linker forms, respectively. Eight conjugation sites were coincidently assigned by both strategies. The assignment of the conjugation sites was manually validated by observed regularities (z[≥]3+, XIC, immonium ions, specific linker fragment ions) not considered by the identification software (PEAKS, Kojak and pLink2). The RBD was also conjugated, but to a lesser extent, to ten other low abundance carrier proteins. To our knowledge, this work is the first report of conjugation site assignment in a TT-based conjugate vaccine.

biochemistry↗

bioRxiv2024

Role of Non-Exponential Reversal times in Aggregation Models of Bacterial Populations

In this paper, we consider 1D agent-based and kinetic models of aggregation with reversals. In particular, we fit a Gamma distribution to represent the run times in myxobacteria and analyze numerically the importance of non-exponential reversal times. We demonstrate that non-exponential reversal times aid aggregation and result in tighter aggregates. We compare and contrast the behavior of agent-based and kinetic models, and also consider kinetic models with aggregation driven by chemotaxis. Thus, incorporating non-exponential reversal times into models of aggregation can be particularly important for reproducing experimental data, such as aggregate persistence and dispersal.

biophysics↗

bioRxiv2023

Pathological beige remodeling induced by cancer cachexia depends on the disease severity and involves mainly the trans-differentiation of mature white adipocytes

In cancer associated cachexia (CAC), white adipose tissue undergoes morphofunctional and inflammatory changes that lead to tissue dysfunction and remodeling. In addition to metabolic changes in white adipose tissues (WAT), adipose tissue atrophy has been implicated in several clinical complications and poor prognoses associated with cachexia. Adipocyte atrophy may be associated with increased beige remodeling in human CAC as evidenced by the "beige remodeling" observed in preclinical models of CAC. Even though beige remodeling is associated with CAC-induced WAT dysfunction, there are still some open questions regarding their cellular origins. In this study, we investigated the development of beige remodeling in CAC from a broader perspective. In addition, we used a grading system to identify the scAT as being affected by mice weight loss early and intensely. Using different in vitro and ex-vivo techniques, we demonstrated that Lewis LLC1 cells can induce a switch from white to beige adipocytes, which is specific to this type of tumor cell. During the more advanced stages of CAC, beige adipocytes are mainly formed from the transdifferentiation of cells. According to our results, humanizing the CAC classification system is an efficient approach to defining the onset of the syndrome in a more homogeneous manner. Pathological beige remodeling occurred early in the disease course and exhibited phenotypic characteristics specific to LLC cells secretomes. Developing therapeutic strategies that recruit beige adipocytes in vivo may be better guided by an understanding of the cellular origins of beige adipocytes emitted by CAC.

cell biology↗

bioRxiv2022

Protein arginine and lysine methylation in Trypanosoma cruzi

Post-translational methylation of proteins, which occurs in arginines and lysines, modulates several biological processes at different levels of cell signaling. Recently, methylation has been demonstrated in the regulation beyond histones, for example, in the dynamics of protein-protein and protein-nucleic acid interactions. However, the presence and role of non-histone methylation in Trypanosoma cruzi, the etiologic agent of Chagas disease, has not yet been elucidated. Here, we applied mass spectrometry-based-proteomics (LC-MS/MS) to describe the methylproteome of T. cruzi epimastigotes. A total of 1253 methyl sites in 824 methylated proteins were identified, of these, 712 (86.4%) proteins were identified in two or more biological replicates. Our results of functional enrichment analysis, protein-protein interaction, and co-occurrence with other PTMs, show that protein methylation impacts different levels of biological processes, such translation, RNA and DNA binding, amino acid and carbohydrate metabolism. In addition, 171 methylated proteins were previously reported with phosphorylation sites in T. cruzi, including flagellar proteins and RNA binding proteins, indicating that there may be an interplay between these different modifications in non-histone proteins. Our results show that a broad spectrum of functions are affected by methylation indicating its potential to impact important processes in the biology of the parasite and other trypanosomes. Statement of the significanceTrypanosoma cruzi is a protozoan parasite that causes Chagas disease in humans and faces different environmental changes throughout its life cycle. Protein methylation is an important post-translational modification by which cells respond and adapt to the environment. We applied mass spectrometry-based proteomics and reported the first proteomic analysis of arginine and lysine methylation in T. cruzi. Our data demonstrate that protein methylation is broad and impacts different cellular processes in T. cruzi. This study represents a significant advance in the investigation of the importance of protein methylation in trypanosomes.

genomics↗

bioRxiv2019

RNA processing machineries in Archaea: the 5’-3’ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3’-5’ exoribonucleolytic RNA exosome machinery

A network of RNA helicases, endoribonucleases, and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focused on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5-3 exoribonuclease of the {beta}-CASP family conserved in Euryarchaea, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, and that this occurs in the vicinity of the ribosome. Proteomic landscapes and direct protein-protein interaction analyses demonstrated that aRNase J interplay with ASH-Ski2 and the Csl4 cap exosome subunit. These in vitro data are strengthened by our phylogenomic studies showing a taxonomic co-distribution of aRNase J and ASH-Ski2 among the archaeal phylogeny. Finally, our T. barophilus whole-cell extract fractionation experiments provide evidences that an aRNase J/ASH-Ski2 complex might exist in vivo and hint at an association of aRNase J with the ribosome or polysomes that is stressed in absence of ASH-Ski2. While aRNase J homologues are found among bacteria, the RNA exosome and the Ski2-like RNA helicase have eukaryotic homologues, underlining the mosaic aspect of archaeal RNA machines. Altogether, these results suggest, for the first time, a fundamental role of {beta}-CASP RNase/helicase complex in archaeal RNA metabolism. Finally, our results position aRNase J at the junction of RNA surveillance and translation processes, thus opening new perspectives and evolutionary scenario on RNA processing players in Archaea.

molecular biology↗