Biology subjects

Nunes-da-Fonseca, R.

Publications and source records attributed to Nunes-da-Fonseca, R..

4 recordsLinked to original sources

bioRxiv2025

Genomic plasticity of the Azospirillum genus in a biotechnological context

Extensive agriculture and the use of chemical fertilizers cause notable environmental impacts on multiple levels, from reducing soil microbiota diversity to groundwater contamination. In this context, the usage of plant growth-promoting bacteria (PGPB) presents a sustainable alternative to enhance crop production while mitigating these adverse effects. Azospirillum, a bacterial genus renowned for its beneficial capabilities, particularly phytohormone production, is a key component of many commercial inoculants. In this work, we performed a comparative genomic analysis of all publicly available Azospirillum genomes and four novel isolates belonging to our microbial collection. Our analysis identified a species complex within the genus, which we designate the A. brasilense species complex, comprising species already used in commercial bioconsortia. This complex is characterized by a core set of exclusive genes linked to chemotaxis and host-recognition capability. Furthermore, we also validated the biosafety of the A. brasilense species complex and confirmed the plant growth-promoting potential of our novel isolates, highlighting their suitability for developing new biofertilizers.

microbiology↗

bioRxiv2025

The small ORFeome of Tribolium castaneum reveals deeply conserved small ORFs broadly expressed across tissues

Small open reading frames (small ORFs/smORFs/sORFs) were historically overlooked due to their short length (<100 codons) and detection challenges. It is widely accepted that small ORFs are rarely conserved across distant taxa, particularly in deeply rooted ancestors. Growing evidence supports their biological relevance and potential roles in gene innovation. Here, we integrated genomic, transcriptomic, and proteomic datasets to identify and characterize 454 putative small ORFs in Tribolium castaneum. Conservation analyses revealed 230 small ORFs conserved within Coleoptera, 167 in insects, 85 in arthropods, 39 in eukaryotes, and six in bacteria. Conserved small ORFs displayed higher GC content ([~]44.87%), with bacterial-conserved sequences exceeding 50%. Functional enrichment revealed dozens of small ORFs associated with catalytic, transporter, structural, and regulatory roles. Binding site predictions indicated 254 small ORFs possess protein-protein interaction potential. Expression profiles across 14 RNA-seq libraries spanning multiple developmental stages showed 40.1% of small ORFs expressed (TPM >1) in at least one sample, and 16.5% expressed in five or more libraries. Conserved small ORFs showed broader and more stable expression, while lineage-specific ones displayed restricted expression, mostly in gonads or embryos. Isoformic and small CDSs were the most widely expressed classes. Notably, 29 small ORFs exhibited transcriptional and translational support (Swiss-Prot and/or Ribo-seq), 28 being small CDSs. A total of 390 small ORFs had potential paralogs, supporting gene duplication as a mechanism for small ORF emergence. Altogether, our findings reinforce that small ORFs, contrary to initial assumptions, can be deeply conserved and potentially perform key roles in evolutionary processes.

genomics↗

bioRxiv2020

The smORF-containing gene mille-pattes is required for moulting and Trypanosoma cruzi metacyclogenesis in the Chagas disease vector Rhodnius prolixus

Chagas disease is estimated to affect 8 million people worldwide and is responsible for circa 10,000 deaths in Latin America every year. Vector control has been developed as the main strategy to control disease spreading. The identification of new targets is essential, and genes containing small open reading frames (smORFs - < 100 amino acids) are present as hundreds of putative new candidate targets in insect genomes. Here, we show that the prototypic smORF containing gene mille-pattes/polished-rice/tarsalless (mlpt/pri/tal) is essential for post-embryonic development of the kissing bug Rhodnius prolixus and for the metacyclogenesis of the Trypanosoma cruzi parasite during nymphal stages. Injection of double-stranded RNA against mlpt (Rp-dsmlpt) during nymphal stages leads to a plethora of phenotypes which impairs post-embryonic development. First, nymphs of fourth or fifth stage injected with Rp-dsmlpt do not moult. Second, vector digestive physiology is largely modified, and haemozoin is significantly increased in the posterior midgut of Rp-dsmlpt nymphs. Third, Rp-mlpt knockdown inhibits the metacyclogenesis of Trypanosoma cruzi, the etiologic agent of Chagas disease. Thus, our study provides the first evidence of a smORF-containing gene regulating vector physiology, parasitic cycle and disease transmission.

molecular biology↗

bioRxiv2019

Multiple roles of the polycistronic gene tarsaless/mille-pattes/polished-rice during embryogenesis of the kissing bug Rhodnius prolixus

Genes encoding small open-reading frames (smORFs) have been characterized as essential players of developmental processes. The smORF tarsaless/mille-pattes/polished-rice has been thoroughly investigated in holometabolous insects, such as the fruit fly Drosophila melanogaster and the red flour beetle Tribolium castaneum, while its function in hemimetabolous insects remains unknown. Thus, we analyzed the function of the tal/pri/mlpt ortholog in a hemimetabolous insect, the kissing bug Rhodnius prolixus (Rp). First, sequence analysis shows that Rp-tal/pri/mlpt polycistronic mRNA encodes two small peptides (11 to 14 amino acids) containing a LDPTG motif. Interestingly, a new hemipteran-specific conserved peptide of approximately 80 amino acids was also identified by in silico analysis. In silico docking analysis supports the high-affinity binding of the small LDPTG peptides to the transcription factor Shavenbaby. Rp-tal/pri/mlpt in situ hybridization and knockdown via RNA interference showed a conserved role of Rp-tal/pri/mlpt during embryogenesis, with a major role in the regulation of thoracic versus abdominal segmentation, leg development and head formation. Altogether, our study shows that tal/pri/mlpt segmentation role is conserved in the common ancestor of Paraneoptera and suggests that polycistronic genes might generate order specific smORFs.

developmental biology↗