bioRxiv Science⌕ Search

Biology subjects

Godoy, V.

Publications and source records attributed to Godoy, V..

7 recordsLinked to original sources
bioRxiv2025

Understanding the genetic diversity of bacteria isolated from across the Atacama Desert

Despite being one of the driest and harshest deserts on Earth, the Atacama Desert is home to a variety of bacterial life. Microorganisms that reside here may have developed adaptations to help them survive this unique environment. In this study, we used bioinformatic and genetic methods to assess the abundance of phyla that are present in this environment and what types of adaptations individual bacteria have obtained. To assess bacterial diversity, we used 16S rRNA sequencing on soil samples and determined the relative composition of different phyla and archaea at sixteen locations. A selection of eight cultivatable organisms which produce pigments were subjected to whole genome sequencing (WGS). Using these sequences, we screened for stress-tolerance capabilities including pigment production pathways, biofilm-related genes, antibiotic production, and genome stability. We found that all strains we sequenced are predicted to produce bioactive compounds. We also found that the pigments that these bacteria produce have antioxidant, iron and ion chelating, and/or antibiotic properties. This characterization allows us to assess adaptive strategies of bacteria which is important in the fields of agriculture, biotechnology and health.

microbiology↗
bioRxiv2024

Multiple transcription factors regulate the expression of genes for error prone DNA polymerases in Acinetobacter baumannii

Acinetobacter baumannii is an opportunistic pathogen causing several infections that are increasingly diSicult to treat due to its ability to rapidly gain antibiotic resistances. These resistances can arise due to mutations during the DNA damage response (DDR), through the activity of error-prone DNA polymerases, such as DNA polymerase V (DNA Pol V). Currently, the DDR in A. baumannii is not well understood and the regulation of genes encoding multiple copies of DNA Pol V is not fully characterized. Through genome wide mutagenesis, we have identified a novel TetR-like family regulator of genes that encode DNA Pol V, which we have named Error-prone polymerase regulator, EppR. We have found that EppR represses the expression of the genes encoding DNA Pol V and itself through direct binding to a conserved EppR motif in their promoters. Lastly, we show that EppR also regulates UmuDAb, previously identified as a regulator of genes encoding DNA Pol V. These two gene products are functionally required to ensure regulation of expression of genes encoding DNA Pol Vs and umuDAb. With these results, we propose a co-repressor model for the regulation of genes encoding DNA Pol V and umuDAb. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/615892v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@502a49org.highwire.dtl.DTLVardef@10844bcorg.highwire.dtl.DTLVardef@1d8be41org.highwire.dtl.DTLVardef@b2a68e_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

microbiology↗
bioRxiv2024

Whole-Genome Sequencing of a Janthinobacterium sp. Isolated from the Patagonian Desert

Janthinobacterium is a genus of Gram-negative environmental bacteria that survive extreme conditions by forming biofilms and producing pigments. Janthinobacterium sp. LS2A, an extremophile isolated from soil in the Chilean Patagonia, contains seven known biosynthetic gene clusters, including the purple pigment violacein, which may aid in its survival in harsh environments.

genomics↗
bioRxiv2023

Discovery of a novel MarR-type transcriptional regulator that controls cell death in Bacillus subtilis biofilms

Pulcherriminic acid (PA) is a cyclic-L-leu-L-leu di-peptide produced by Bacillus subtilis during biofilm formation. When secreted, PA strongly chelates extracellular iron and forms a reddish- brown pigment, pulcherrimin. Production of pulcherriminic acid and formation of pulcherrimin modulate iron homeostasis in B. subtilis. Pulcherriminic acid also functions as an antioxidant to protect cells from increasing oxidative stress during biofilm formation. We previously showed that PA is involved in gene regulation, differentially regulating hundreds of genes in B. subtilis. One of the strongly upregulated genes by PA is yhjH, encoding a putative MarR-type transcription repressor. In this study, we characterized the regulation of the yhjH gene by PA, by PchR, a known transcription repressor for PA biosynthesis, and by YhjH itself. We also found that high expression of yhjH triggers rapid cell lysis in B. subtilis. Results from RNA-seq suggest that YhjH differentially regulates about 180 genes, among which there is a significant number of prophage genes. Lastly, we propose that YhjH be re-named as PcdR, for "pulcherriminic acid cell death regulator".

microbiology↗
bioRxiv2022

RecA balances genomic stability and evolution using many successive mismatch tolerant homology tests

A double-strand break (DSB) must usually be repaired with as little alteration to the genome as possible, though some rare alterations provide valuable genomic evolution. In E.coli, a DSB undergoes resection to give 3 ssDNA tails. These invading strand tails are loaded with RecA protein and then rapidly search the genome for the corresponding (allelic) partner. Thus, a searching ssDNA/RecA filament must almost never make stable non-allelic contact; therefore, it has been puzzling that RecA forms stable products that join partially homologous sequences. Homology testing by RecA family proteins begins with an 8-bp test, followed by successive homology tests of base pair triplets. Here we introduce a highly simplified homology recognition model to highlight how mismatch sensitivity could affect non-allelic pairing in bacterial genomes. The model predicts that even if each triplet test accepts 2 mismatches, RecA can have [~] 95% probability of establishing allelic pairing after a DSB in E. coli; however, that accuracy requires homology testing {gap}50 contiguous base pairs, consistent with the homology lengths probed in vivo. In contrast, if no mismatches are accepted testing 14 bp is sufficient, and testing more base pairs does not reduce non-allelic pairing because bacterial genomes contain long repeats.

biophysics↗
bioRxiv2018

The sequences near Chi sites allow the RecBCD pathway to avoid genomic rearrangements

Bacterial recombinational repair is initiated by RecBCD, which creates a 3' single-stranded DNA (ssDNA) tail on each side of a double strand break (DSB). Each tail terminates in a Chi site sequence that is usually distant from the break. Once an ssDNA-RecA filament forms on a tail, the tail searches for homologous double-stranded DNA (dsDNA) to use as template for DSB repair. Here we show that the nucleoprotein filaments rarely trigger sufficient synthesis to form an irreversible repair unless a long strand exchange product forms at the 3' end of the filament. Our experimental data and modeling suggest that terminating both filaments with Chi sites allows recombinational repair to strongly suppress fatal genomic rearrangements resulting from mistakenly joining different copies of a repeated sequence after a DSB has occurred within a repeat. Taken together our evidence highlights cellular safe fail mechanisms that bacteria use to avoid potentially lethal situations.

biophysics↗