Biology subjects

Bellieny-Rabelo, D.

Publications and source records attributed to Bellieny-Rabelo, D..

7 recordsLinked to original sources

bioRxiv2020

Novel two-component system-like elements reveal functional domains associated with restriction-modification systems and paraMORC ATPases in bacteria

BackgroundTwo-component systems (TCS) are essential machineries allowing for efficient signal recognition and transmission in bacterial cells. The majority of TCSs utilized by bacteria are composed by a sensor histidine kinase (HK) and a cognate response regulator (RR). In the present study, we report two newly predicted protein domains -- Response_reg_2 (PF19192) and HEF_HK (PF19191) -- in bacteria which exhibit high structural similarity, respectively, with typical domains of RRs and HKs. ResultsAdditionally, the genes encoding for the novel predicted domains exhibit a 91.6% linkage observed across 644 genomic regions recovered from 628 different bacterial strains. The remarkable adjacent co-localization between genes carrying Response_reg_2 and HEF_HK in addition to their conserved structural features, which are highly similar to those from well-known HKs and RRs, raises the possibility of Response_reg_2 and HEF_HK integrating a new TCS in bacteria. The genomic regions in which these predicted two-component systems-like are located additionally exhibit an overrepresented presence of restriction-modification (R-M) systems especially the type II R-M. Among these, there is a conspicuous presence of C-5 cytosine-specific DNA methylases which may indicate a functional association with the newly discovered domains. The solid presence of R-M systems and the presence of the GHKL family domain HATPase_c_3 across most of the HEF_HK-containing genes are also indicative that these genes are evolutionarily related to the paraMORC family of ATPases. ConclusionsThe present study uncovered two novel protein conserved domains and raised the possibility of a TCS-like system undertaking a regulatory role mechanistically linked to R-M systems in a large variety of bacterial lineages.

genomics↗

bioRxiv2019

Transcriptional profiling of potato (Solanum tuberosum L.) during a compatible interaction with the root-knot nematode, Meloidogyne javanica

Root-knot nematode (RKN, Meloidogyne javanica) presents a great challenge to Solanaceae crops, including the potato. In this report, we conducted an investigation to understand the transcriptional regulation of molecular responses in potato roots during a compatible interaction following RKN infection. In this study, analysis of gene expression profiles using RNA-seq of Solanum tuberosum cv Mondial with RKN interaction at 0, 3- and 7-days post-inoculation (dpi). In total, 4,948 and 4,484 genes were respectively detected as differentially expressed genes (DEGs) at 3 and 7 dpi. Functional annotation revealed that genes associated with metabolic process were enriched at the transcriptional level suggesting they have an important role in RKN disease development. Nematode infection caused down-regulation of 282 genes associated with pathogen perception hence interfering with activation plant immune system. Further, late activation of pathogenesis-related genes, down-regulation disease resistance genes and activation of host antioxidant system contributed to a susceptible response. Activation of Jasmonic acid (JA) pathway and protease inhibitors was due to wounding during nematode migration and feeding. Nematode infection suppressed ethylene (ET) and salicylic acid (SA) signalling pathway hindering SA/ET responsive genes involved with defense. Induction of auxin biosynthesis genes, regulation of cytokinin levels and up-regulation of transporter genes facilitated of nematode feeding sites (NFSs) initiation. The regulation of several families of transcription factors (TFs) in the plant, such as WRKY, GRAS, ERF BHLH and MYB, was affected by RKN infection disrupting plant defense signalling pathways. This clearly suggest that TFs played an indispensable role in physiological adaptation for successful RKN disease development. This genome-wide analysis revealed the molecular regulatory networks in potato roots which are successfully manipulated by RKN. Being the first study analysing transcriptome profiling of RKN diseased potato, it will provide unparalleled insight into the mechanism underlying disease development.

pathology↗

bioRxiv2019

Horizontally acquired quorum sensing regulators recruited by the PhoP regulatory network expand host-adaptation repertoire in the phytopathogen Pectobacterium carotovorum

In this study, we examine the impact of transcriptional network rearrangements driven by horizontal gene acquisition in PhoP and SlyA regulons using as a case study the phytopathosystem comprised of potato tubers and the soft rot pathogen Pectobacterium carotovorum subsp. brasiliense (Pcb1692). By comparing those two networks with that of PecS obtained from the closely related Dickeya dadantii, we found that: (a) 24-31% of the genes regulated at late infection are genus-specific (GS) (based on Pectobacterium and Dickeya genera), and that (b) of these, 28.1-44.4% were predicted with high confidence as horizontal gene transfer (HGT) candidates. Further, genome simulation and statistical analyses corroborated the bias in late infection regulons towards the transcriptional control of candidate GS-HGT genes by PhoP, SlyA, and PecS, highlighting the prominence of network rearrangements in these late infection regulons. The evidence further supports the circumscription of two horizontally acquired quorum sensing regulators (carR and expR1) by the PhoP network. By recruiting carR and expR1, the PhoP network also impacts certain host adaptation- and bacterial competition-related systems, seemingly in a quorum sensing-dependent manner, such as the type VI secretion system, carbapenem biosynthesis, and plant cell walls degrading enzymes (PCWDE) such as cellulases and pectate lyases. Conversely, polygalacturonases and the type III secretion system (T3SS) exhibit a transcriptional pattern that suggests quorum sensing-independent regulation by the PhoP network. This includes a yet uncharacterized novel phage-related gene family within the T3SS gene cluster that has been recently acquired by two Pectobacterium species. The evidence further suggests a PhoP-dependent regulation of carbapenem and PCWDE-encoding genes based on the synthesized products optimum pH. The PhoP network also controls slyA expression in planta, which seems to impact the carbohydrate metabolism regulation, especially at early infection when 69.6% of the SlyA-regulated genes from that category also require PhoP to achieve normal expression levels.\n\nAUTHOR SUMMARYExchanging genetic material through horizontal transfer is a critical mechanism that drives bacteria to efficiently adapt to host defenses. In this report, we demonstrate that a specific plant pathogenic species (from the Pectobacterium genus) successfully integrated a population density-based behaviour system (quorum sensing) acquired through horizontal transfer into a resident stress-response gene regulatory network controlled by the PhoP protein. Evidence found here underscores that subsets of bacterial weaponry critical for colonization, typically known to respond to quorum sensing, are also controlled by PhoP. Some of these traits include different types of enzymes that can efficiently break plant cell walls depending on the environmental acidity level. Thus, we hypothesize that PhoP ability to elicit regulatory responses based on acidity and nutrient availability fluctuations may have strongly impacted the fixation of its regulatory connection with quorum sensing. In addition, another global gene regulator known as SlyA was found under the PhoP regulatory network. The SlyA regulator controls a series of carbohydrate metabolism-related traits, which also seem to be regulated by PhoP. By centralizing quorum sensing and slyA under PhoP scrutiny, Pectobacterium cells added an advantageous layer of control over those two networks that potentially enhances colonization efficiency.

microbiology↗

bioRxiv2018

The impact of type VI secretion system, bacteriocins and antibiotics on competition amongst Soft-Rot Enterobacteriaceae: Regulation of carbapenem biosynthesis by iron and the transcriptional regulator Fur

Plant microbial communities complexity provide a rich model for investigation on biochemical and regulatory strategies involved in interbacterial competition. Within these niches, the soft rot Enterobacteriaceae (SRE) comprise an emerging group of plant-pathogens inflicting soft rot/black-leg diseases and causing economic losses worldwide in a variety of crops. In this report, a range of molecular and computational techniques are utilized to survey the contribution of antimicrobial factors such as bacteriocins, carbapenem antibiotic and type VI secretion system (T6SS) in interbacterial competition among plant-pathogens/endophytes using an aggressive SRE as a case study (Pectobacterium carotovorum subsp. brasiliense strain PBR1692 - Pcb1692). A preliminary screening using next-generation sequencing of 16S rRNA comparatively analysing healthy and diseased potato tubers, followed by in vitro competition assays, corroborated the aggressiveness of Pcb1692 against several relevant taxa sharing this niche ranging from Proteobacteria to Firmicutes. The results showed growth inhibition of several Proteobacteria by Pcb1692 depends either on carbapenem or pyocin production. Whereas for targeted Firmicutes, only pyocin seems to play a role in growth inhibition by Pcb1692. Further analyses elucidated that although T6SS confers no relevant advantage during in vitro competition, a significant attenuation in competition by the mutant strain lacking a functional T6SS was observed in planta. Furthermore, production of carbapenem by Pcb1692 was observably dependent on the presence of environmental iron and oxygen. Additionally, upon deletion of fur, slyA and expI regulators, carbapenem production ceased, implying a complex regulatory mechanism involving these three genes. Potential Fur binding sites found upstream of slyA, carR and expR in Pectobacterium genomes harboring carbapenem-associated genes further suggests a conserved regulatory pattern in the genus, in which carbapenem might be modulated in response to iron through the control exerted by Fur over secondary regulators. Furthermore, we unveiled the striking role played by S-pyocin in growth inhibition within the SRE group.\n\nAuthors SummaryFor many phytopathogenic bacteria, more is known about interactions within the host and virulence factors used for host colonisation while relatively less is known about microbe-microbe interactions and factors that shape niche colonisation. The soft rot Enterobacteriaceae (SRE) comprise an emerging group of phytopathogens causing soft rot/black-leg diseases in a variety of crops leading to huge economic losses worldwide. In this report, a range of molecular and computational techniques are utilized to survey the contribution of antimicrobial factors such as bacteriocins, carbapenem antibiotic and type VI secretion system (T6SS) in interbacterial competition among plant-pathogens/endophytes using an aggressive SRE as a case study (Pcb1692). Our results show that Pcb1692 inhibits growth of other SRE and several potato endophytes using either the type VI secretion, carbapenem or bacteriocins. Carbapenem plays a role in both inter and intrabacterial competition in vitro, while the Pcb1692T6SS plays a role in interbacterial competition in planta (in potato tubers). We also demonstrate that carbapenem regulation requires the presence of environmental iron and oxygen in a complex network consisting of Pcb1692 Fur, SlyA, and ExpI. The presence of these gene homologs in several SREs suggests that they too can deploy similar antimicrobials to target other bacteria.

microbiology↗

bioRxiv2018

Transcriptome and Comparative Genomics analyses reveal new functional insights on key determinants of pathogenesis and interbacterial competition in Pectobacterium and Dickeya spp

Soft-rot Enterobacteriaceae (SRE) typified by Pectobacterium and Dickeya genera are phytopathogenic bacteria inflicting soft-rot disease in crops worldwide. By combining genomic information from 100 SRE with whole-transcriptome datasets, we identified novel genomic and transcriptional associations amongst key pathogenicity themes in this group. Comparative genomics revealed solid linkage between the type I secretion system (T1SS) and the carotovoricin bacteriophage (Ctv) conserved in 96.7% of Pectobacterium genomes. Moreover, their co-activation during infection might indicate a novel functional association involving T1SS/Ctv. Another bacteriophage-borne genomic region mostly confined in less than 10% of Pectobacterium organisms was found, presumably comprising a novel lineage-specific prophage in the genus. We also detected the transcriptional co-regulation of a previously predicted toxin/immunity pair (WHH and SMI1_KNR4 families) along with type VI secretion system (T6SS) and hcp/vgrG genes suggesting a role in disease development as T6SS-dependent effectors. Further, we showed that another predicted T6SS-dependent endonuclease (AHH-family) exhibited toxicity in ectopic expression assays indicating antibacterial activity. Additionally, we report the striking conservation of group-4-capsule (GFC) cluster in 100 SRE strains which consistently features adjacently conserved serotype-specific gene-arrays comprising a previously unknown organization in GFC clusters. Also, extensive sequence variations found in gfcA orthologs suggest a serotype-specific role in the GfcABCD machinery.

genomics↗

bioRxiv2017

Expansion and diversification of the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) in land plants

Gibberellic acid (gibberellins, GA) controls key developmental processes in the life-cycle of land plants. By interacting with the GIBBERELLIN INSENSITIVE DWARF1 (GID1) receptor, GA regulates the expression of a wide range of genes through different pathways. Here we report the systematic identification and classification of GID1s in 52 plants genomes, encompassing from bryophytes and lycophytes, to several monocots and eudicots. We investigated the evolutionary relationship of GID1s using a comparative genomics framework and found strong support a previously proposed phylogenetic classification of this family in land plants. We identified lineage-specific expansions of particular subfamilies (i.e. GID1ac and GID1b) in different eudicot lineages (e.g. GID1b in legumes). Further, we found both, shared and divergent structural features between GID1ac and GID1b subgroups in eudicots, which provide mechanistic insights on their functions. Gene expression data from several species show that at least one GID1 gene is expressed in every sampled tissue, with a strong bias of GID1b expression towards underground tissues and dry legume seeds (typically with low GA levels). Taken together, our results support that GID1ac retained canonical GA signaling roles, whereas GID1b specialized in conditions of low GA concentrations. We propose that this functional specialization occurred initially at the gene expression level and was later fine-tuned by specific mutations that conferred greater GA affinity to GID1b, including a Phe residue in the GA-binding pocket. Finally, we discuss the importance of our findings to understand the diversification of GA perception mechanisms in land plants.

plant biology↗

bioRxiv2017

De novo transcriptome sequencing and comparative analysis of midgut tissues of four non-model insects pertaining to Hemiptera, Coleoptera, Diptera and Lepidoptera

Despite the great morphological diversity of insects, there is a regularity in their digestive functions, which is apparently related to their physiology. In the present work we report the de novo midgut transcriptomes of four non-model insects from four distinct orders: Spodoptera frugiperda (Lepidoptera), Musca domestica (Diptera), Tenebrio molitor (Coleoptera) and Dysdercus peruvianus (Hemiptera). We employed a computational strategy to merge assemblies obtained with two different algorithms, which substantially increased the quality of the final transcriptomes. Unigenes were annotated and analyzed using the eggNOG database, which allowed us to assign some level of functional and evolutionary information to 79.7% to 93.1% of the transcriptomes. We found interesting transcriptional patterns, such as: i) the intense use of lysozymes in digestive functions of M. domestica larvae, which are streamlined and adapted to feed on bacteria; ii) the up-regulation of orthologous UDP-glycosyl transferase and cytochrome P450 genes in the whole midguts different species, supporting the presence of an ancient defense frontline to counter xenobiotics; iii) evidence supporting roles for juvenile hormone binding proteins in the midgut physiology, probably as a way to activate genes that help fight anti-nutritional substances (e.g. protease inhibitors). The results presented here shed light on the digestive and structural properties of the digestive systems of these distantly related species. Furthermore, the produced datasets will also be useful for scientists studying these insects.

genomics↗