T9GPred: A Comprehensive Computational Tool for the Prediction of Type 9 Secretion System, Gliding Motility, and the Associated Secreted Proteins

C-terminal glycosylation of type IX secretion system cargo proteins in Prevotella intermedia with both short and long secretion signals

Prevotella intermedia is a Gram-negative bacterium that is associated with periodontitis and acute necrotizing ulcerative gingivitis. P. intermedia utilizes the type IX secretion system (T9SS) to secrete and anchor virulence factors to the cell surface, presumably via C-terminal glycosylation. The identity of the linking sugar and the sites of modification on the cargo are unknown. Here, we employed hidden Markov models to predict cargo proteins in P. intermedia and conducted LC-MS/MS analyses of partially deglycosylated fractions to characterize the C-terminal glycosylation. A total of 80 cargo proteins were predicted based on the presence of a T9SS C-terminal domain (CTD) signal, and these were divided into 48 short CTDs and 32 long CTDs. Cleavage sites for five short and four long CTDs were experimentally determined, and glycosylation was observed at the mature C-terminus of six cargo. Two glycans were identified of delta masses 419.198 and 433.185 Da, corresponding to novel C-terminal amide linkages to N-alanyl dHex-HexNAc and N-alanyl (Me-dHex)-HexNAc, respectively. This indicated that both short and long CTDs supported cleavage and glycosylation. AlphaFold multimer modelling predicted that both kinds of CTDs could bind to the PorV shuttle protein in the same manner, with the conserved CTD motifs interacting with the same sites in PorV.

Complete genome and carbohydrate-active enzymes of Arenibacter antarcticus KCTC 52924T isolated from deep sea sediment of Ross Sea, Antarctica

Members of the genus Arenibacter were widely distributed in oceanic habitats around the world and have been studied for a variety of useful properties, including antigen deactivation, pollutant degradation, and the production of antimicrobial agents. Arenibacter antarcticus KCTC 52924T of our interest is an aerobic, non-motile, Gram-negative, psychrotolerant type strain isolated from the deep-sea sediment of Ross Sea, Antarctica. The extreme conditions of this habitat are believed to have diversified the substrate spectrum and range of operational conditions of the enzymes, offering both scientific interest and potential industrial benefits. Here, we obtained the complete genome sequence of this promising strain, which consists of 4,694,007 bp (G + C content of 38.8 %) with a single chromosome, 3917 protein-coding genes, 43 tRNAs, and 3 rRNA operons. The functional annotations of the genome reveal four metabolite biosynthesis clusters and a variety of carbohydrate-active enzymes with potential biotechnological applications. Additionally, several interesting features related to environmental interactions were identified. Therefore, this genome data and its genomic potentials figured out in this study serve as a conner stone in further study aimed at understanding physiology of this strain which may be valuable in biotechnological purpose.

Differential gliding motility responses of Chryseobacterium sp. strain PMSZPI isolated from uranium ore deposit on hard and soft substrates

The Bacteroidota bacterium, Chryseobacterium sp. strain PMSZPI isolated from sub-surface soil of uranium ore deposit was shown to move on solid surfaces via gliding motility resulting in the formation of thin spreading colonies. In this study, we attempted to understand the influence of the surfaces, soft or hard/rigid, on the motility behaviour of PMSZPI cells. The computational tool T9GPred in combination with LC-MS/MS analysis established the presence of orthologs of vital gliding motility proteins in PMSZPI. We analyzed the single cell or population motility phenotypes of PMSZPI under spreading and non-spreading conditions. A low percentage of agar or soft agar (0.35 %) with low nutrient levels induced more active gliding motility in individual cells leading to increased colony spreading. Microscopic analyses indicated the self-assembly of the gliding cells into irregular edged or spherical microcolonies based on the agar concentration. Cells moved at a speed of 0.6 µm s-1 on low-percentage gliding permissive agar (0.35 %) surface in contrast to significant inhibition of motility on rigid or hard agar (1.5 %) surface. RNA sequencing and real-time quantitative PCR (qPCR) analysis revealed increased expression of gliding motility genes under low agar conditions consistent with increased spreading behaviour. These findings provide the first glimpse into the gliding motility behaviour of a Bacteroidota bacterium from metal enriched environment that apparently could have implications on bacterial adaptation to changing surface environments.

Proteomic characterization of Tenacibaculum dicentrarchi under iron limitation reveals an upregulation of proteins related to iron oxidation and reduction metabolism, iron uptake systems and gliding motility

A strategy for vaccine design involves identifying proteins that could be involved in pathogen-host interactions. The aim of this proteomic study was to determine how iron limitation affects the protein expression of Tenacibaculum dicentrarchi, with a primary focus on virulence factors and proteins associated with iron uptake. The proteomic analysis was carried out using two strains of T. dicentrarchi grown under normal (control) and iron-limited conditions, mimicking the host environment. Our findings revealed differences in the proteins expressed by the type strain CECT 7612T and the Chilean strain TdCh05 of T. dicentrarchi. Nonetheless, both share a common response to iron deprivation, with an increased expression of proteins associated with iron oxidation and reduction metabolism (e.g., SufA, YpmQ, SufD), siderophore transport (e.g., ExbD, TonB-dependent receptor, HbpA), heme compound biosynthesis, and iron transporters under iron limitation. Proteins involved in gliding motility, such as GldL and SprE, were also upregulated in both strains. A negative differential regulation of metabolic proteins, particularly those associated with amino acid biosynthesis, was observed under iron limitation, reflecting the impact of iron availability on bacterial metabolism. Additionally, the TdCh05 strain exhibited unique proteins associated with gliding motility machinery and phage infection control compared to the type strain. These groups of proteins have been identified as virulence factors within the Flavobacteriaceae family, including the genus Tenacibaculum. These results build upon our previous report on iron acquisition mechanisms and could lay the groundwork for future studies aimed at elucidating the role of some of the described proteins in the infectious process of tenacibaculosis, as well as in the development of potential vaccines.

Radiation-Tolerant Fibrivirga spp. from Rhizosphere Soil: Genome Insights and Potential in Agriculture

The rhizosphere of plants contains a wide range of microorganisms that can be cultivated and used for the benefit of agricultural practices. From garden soil near the rhizosphere region, Strain ES10-3-2-2 was isolated, and the cells were Gram-negative, aerobic, non-spore-forming rods that were 0.3-0.8 µm in diameter and 1.5-2.5 µm in length. The neighbor-joining method on 16S rDNA similarity revealed that the strain exhibited the highest sequence similarities with "Fibrivirga algicola JA-25" (99.2%) and Fibrella forsythia HMF5405T (97.3%). To further explore its biotechnological potentialities, we sequenced the complete genome of this strain employing the PacBio RSII sequencing platform. The genome of Strain ES10-3-2-2 comprises a 6,408,035 bp circular chromosome with a 52.8% GC content, including 5038 protein-coding genes and 52 RNA genes. The sequencing also identified three plasmids measuring 212,574 bp, 175,683 bp, and 81,564 bp. Intriguingly, annotations derived from the NCBI-PGAP, eggnog, and KEGG databases indicated the presence of genes affiliated with radiation-resistance pathway genes and plant-growth promotor key/biofertilization-related genes regarding Fe acquisition, K and P assimilation, CO2 fixation, and Fe solubilization, with essential roles in agroecosystems, as well as genes related to siderophore regulation. Additionally, T1SS, T6SS, and T9SS secretion systems are present in this species, like plant-associated bacteria. The inoculation of Strain ES10-3-2-2 to Arabidopsis significantly increases the fresh shoot and root biomass, thereby maintaining the plant quality compared to uninoculated controls. This work represents a link between radiation tolerance and the plant-growth mechanism of Strain ES10-3-2-2 based on in vitro experiments and bioinformatic approaches. Overall, the radiation-tolerant bacteria might enable the development of microbiological preparations that are extremely effective at increasing plant biomass and soil fertility, both of which are crucial for sustainable agriculture.