Characteristics and Evolutionary Analysis of Photosynthetic Gene Clusters on Extrachromosomal Replicons: from Streamlined Plasmids to Chromids

ABSTRACT Aerobic anoxygenic photoheterotrophic bacteria (AAPB) represent a bacteriochlorophyll a-containing functional group. Substantial evidence indicates that highly conserved photosynthetic gene clusters (PGCs) of AAPB can be transferred between species, genera, and even phyla. Furthermore, analysis of recently discovered PGCs carried by extrachromosomal replicons (exPGCs) suggests that extrachromosomal replicons (ECRs) play an important role in the transfer of PGCs. In this study, 13 Roseobacter clade genomes from seven genera that harbored exPGCs were used to analyze the characteristics and evolution of PGCs. The identification of plasmid-like and chromid-like ECRs among PGC-containing ECRs revealed two different functions: the spread of PGCs among strains and the maintenance of PGCs within genomes. Phylogenetic analyses indicated two independent origins of exPGCs, corresponding to PufC-containing and PufX-containing puf operons. Furthermore, the two different types of operons were observed within different strains of the same Tateyamaria and Jannaschia genera. The PufC-containing and PufX-containing operons were also differentially carried by chromosomes and ECRs in the strains, respectively, which provided clear evidence for ECR-mediated PGC transfer. Multiple recombination events of exPGCs were also observed, wherein the majority of exPGCs were inserted by replication modules at the same genomic positions. However, the exPGCs of the Jannaschia strains comprised superoperons without evidence of insertion and therefore likely represent an initial evolutionary stage where the PGC was translocated from chromosomes to ECRs without further combinations. Finally, a scenario of PGC gain and loss is proposed that specifically focuses on ECR-mediated exPGC transfer to explain the evolution and patchy distribution of AAPB within the Roseobacter clade. IMPORTANCE The evolution of photosynthesis was a significant event during the diversification of biological life. Aerobic anoxygenic photoheterotrophic bacteria (AAPB) share physiological characteristics with chemoheterotrophs and represent an important group associated with bacteriochlorophyll-dependent phototrophy in the environment. Here, characterization and evolutionary analyses were conducted for 13 bacterial strains that contained photosynthetic gene clusters (PGCs) carried by extrachromosomal replicons (ECRs) to shed light on the evolution of chlorophototrophy in bacteria. This report advances our understanding of the importance of ECRs in the transfer of PGCs within marine photoheterotrophic bacteria.

Download Full-text

Characteristics and Evolutionary analysis of Photosynthetic Gene Clusters on Extrachromosomal Replicons: from streamlined plasmids to chromids

10.1101/663864 ◽

2019 ◽

Author(s):

Yanting Liu ◽

Qiang Zheng ◽

Wenxin Lin ◽

Nianzhi Jiao

Keyword(s):

Heterotrophic Bacteria ◽

Phylogenetic Analyses ◽

Gene Clusters ◽

Evolutionary Stage ◽

Evolutionary Analysis ◽

Bacterial Strains ◽

Photosynthetic Gene ◽

Different Strains ◽

Evolution Of Photosynthesis ◽

Shed Light

AbstractAerobic anoxygenic photoheterotrophic bacteria (AAPB) represent intermediates in the evolution from photoautotrophic to heterotrophic metabolisms. Substantial evidence indicates that highly conserved photosynthetic gene clusters (PGCs) of AAPB can be transferred between species, genera, and even phyla. Furthermore, analysis of recently discovered PGCs carried by extrachromosomal replicons (exPGCs) suggests that extrachromosomal replicons (ECRs) play an important role in the transfer of PGCs. In the present study, thirteenRoseobacterclade genomes from seven genera that harbored exPGCs were used to analyze characteristics and evolution of PGCs. The identification of plasmid-like and chromid-like ECRs from PGC-containing ECRs revealed two different functions: the spread of PGCs among strains and the maintenance of PGCs within genomes. Phylogenetic analyses indicated two independent origins of exPGCs, corresponding to PufC-containing and PufX-containing photosynthetic reaction complexes. Furthermore, the two different types of complexes were observed within different strains of the sameTateyamariaandJannaschiagenera. The two different complexes were also differentially carried by chromosomes and ECRs in the strains, respectively, which provided clear evidence for ECR-mediated PGC transfer. Multiple recombination events of exPGCs were also observed, wherein the majority of exPGCs were inserted by replication modules at the same genomic positions. However, the exPGCs of theJannaschiastrains comprised superoperons without evidence of insertion, and therefore likely represent an initial evolutionary stage where the PGC was translocated from chromosomes to ECRs without further combinations. Lastly, a scenario of PGC gain and loss is proposed that specifically focuses on ECR-mediated exPGC transfer to explain the evolution and patchy distribution of AAPB within theRoseobacterclade.ImportanceThe evolution of photosynthesis was a significant event during the diversification of biological life. Aerobic anoxygenic heterotrophic bacteria (AAPB) share physiological characteristics with both photoautotrophs and heterotrophs and are therefore suggested to be evolutionary intermediates between the two lifestyles. Here, characterization and evolutionary analyses were conducted for thirteen bacterial strains that contained photosynthetic gene clusters (PGCs) carried by extrachromosomal replicons (ECRs) to shed light on the evolution of photosynthesis in bacteria. Specifically, these analyses improved the “Think Pink” scenario of PGC transfer that is mediated by ECRs inRoseobacterclade strains. This study advances our understanding of the importance of ECRs in the transfer of PGCs within marine photoheterotrophic bacteria.

Download Full-text

The Type VI Secretion System of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility

10.21203/rs.3.rs-48039/v2 ◽

2020 ◽

Author(s):

Nathaly Andrea Montenegro Benavides ◽

Alejandro Alvarez Borrero ◽

Mario Luis Arrieta Ortiz ◽

Luis Miguel Rodriguez-R. ◽

David Octavio Botero Rozo ◽

...

Keyword(s):

Gene Knockout ◽

Phylogenetic Analyses ◽

Gene Clusters ◽

Secretion System ◽

Type Vi Secretion System ◽

Cellular Processes ◽

Protein Secretion System ◽

Different Strains

Abstract Background: The type VI protein secretion system (T6SS) is important in diverse cellular processes in Gram-negative bacteria, including interactions with other bacteria and with eukaryotic hosts. In this study we analyze the evolution of the T6SS in the genus Xanthomonas and evaluate its importance of the T6SS for virulence and in vitro motility in Xanthomonas phaseoli pv. manihotis (Xpm), the causal agent of bacterial blight in cassava (Manihot esculenta). We delineate the organization of the T6SS gene clusters in Xanthomonas and then characterize proteins of this secretion system in Xpm strain CIO151. Results: We describe the presence of three different clusters in the genus Xanthomonas that vary in their organization and degree of synteny between species. Using a gene knockout mutagenesis, we also found that vgrG and hcp are required for maximal aggressiveness of Xpm on cassava plants while clpV is important for both motility and maximal aggressiveness. Conclusion: We characterized the T6SS in 15 different strains in Xanthomonas and our phylogenetic analyses suggest that the T6SS might have been acquired by a very ancient event of horizontal gene transfer and maintained through evolution, hinting at their importance for the adaptation of Xanthomonas to their hosts. Finally, we demonstrated that the T6SS of Xpm is functional, and significantly contributes to virulence and motility. This is the first experimental study that demonstrates the role of the T6SS in the Xpm-cassava interaction and the T6SS organization in the genus Xanthomonas.

Download Full-text

The Type VI Secretion System of Xanthomonas Phaseoli pv. Manihotis is Involved in Virulence and in vitro Motility

10.21203/rs.3.rs-48039/v1 ◽

2020 ◽

Author(s):

Nathaly Andrea Montenegro Benavides ◽

Alejandro Alvarez Borrero ◽

Mario Luis Arrieta Ortiz ◽

Luis Miguel Rodriguez-R. ◽

David Octavio Botero Rozo ◽

...

Keyword(s):

Gene Knockout ◽

Phylogenetic Analyses ◽

Gene Clusters ◽

Secretion System ◽

Type Vi Secretion System ◽

In Vitro Motility ◽

Cellular Processes ◽

Protein Secretion System ◽

Different Strains

Download Full-text

The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility

BMC Microbiology ◽

10.1186/s12866-020-02066-1 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Nathaly Andrea Montenegro Benavides ◽

Alejandro Alvarez B. ◽

Mario L. Arrieta-Ortiz ◽

Luis Miguel Rodriguez-R ◽

David Botero ◽

...

Keyword(s):

Gene Knockout ◽

Phylogenetic Analyses ◽

Gene Clusters ◽

Secretion System ◽

Type Vi Secretion System ◽

In Vitro Motility ◽

Cellular Processes ◽

Protein Secretion System ◽

Different Strains

Abstract Background The type VI protein secretion system (T6SS) is important in diverse cellular processes in Gram-negative bacteria, including interactions with other bacteria and with eukaryotic hosts. In this study we analyze the evolution of the T6SS in the genus Xanthomonas and evaluate its importance of the T6SS for virulence and in vitro motility in Xanthomonas phaseoli pv. manihotis (Xpm), the causal agent of bacterial blight in cassava (Manihot esculenta). We delineate the organization of the T6SS gene clusters in Xanthomonas and then characterize proteins of this secretion system in Xpm strain CIO151. Results We describe the presence of three different clusters in the genus Xanthomonas that vary in their organization and degree of synteny between species. Using a gene knockout strategy, we also found that vgrG and hcp are required for maximal aggressiveness of Xpm on cassava plants while clpV is important for both motility and maximal aggressiveness. Conclusion We characterized the T6SS in 15 different strains in Xanthomonas and our phylogenetic analyses suggest that the T6SS might have been acquired by a very ancient event of horizontal gene transfer and maintained through evolution, hinting at their importance for the adaptation of Xanthomonas to their hosts. Finally, we demonstrated that the T6SS of Xpm is functional, and significantly contributes to virulence and motility. This is the first experimental study that demonstrates the role of the T6SS in the Xpm-cassava interaction and the T6SS organization in the genus Xanthomonas.

Download Full-text

The Type VI Secretion System of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility

10.21203/rs.3.rs-48039/v3 ◽

2020 ◽

Author(s):

Nathaly Andrea Montenegro Benavides ◽

Alejandro Alvarez Borrero ◽

Mario Luis Arrieta Ortiz ◽

Luis Miguel Rodriguez-R. ◽

David Octavio Botero Rozo ◽

...

Keyword(s):

Gene Knockout ◽

Phylogenetic Analyses ◽

Gene Clusters ◽

Secretion System ◽

Type Vi Secretion System ◽

Cellular Processes ◽

Protein Secretion System ◽

Different Strains

Abstract Background: The type VI protein secretion system (T6SS) is important in diverse cellular processes in Gram-negative bacteria, including interactions with other bacteria and with eukaryotic hosts. In this study we analyze the evolution of the T6SS in the genus Xanthomonas and evaluate its importance of the T6SS for virulence and in vitro motility in Xanthomonas phaseoli pv. manihotis (Xpm), the causal agent of bacterial blight in cassava (Manihot esculenta). We delineate the organization of the T6SS gene clusters in Xanthomonas and then characterize proteins of this secretion system in Xpm strain CIO151. Results: We describe the presence of three different clusters in the genus Xanthomonas that vary in their organization and degree of synteny between species. Using a gene knockout strategy, we also found that vgrG and hcp are required for maximal aggressiveness of Xpm on cassava plants while clpV is important for both motility and maximal aggressiveness. Conclusion: We characterized the T6SS in 15 different strains in Xanthomonas and our phylogenetic analyses suggest that the T6SS might have been acquired by a very ancient event of horizontal gene transfer and maintained through evolution, hinting at their importance for the adaptation of Xanthomonas to their hosts. Finally, we demonstrated that the T6SS of Xpm is functional, and significantly contributes to virulence and motility. This is the first experimental study that demonstrates the role of the T6SS in the Xpm-cassava interaction and the T6SS organization in the genus Xanthomonas.

Download Full-text

Genome Analysis of Streptomyces nojiriensis JCM 3382 and Distribution of Gene Clusters for Three Antibiotics and an Azasugar across the Genus Streptomyces

Microorganisms ◽

10.3390/microorganisms9091802 ◽

2021 ◽

Vol 9 (9) ◽

pp. 1802

Author(s):

Jin-Soo Park ◽

Da-Eun Kim ◽

Sung-Chul Hong ◽

Seung-Young Kim ◽

Hak Cheol Kwon ◽

...

Keyword(s):

Genome Analysis ◽

Gene Clusters ◽

Biosynthetic Gene ◽

Chemical Profile ◽

Biosynthetic Gene Clusters ◽

Genus Streptomyces ◽

Streptomyces Spp ◽

Spectroscopic Analyses ◽

Different Types ◽

Different Strains

Streptomyces spp. have been major contributors of novel natural products that are used in many application areas. We found that the nojirimycin (NJ) producer JCM 3382 has antimicrobial activity against Staphylococcus aureus via cellular degradation. Genome analysis revealed 30 biosynthetic gene clusters, including those responsible for producing antibiotics, including an azasugar NJ. In-depth MS/MS analysis confirmed the production of 1-deoxynojirimycin (DNJ) along with NJ. In addition, the production of tambromycins, setomimycin, and linearmycins was verified by spectroscopic analyses, including LC-MS and NMR. The distribution of the clusters of genes coding for antibiotics in 2061 Streptomyces genomes suggested potential producers of tambromycin, setomimycin, and linearmycin. For a DNJ gene cluster, homologs of gabT1 and gutB1 were commonly found; however, yktC1 was identified in only 112 genomes. The presence of several types of clusters suggests that different strains may produce different types of azasugars. Chemical-profile-inspired comparative genome analysis may facilitate a more accurate assessment of the biosynthetic potential to produce secondary metabolites.

Download Full-text

Antioxidant and Antibacterial Activities of Artemisia herba-alba Asso Essential Oil from Middle Atlas, Morocco

Phytothérapie ◽

10.3166/phyto-2018-0057 ◽

2018 ◽

Vol 16 (S1) ◽

pp. S48-S54

Author(s):

Y. Ez zoubi ◽

S. Lairini ◽

A. Farah ◽

K. Taghzouti ◽

A. El Ouali Lalami

Keyword(s):

Antibacterial Activity ◽

Essential Oil ◽

Foodborne Pathogens ◽

Food Systems ◽

Antibacterial Activities ◽

Culture Collection ◽

Bornyl Acetate ◽

Bacterial Strains ◽

Disk Diffusion Assay ◽

Different Strains

The purpose of this study was to determine the chemical composition and to evaluate the antioxidant and antibacterial effects of the Moroccan Artemisia herba-alba Asso essential oil against foodborne pathogens. The essential oil of Artemisia herba-alba was analyzed by gas chromatography coupled with mass spectroscopy. The antibacterial activity was assessed against three bacterial strains isolated from foodstuff and three bacterial strains referenced by the ATCC (American Type Culture Collection) using the disk diffusion assay and the macrodilution method. The antioxidant activity was evaluated using the DPPH (2, 2-diphenyl-1- picrylhydrazyl) method. The fourteen compounds of the Artemisia herba-alba essential oil were identified; the main components were identified as β-thujone, chrysanthenone, α-terpineol, α-thujone, α-pinene, and bornyl acetate. The results of the antibacterial activity obtained showed a sensitivity of the different strains to Artemisia herba-alba essential oil with an inhibition diameter of 8.50 to 17.00 mm. Concerning the MICs (minimum inhibitory concentrations), the essential oil exhibited much higher antibacterial activity with MIC values of 2.5 μl/ml against Bacillus subtilis ATCC and Lactobacillus sp. The essential oil was found to be active by inhibiting free radicals with an IC50 (concentration of an inhibitor where the response is reduced by half) value of 2.9 μg/ml. These results indicate the possible use of the essential oil on food systems as an effective inhibitor of foodborne pathogens, as a natural antioxidant, and for potential pharmaceutical applications. However, further research is needed in order to determine the toxicity, antibacterial, and antioxidant effects in edible products.

Download Full-text

A Closer Look at the Cellular and Molecular Components of the Deep/Muscular Fasciae

International Journal of Molecular Sciences ◽

10.3390/ijms22031411 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1411

Author(s):

Caterina Fede ◽

Carmelo Pirri ◽

Chenglei Fan ◽

Lucia Petrelli ◽

Diego Guidolin ◽

...

Keyword(s):

Extracellular Matrix ◽

Connective Tissue ◽

Treatment Strategies ◽

Clear Understanding ◽

Pathological Characteristics ◽

Appropriate Treatment ◽

Different Types ◽

Molecular Components ◽

Entire Network ◽

Shed Light

The fascia can be defined as a dynamic highly complex connective tissue network composed of different types of cells embedded in the extracellular matrix and nervous fibers: each component plays a specific role in the fascial system changing and responding to stimuli in different ways. This review intends to discuss the various components of the fascia and their specific roles; this will be carried out in the effort to shed light on the mechanisms by which they affect the entire network and all body systems. A clear understanding of fascial anatomy from a microscopic viewpoint can further elucidate its physiological and pathological characteristics and facilitate the identification of appropriate treatment strategies.

Download Full-text

Whole-Body Regeneration in Sponges: Diversity, Fine Mechanisms, and Future Prospects

Genes ◽

10.3390/genes12040506 ◽

2021 ◽

Vol 12 (4) ◽

pp. 506

Author(s):

Alexander Ereskovsky ◽

Ilya E. Borisenko ◽

Fyodor V. Bolshakov ◽

Andrey I. Lavrov

Keyword(s):

Single Species ◽

Whole Body ◽

Phylogenetic Position ◽

Main Body ◽

Regenerative Processes ◽

Cellular Mechanisms ◽

Different Types ◽

Dissociated Cells ◽

Shed Light ◽

Regeneration Processes

While virtually all animals show certain abilities for regeneration after an injury, these abilities vary greatly among metazoans. Porifera (Sponges) is basal metazoans characterized by a wide variety of different regenerative processes, including whole-body regeneration (WBR). Considering phylogenetic position and unique body organization, sponges are highly promising models, as they can shed light on the origin and early evolution of regeneration in general and WBR in particular. The present review summarizes available data on the morphogenetic and cellular mechanisms accompanying different types of WBR in sponges. Sponges show a high diversity of WBR, which principally could be divided into (1) WBR from a body fragment and (2) WBR by aggregation of dissociated cells. Sponges belonging to different phylogenetic clades and even to different species and/or differing in the anatomical structure undergo different morphogeneses after similar operations. A common characteristic feature of WBR in sponges is the instability of the main body axis: a change of the organism polarity is described during all types of WBR. The cellular mechanisms of WBR are different across sponge classes, while cell dedifferentiations and transdifferentiations are involved in regeneration processes in all sponges. Data considering molecular regulation of WBR in sponges are extremely scarce. However, the possibility to achieve various types of WBR ensured by common morphogenetic and cellular basis in a single species makes sponges highly accessible for future comprehensive physiological, biochemical, and molecular studies of regeneration processes.

Download Full-text

Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts

Genome Biology and Evolution ◽

10.1093/gbe/evz155 ◽

2019 ◽

Cited By ~ 4

Author(s):

Sergio A Muñoz-Gómez ◽

Keira Durnin ◽

Laura Eme ◽

Christopher Paight ◽

Christopher E Lane ◽

...

Keyword(s):

Life Style ◽

Metabolic Pathways ◽

Evolutionary History ◽

Phylogenetic Analyses ◽

Phylogenetic Position ◽

Biosynthetic Pathways ◽

History Of ◽

Sea Squirts ◽

Shed Light ◽

Apicoplast Genome

Abstract A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to (1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, (2) search for the apicoplast genome of Nephromyces, and (3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the non-photosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.

Download Full-text