scholarly journals Oxygenation properties of hemoglobin and the evolutionary origins of isoform multiplicity in an amphibious air-breathing fish, the blue-spotted mudskipper (Boleophthalmus pectinirostris)

2019 ◽  
Author(s):  
Jay F. Storz ◽  
Chandrasekhar Natarajan ◽  
Magnus K. Grouleff ◽  
Michael Vandewege ◽  
Federico G. Hoffmann ◽  
...  
Keyword(s):  
Globin Gene ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Comparative Genomic ◽  
Air Breathing ◽  
Aerial Respiration ◽  
Evolutionary Origins ◽  
Amino Acid Divergence ◽  
Boleophthalmus Pectinirostris ◽  
And Function

ABSTRACTAmong the numerous lineages of teleost fish that have independently transitioned from obligate water-breathing to facultative air-breathing, evolved properties of hemoglobin (Hb)-O2 transport may have been shaped by the prevalence and severity of aquatic hypoxia (which influences the extent to which fish are compelled to switch to aerial respiration) as well as the anatomical design of air-breathing structures and the cardiovascular system. Here we examine the structure and function of Hbs in an amphibious, facultative air-breathing fish, the blue-spotted mudskipper (Boleophthalmus pectinirostris). We also characterized the genomic organization of the globin gene clusters of the species and we integrated phylogenetic and comparative genomic analyses to unravel the duplicative history of the genes that encode the subunits of structurally distinct mudskipper Hb isoforms (isoHbs). The B. pectinirostris isoHbs exhibit high intrinsic O2-affinities, similar to those of hypoxia-tolerant, water-breathing teleosts, and remarkably large Bohr effects. Genomic analysis of conserved synteny revealed that the genes that encode the α-type subunits of the two main adult isoHbs are members of paralogous gene clusters that represent products of the teleost-specific whole-genome duplication. Experiments revealed no appreciable difference in the oxygenation properties of co-expressed isoHbs in spite of extensive amino acid divergence between the alternative α-chain subunit isoforms. It therefore appears that the ability to switch between aquatic and aerial respiration does not necessarily require a division of labor between functionally distinct isoHbs with specialized oxygenation properties.Summary statementThe blue-spotted mudskipper routinely switches between aquatic and aerial respiration. This respiratory versatility is associated with properties of hemoglobin-oxygen transport that are similar to those found in hypoxia-adapted water-breathing fishes.

scholarly journals Insights into the cultured bacterial fraction of corals

2020 ◽  
Author(s):  
Michael Sweet ◽  
Helena Villela ◽  
Tina Keller-Costa ◽  
Rodrigo Costa ◽  
Stefano Romano ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Gene Clusters ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Comprehensive Overview ◽  
Associated Bacteria ◽  
Reef Restoration ◽  
Coral Holobiont ◽  
Metabolic Interactions ◽  
And Function

Abstract Bacteria associated with coral hosts are diverse and abundant, with recent studies suggesting involvement of these symbionts in host resilience to anthropogenic stress. Despite the putative importance of bacteria, the work dedicated to culturing coral-associated bacteria has received little attention. Combining published and unpublished data, here we report a comprehensive overview of the diversity and function of culturable, coral-associated bacteria. A total of 3055 isolates from 52 studies were considered by our meta-survey. Of these, 1045 had full length 16S rRNA gene sequences, spanning 138 formally described and 12 putatively novel bacterial genera across the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria phyla. We performed comparative genomic analysis using the available genomes of 74 strains and identified potential signatures of beneficial bacterial-coral symbioses among them. Our analysis revealed >400 biosynthetic gene clusters that underlie the biosynthesis of antioxidant, antimicrobial, cytotoxic, and other secondary metabolites. Moreover, we uncovered genomic features - not previously described for coral-bacterial symbioses - involved in host colonization and host-symbiont recognition, antiviral defence mechanisms, and/or integrated metabolic interactions, which we suggest as novel targets for the screening of coral probiotics. Our results highlight the importance of bacterial cultures to elucidate coral holobiont functioning, and guide the selection of probiotic candidates to promote coral resilience and improve reef restoration efforts.

scholarly journals Genome Reduction and Secondary Metabolism of the Marine Sponge-Associated Cyanobacterium Leptothoe

Marine Drugs ◽  
2021 ◽  
Vol 19 (6) ◽  
pp. 298
Author(s):  
Despoina Konstantinou ◽  
Rafael V. Popin ◽  
David P. Fewer ◽  
Kaarina Sivonen ◽  
Spyros Gkelis
Keyword(s):  
Natural Products ◽  
Microbial Communities ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Marine Sponges ◽  
Genome Reduction ◽  
Extracellular Polysaccharides ◽  
Comparative Genomic ◽  
Symbiotic Relationships ◽  
Genes Encoding

Sponges form symbiotic relationships with diverse and abundant microbial communities. Cyanobacteria are among the most important members of the microbial communities that are associated with sponges. Here, we performed a genus-wide comparative genomic analysis of the newly described marine benthic cyanobacterial genus Leptothoe (Synechococcales). We obtained draft genomes from Le. kymatousa TAU-MAC 1615 and Le. spongobia TAU-MAC 1115, isolated from marine sponges. We identified five additional Leptothoe genomes, host-associated or free-living, using a phylogenomic approach, and the comparison of all genomes showed that the sponge-associated strains display features of a symbiotic lifestyle. Le. kymatousa and Le. spongobia have undergone genome reduction; they harbored considerably fewer genes encoding for (i) cofactors, vitamins, prosthetic groups, pigments, proteins, and amino acid biosynthesis; (ii) DNA repair; (iii) antioxidant enzymes; and (iv) biosynthesis of capsular and extracellular polysaccharides. They have also lost several genes related to chemotaxis and motility. Eukaryotic-like proteins, such as ankyrin repeats, playing important roles in sponge-symbiont interactions, were identified in sponge-associated Leptothoe genomes. The sponge-associated Leptothoe stains harbored biosynthetic gene clusters encoding novel natural products despite genome reduction. Comparisons of the biosynthetic capacities of Leptothoe with chemically rich cyanobacteria revealed that Leptothoe is another promising marine cyanobacterium for the biosynthesis of novel natural products.

scholarly journals Neonatal Salivary Analysis Reveals Global Developmental Gene Expression Changes in the Premature Infant

2010 ◽  
Vol 56 (3) ◽  
pp. 409-416 ◽  
Author(s):  
Jill L Maron ◽  
Kirby L Johnson ◽  
David M Rocke ◽  
Michael G Cohen ◽  
Albert J Liley ◽  
...  
Keyword(s):  
Gene Expression ◽  
System Development ◽  
Newborn Care ◽  
Genomic Analysis ◽  
Nervous System Development ◽  
Comparative Genomic ◽  
Tissue Development ◽  
Bioinformatics Analyses ◽  
Noninvasive Technique ◽  
And Function

Abstract Background: There is an important need to develop noninvasive biomarkers to detect disease in premature neonates. Our objective was to determine if salivary genomic analysis provides novel information about neonatal expression of developmental genes. Methods: Saliva (50–200 μL) was prospectively collected from 5 premature infants at 5 time points: before, starting, and advancing enteral nutrition; at the introduction of oral feeds; and at advanced oral feeds. Salivary RNA was extracted, amplified, and hybridized onto whole-genomic microarrays. Results: Bioinformatics analyses identified 9286 gene transcripts with statistically significant gene expression changes across individuals over time. Of these genes, 3522 (37.9%) were downregulated, and 5764 (62.1%) were upregulated. Gene expression changes were highly associated with developmental pathways. Significantly downregulated expression was seen in embryonic development, connective tissue development and function, hematologic system development and function, and survival of the organism (10−14 < P < 10−3). Conversely, genes associated with behavior, nervous system development, tissue development, organ development, and digestive system development were significantly upregulated (10−11 < P < 10−2). Conclusions: Comparative genomic salivary analyses provide robust, comprehensive, real-time information regarding nearly all organs and tissues in the developing preterm infant. This innovative and noninvasive technique represents a new approach for monitoring health, disease, and development in this vulnerable patient population. By comparing these data in healthy infants with data from infants who develop medical complications, we expect to identify new biomarkers that will ultimately improve newborn care.

scholarly journals Whole Genome Sequencing Based Taxonomic Classification, and Comparative Genomic Analysis of Potentially Human Pathogenic Enterobacter spp. Isolated from Chlorinated Wastewater in the North West Province, South Africa

2021 ◽  
Vol 9 (9) ◽  
pp. 1928
Author(s):  
Tawanda E. Maguvu ◽  
Cornelius C. Bezuidenhout
Keyword(s):  
Bacterial Species ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Comparative Genomic Analysis ◽  
Taxonomic Classification ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Human Pathogens ◽  
Wastewater Treatment Process ◽  
North West

Comparative genomics, in particular, pan-genome analysis, provides an in-depth understanding of the genetic variability and dynamics of a bacterial species. Coupled with whole-genome-based taxonomic analysis, these approaches can help to provide comprehensive, detailed insights into a bacterial species. Here, we report whole-genome-based taxonomic classification and comparative genomic analysis of potential human pathogenic Enterobacter hormaechei subsp. hoffmannii isolated from chlorinated wastewater. Genome Blast Distance Phylogeny (GBDP), digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANI) confirmed the identity of the isolates. The algorithm PathogenFinder predicted the isolates to be human pathogens with a probability of greater than 0.78. The potential pathogenic nature of the isolates was supported by the presence of biosynthetic gene clusters (BGCs), aerobactin, and aryl polyenes (APEs), which are known to be associated with pathogenic/virulent strains. Moreover, analysis of the genome sequences of the isolates reflected the presence of an arsenal of virulence factors and antibiotic resistance genes that augment the predictions of the algorithm PathogenFinder. The study comprehensively elucidated the genomic features of pathogenic Enterobacter isolates from wastewaters, highlighting the role of wastewaters in the dissemination of pathogenic microbes, and the need for monitoring the effectiveness of the wastewater treatment process.

Lack of defense systems drives Enterococcus easily evolved into lysogens

2019 ◽  
Author(s):  
Shengyi Han ◽  
JianHua Zhou ◽  
Lina Ma ◽  
Chengxiu Ma ◽  
Qiaoying Zeng ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Potential Contribution ◽  
Systematic Analysis ◽  
Evolutionary Origins ◽  
Distribution Potential ◽  
Foreign Genes ◽  
The Relationship

Abstract Background: Enterococcus are important opportunistic pathogens that readily acquire foreign genes and could be easily lysogenized by phages. But no comparative genomic analysis of Enterococcus prophages had been undertaken to date. The prophage distribution, potential contribution and the relationship with Enterococcus defensive system remain unclear. Result: This study presents a comparative analysis of 563 putative prophages identified in 107 chromosomes and 301 plasmids of Enterococcus. Our result suggested that lysogens are highly prevalent in Enterococcus and Enterococcus genomes have more prophages than other bacteria, the number of prophages are related with strains pathogenicity, groups and isolated regions, and the prophages distribution present phylogeographic pattern. By analyzing the prophages characteristic, it is found that prophages can be divided into many clusters, but most of prophages have distant genetic relationship with sequenced phages and remain unreported; Prophages integrated into chromosomes and plasmids have different evolutionary origins, and show different genomes size, GC% and genes characteristic. It should be noted that all antibiotic resistance genes are carried by plasmids prophages and E. faecium plasmid prophages play important roles in transmission of vancomycin resistance genes through plasmid conjugation transfer and phages transduction. By investigating and statistical analyzing the relationship between major defend systems and the number of prophages, it indicated that R-M system often absent in Enterococcus, orphan CRISPR array prevalent in most of Enterococcus, and the presence of CRISPR-spacers and the absence of prophages in lysogen is inversely related. Conclusion: To our knowledge, this is the first systematic analysis of Enterococcus prophages distribution, potential contribution and phylogeny, and elucidate the relationship between defense system and lysogeny in Enterococcus. This information helps to understand how prophages affect its hosts diversity, fitness and evolution.

scholarly journals Whole-Genome Sequencing of Corallococcus sp. Strain EGB Reveals the Genetic Determinants Linking Taxonomy and Predatory Behavior

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1421
Author(s):  
Yuqiang Zhao ◽  
Yanxin Wang ◽  
Chengyao Xia ◽  
Xu Li ◽  
Xianfeng Ye ◽  
...  
Keyword(s):  
Extracellular Enzymes ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Predatory Behavior ◽  
Phytopathogenic Fungi ◽  
Plant Diseases ◽  
Comparative Genomic ◽  
Comprehensive Overview ◽  
Circular Chromosome ◽  
Pan Genome

Corallococcus sp. strain EGB is a Gram-negative myxobacteria isolated from saline soil, and has considerable potential for the biocontrol of phytopathogenic fungi. However, the detailed mechanisms related to development and predatory behavior are unclear. To obtain a comprehensive overview of genetic features, the genome of strain EGB was sequenced, annotated, and compared with 10 other Corallococcus species. The strain EGB genome was assembled as a single circular chromosome of 9.4 Mb with 7916 coding genes. Phylogenomics analysis showed that strain EGB was most closely related to Corallococcus interemptor AB047A, and it was inferred to be a novel species within the Corallococcus genus. Comparative genomic analysis revealed that the pan-genome of Corallococcus genus was large and open. Only a small proportion of genes were specific to strain EGB, and most of them were annotated as hypothetical proteins. Subsequent analyses showed that strain EGB produced abundant extracellular enzymes such as chitinases and β-(1,3)-glucanases, and proteases to degrade the cell-wall components of phytopathogenic fungi. In addition, 35 biosynthetic gene clusters potentially coding for antimicrobial compounds were identified in the strain EGB, and the majority of them were present in the dispensable pan-genome with unexplored metabolites. Other genes related to secretion and regulation were also explored for strain EGB. This study opens new perspectives in the greater understanding of the predatory behavior of strain EGB, and facilitates a potential application in the biocontrol of fungal plant diseases in the future.

scholarly journals PlantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters

2016 ◽  
Author(s):  
Satria A. Kautsar ◽  
Hernando G. Suarez Duran ◽  
Kai Blin ◽  
Anne Osbourn ◽  
Marnix H. Medema
Keyword(s):  
Genome Mining ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Plant Genome ◽  
Gene Clustering ◽  
Comparative Genomic ◽  
Biosynthetic Gene ◽  
Automated Identification ◽  
Biosynthetic Gene Clusters ◽  
Rich Diversity

ABSTRACTPlant specialized metabolites are chemically highly diverse, play key roles in host-microbe interactions, have important nutritional value in crops and are frequently applied as medicines. It has recently become clear that plant biosynthetic pathway-encoding genes are sometimes densely clustered in specific genomic loci: biosynthetic gene clusters (BGCs). Here, we introduce plantiSMASH, a versatile online analysis platform that automates the identification of candidate plant BGCs. Moreover, it allows integration of transcriptomic data to prioritize candidate BGCs based on the coexpression patterns of predicted biosynthetic enzyme-coding genes, and facilitates comparative genomic analysis to study the evolutionary conservation of each cluster. Applied on 48 high-quality plant genomes, plantiSMASH identifies a rich diversity of candidate plant BGCs. These results will guide further experimental exploration of the nature and dynamics of gene clustering in plant metabolism. Moreover, spurred by the continuing decrease in costs of plant genome sequencing, they will allow genome mining technologies to be applied to plant natural product discovery.The plantiSMASH web server, precalculated results and source code are freely available from http://plantismash.secondarymetabolites.org.

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