scholarly journals Colocality to Cofunctionality: Eukaryotic Gene Neighborhoods as a Resource for Function Discovery

2020 ◽  
Author(s):  
Fatima Foflonker ◽  
Crysten E Blaby-Haas
Keyword(s):  
Green Algae ◽  
Sequence Similarity ◽  
Phosphoglycerate Kinase ◽  
Orthologous Gene ◽  
Model Organisms ◽  
Comparative Genomic ◽  
Evolutionary Origins ◽  
Eukaryotic Gene ◽  
Arsenic Detoxification ◽  
Function Discovery

Abstract Diverging from the classic paradigm of random gene order in eukaryotes, gene proximity can be leveraged to systematically identify functionally related gene neighborhoods in eukaryotes, utilizing techniques pioneered in bacteria. Current methods of identifying gene neighborhoods typically rely on sequence similarity to characterized gene products. However, this approach is not robust for nonmodel organisms like algae, which are evolutionarily distant from well-characterized model organisms. Here, we utilize a comparative genomic approach to identify evolutionarily conserved proximal orthologous gene pairs conserved across at least two taxonomic classes of green algae. A total of 317 gene neighborhoods were identified. In some cases, gene proximity appears to have been conserved since before the streptophyte–chlorophyte split, 1,000 Ma. Using functional inferences derived from reconstructed evolutionary relationships, we identified several novel functional clusters. A putative mycosporine-like amino acid, “sunscreen,” neighborhood contains genes similar to either vertebrate or cyanobacterial pathways, suggesting a novel mosaic biosynthetic pathway in green algae. One of two putative arsenic-detoxification neighborhoods includes an organoarsenical transporter (ArsJ), a glyceraldehyde 3-phosphate dehydrogenase-like gene, homologs of which are involved in arsenic detoxification in bacteria, and a novel algal-specific phosphoglycerate kinase-like gene. Mutants of the ArsJ-like transporter and phosphoglycerate kinase-like genes in Chlamydomonas reinhardtii were found to be sensitive to arsenate, providing experimental support for the role of these identified neighbors in resistance to arsenate. Potential evolutionary origins of neighborhoods are discussed, and updated annotations for formerly poorly annotated genes are presented, highlighting the potential of this strategy for functional annotation.

scholarly journals Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes

2017 ◽  
Author(s):  
Monica R. Sanchez ◽  
Celia Payen ◽  
Frances Cheong ◽  
Blake T. Hovde ◽  
Sarah Bissonnette ◽  
...  
Keyword(s):  
Insertional Mutagenesis ◽  
Gene Annotation ◽  
Experimental Testing ◽  
Sequence Similarity ◽  
Normal Function ◽  
Essential Genes ◽  
Model Organisms ◽  
Comparative Genomic ◽  
Saccharomyces Uvarum ◽  
Cellular Processes

AbstractTo understand how complex genetic networks perform and regulate diverse cellular processes, the function of each individual component must be defined. Comprehensive phenotypic studies of mutant alleles have been successful in model organisms in determining what processes depend on the normal function of a gene. These results are often ported to newly sequenced genomes by using sequence homology. However, sequence similarity does not always mean identical function or phenotype, suggesting that new methods are required to functionally annotate newly sequenced species. We have implemented comparative analysis by high-throughput experimental testing of gene dispensability in Saccharomyces uvarum, a sister species of S. cerevisiae. We created haploid and heterozygous diploid Tn7 insertional mutagenesis libraries in S. uvarum to identify species dependent essential genes, with the goal of detecting genes with divergent functions and/or different genetic interactions. Comprehensive gene dispensability comparisons with S. cerevisiae predicted diverged dispensability at 12% of conserved orthologs, and validation experiments confirmed 22 differentially essential genes. Surprisingly, despite their differences in essentiality, these genes were capable of cross-species complementation, demonstrating that trans-acting factors that are background-dependent contribute to differential gene essentiality. This study demonstrates that direct experimental testing of gene disruption phenotypes across species can inform comparative genomic analyses and improve gene annotation. Our method can be widely applied in microorganisms to further our understanding of genome evolution.

scholarly journals Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity

2021 ◽  
Vol 7 (5) ◽  
pp. 337
Author(s):  
Daniel Peterson ◽  
Tang Li ◽  
Ana M. Calvo ◽  
Yanbin Yin
Keyword(s):  
Comparative Genomics ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Phytopathogenic Fungi ◽  
Secreted Proteins ◽  
Economic Losses ◽  
Comparative Genomic ◽  
Signal Peptides ◽  
Comparative Genomics Analysis

Phytopathogenic Ascomycota are responsible for substantial economic losses each year, destroying valuable crops. The present study aims to provide new insights into phytopathogenicity in Ascomycota from a comparative genomic perspective. This has been achieved by categorizing orthologous gene groups (orthogroups) from 68 phytopathogenic and 24 non-phytopathogenic Ascomycota genomes into three classes: Core, (pathogen or non-pathogen) group-specific, and genome-specific accessory orthogroups. We found that (i) ~20% orthogroups are group-specific and accessory in the 92 Ascomycota genomes, (ii) phytopathogenicity is not phylogenetically determined, (iii) group-specific orthogroups have more enriched functional terms than accessory orthogroups and this trend is particularly evident in phytopathogenic fungi, (iv) secreted proteins with signal peptides and horizontal gene transfers (HGTs) are the two functional terms that show the highest occurrence and significance in group-specific orthogroups, (v) a number of other functional terms are also identified to have higher significance and occurrence in group-specific orthogroups. Overall, our comparative genomics analysis determined positive enrichment existing between orthogroup classes and revealed a prediction of what genomic characteristics make an Ascomycete phytopathogenic. We conclude that genes shared by multiple phytopathogenic genomes are more important for phytopathogenicity than those that are unique in each genome.

scholarly journals Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas sp. AAP5

2021 ◽  
Vol 9 (4) ◽  
pp. 768
Author(s):  
Karel Kopejtka ◽  
Yonghui Zeng ◽  
David Kaftan ◽  
Vadim Selyanin ◽  
Zdenko Gardian ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Close Phylogenetic Relationship

An aerobic, yellow-pigmented, bacteriochlorophyll a-producing strain, designated AAP5 (=DSM 111157=CCUG 74776), was isolated from the alpine lake Gossenköllesee located in the Tyrolean Alps, Austria. Here, we report its description and polyphasic characterization. Phylogenetic analysis of the 16S rRNA gene showed that strain AAP5 belongs to the bacterial genus Sphingomonas and has the highest pairwise 16S rRNA gene sequence similarity with Sphingomonas glacialis (98.3%), Sphingomonas psychrolutea (96.8%), and Sphingomonas melonis (96.5%). Its genomic DNA G + C content is 65.9%. Further, in silico DNA-DNA hybridization and calculation of the average nucleotide identity speaks for the close phylogenetic relationship of AAP5 and Sphingomonas glacialis. The high percentage (76.2%) of shared orthologous gene clusters between strain AAP5 and Sphingomonas paucimobilis NCTC 11030T, the type species of the genus, supports the classification of the two strains into the same genus. Strain AAP5 was found to contain C18:1ω7c (64.6%) as a predominant fatty acid (>10%) and the polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, six unidentified glycolipids, one unidentified phospholipid, and two unidentified lipids. The main respiratory quinone was ubiquinone-10. Strain AAP5 is a facultative photoheterotroph containing type-2 photosynthetic reaction centers and, in addition, contains a xathorhodopsin gene. No CO2-fixation pathways were found.

scholarly journals Microbial Functional Responses to Cholesterol Catabolism in Denitrifying Sludge

mSystems ◽  
2018 ◽  
Vol 3 (5) ◽  
Author(s):  
Sean Ting-Shyang Wei ◽  
Yu-Wei Wu ◽  
Tzong-Huei Lee ◽  
Yi-Shiang Huang ◽  
Cheng-Yu Yang ◽  
...  
Keyword(s):  
16S Rrna ◽  
De Novo ◽  
Anthropogenic Impacts ◽  
Sequence Similarity ◽  
Community Level ◽  
Model Organisms ◽  
Substrate Uptake ◽  
Functional Responses ◽  
Content Type ◽  
Rare Biosphere

ABSTRACTThe 2,3-secopathway, the pathway for anaerobic cholesterol degradation, has been established in the denitrifying betaproteobacteriumSterolibacterium denitrificans. However, knowledge of how microorganisms respond to cholesterol at the community level is elusive. Here, we applied mesocosm incubation and 16S rRNA sequencing to reveal that, in denitrifying sludge communities, three betaproteobacterial operational taxonomic units (OTUs) with low (94% to 95%) 16S rRNA sequence similarity toStl. denitrificansare cholesterol degraders and members of the rare biosphere. Metatranscriptomic and metabolite analyses show that these degraders adopt the 2,3-secopathway to sequentially catalyze the side chain and sterane of cholesterol and that two molybdoenzymes—steroid C25 dehydrogenase and 1-testosterone dehydrogenase/hydratase—are crucial for these bioprocesses, respectively. The metatranscriptome further suggests that these betaproteobacterial degraders display chemotaxis and motility toward cholesterol and that FadL-like transporters may be the key components for substrate uptake. Also, these betaproteobacteria are capable of transporting micronutrients and synthesizing cofactors essential for cellular metabolism and cholesterol degradation; however, the required cobalamin is possibly provided by cobalamin-de novo-synthesizing gamma-, delta-, and betaproteobacteria via the salvage pathway. Overall, our results indicate that the ability to degrade cholesterol in sludge communities is reserved for certain rare biosphere members and that C25 dehydrogenase can serve as a biomarker for sterol degradation in anoxic environments.IMPORTANCESteroids are ubiquitous and abundant natural compounds that display recalcitrance. Biodegradation via sludge communities in wastewater treatment plants is the primary removal process for steroids. To date, compared to studies for aerobic steroid degradation, the knowledge of anaerobic degradation of steroids has been based on only a few model organisms. Due to the increase of anthropogenic impacts, steroid inputs may affect microbial diversity and functioning in ecosystems. Here, we first investigated microbial functional responses to cholesterol, the most abundant steroid in sludge, at the community level. Our metagenomic and metatranscriptomic analyses revealed that the capacities for cholesterol approach, uptake, and degradation are unique traits of certain low-abundance betaproteobacteria, indicating the importance of the rare biosphere in bioremediation. Apparent expression of genes involved in cofactorde novosynthesis and salvage pathways suggests that these micronutrients play important roles for cholesterol degradation in sludge communities.

scholarly journals Persicivirga ulvanivorans sp. nov., a marine member of the family Flavobacteriaceae that degrades ulvan from green algae

2011 ◽  
Vol 61 (8) ◽  
pp. 1899-1905 ◽  
Author(s):  
Tristan Barbeyron ◽  
Yannick Lerat ◽  
Jean-François Sassi ◽  
Sophie Le Panse ◽  
William Helbert ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Green Algae ◽  
Electron Acceptor ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
The Family ◽  
Gliding Bacterium

A rod shaped, Gram-stain-negative, chemo-organotrophic, heterotrophic, strictly aerobic, non-gliding bacterium, designated strain PLRT, was isolated from faeces of the mollusc Aplysia punctata (Mollusca, Gastropoda) that had been fed with green algae belonging to the genus Ulva. The novel strain was able to degrade ulvan, a polysaccharide extracted from green algae (Chlorophyta, Ulvophyceae). The taxonomic position of strain PLRT was investigated by using a polyphasic approach. Strain PLRT was dark orange, oxidase-positive, catalase-positive and grew optimally at 25 °C, at pH 7.5 and in the presence of 2.5 % (w/v) NaCl with an oxidative metabolism using oxygen as the electron acceptor. Nitrate could not be used as the electron acceptor. Strain PLRT had a Chargaff’s coefficient (DNA G+C content) of 35.3 mol%. Phylogenetic analysis based on the sequence of the 16S rRNA gene placed the novel strain in the family Flavobacteriaceae (phylum ‘Bacteroidetes’), within a clade comprising Stenothermobacter spongiae, Nonlabens tegetincola, Sandarakinotalea sediminis, Persicivirga xylanidelens and Persicivirga dokdonensis. The closest neighbours of strain PLRT were P. xylanidelens and P. dokdonensis, sharing 95.2 and 95.5 % 16S rRNA gene sequence similarity, respectively. Phylogenetic inference and differential phenotypic characteristics demonstrated that strain PLRT represents a novel species of the genus Persicivirga, for which the name Persicivirga ulvanivorans sp. nov. is proposed. The type strain is PLRT ( = CIP 110082T = DSM 22727T).

scholarly journals Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Marina Athanasouli ◽  
Hanh Witte ◽  
Christian Weiler ◽  
Tobias Loschko ◽  
Gabi Eberhardt ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Model Organisms ◽  
Parasitic Nematodes ◽  
Comparative Genomic ◽  
Orphan Genes ◽  
Community Based ◽  
Pristionchus Pacificus ◽  
Gene Annotations ◽  
Gene Models

Abstract Background Nematode model organisms such as Caenorhabditis elegans and Pristionchus pacificus are powerful systems for studying the evolution of gene function at a mechanistic level. However, the identification of P. pacificus orthologs of candidate genes known from C. elegans is complicated by the discrepancy in the quality of gene annotations, a common problem in nematode and invertebrate genomics. Results Here, we combine comparative genomic screens for suspicious gene models with community-based curation to further improve the quality of gene annotations in P. pacificus. We extend previous curations of one-to-one orthologs to larger gene families and also orphan genes. Cross-species comparisons of protein lengths, screens for atypical domain combinations and species-specific orphan genes resulted in 4311 candidate genes that were subject to community-based curation. Corrections for 2946 gene models were implemented in a new version of the P. pacificus gene annotations. The new set of gene annotations contains 28,896 genes and has a single copy ortholog completeness level of 97.6%. Conclusions Our work demonstrates the effectiveness of comparative genomic screens to identify suspicious gene models and the scalability of community-based approaches to improve the quality of thousands of gene models. Similar community-based approaches can help to improve the quality of gene annotations in other invertebrate species, including parasitic nematodes.

scholarly journals Genomic Virulence Features of Two Novel Species Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., Isolated from Patients with Chronic Pulmonary Diseases

2020 ◽  
Vol 8 (10) ◽  
pp. 1517
Author(s):  
Imen Nouioui ◽  
Carlos Cortés-Albayay ◽  
Meina Neumann-Schaal ◽  
Diego Vicente ◽  
Gustavo Cilla ◽  
...  
Keyword(s):  
Novel Species ◽  
Sequence Similarity ◽  
Genetic Maps ◽  
Pulmonary Diseases ◽  
Comparative Genomic ◽  
Syntenic Block ◽  
Rrna Gene ◽  
Old Patients ◽  
Mycolic Acids ◽  
Chronic Pulmonary Diseases

Strains 335427T and 234509T, isolated from two 76-year-old patients with chronic pulmonary diseases, were the subject of polyphasic taxonomic studies and comparative genomic analyses for virulence factors. The 16 rRNA gene sequence similarity between strains 335427T and 234509T and their closest phylogenetic neighbors Nocardia asiatica NBRC 100129T and Nocardia abscessus NBRC 100374T were 99.5% and 100%, respectively. Digital DNA–DNA hybridization values between the aforementioned studied strains were well below the 70% threshold for assigning prokaryotic strains to a novel species. Strains 335427T and 234509T have genome sizes of 8.49 Mpb and 8.07 Mpb, respectively, with G + C content of 68.5%. Isolate 335427T has C16:0, C18:1 ω9c, C18:0 and C18:0 10 methyl as major fatty acids (>15%) and mycolic acids formed of 52–54 carbon atoms. However, only C18:1 ω9c was detected for isolate 234509T, which had mycolic acids with 44–56 carbon. Based on phenotypic and genetic data, strains 335427T (DSM 109819T = CECT 9924T) and 234509T (DSM 111366T = CECT 30129T) merit recognition as novel species, which are named Nocardia barduliensis sp. nov. and Nocardia gipuzkoensis sp. nov., respectively. All the strains studied had homologous VF-associated genes to those described in M. tuberculosis, including experimentally verified virulence genes in humans related to tuberculosis. The narGHIJ (nitrate reduction pathway) and gvpAFGOJLMK (gas vesicles) genetic maps of strains 335427T, 234509T, NBRC 100129T and NBRC 100374T showed the same syntenic block and raise the question of whether their functions are interlinked during the infection of the human host. However, further research is required to decipher the role of the gas vesicle in the pathogenicity mechanism of Nocardia spp.

scholarly journals Searching for a “Hidden” Prophage in a Marine Bacterium

2009 ◽  
Vol 76 (2) ◽  
pp. 589-595 ◽  
Author(s):  
Yanlin Zhao ◽  
Kui Wang ◽  
Hans-Wolfgang Ackermann ◽  
Rolf U. Halden ◽  
Nianzhi Jiao ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Genomic Analysis ◽  
Bioinformatic Analysis ◽  
Open Reading Frames ◽  
Careful Examination ◽  
Comparative Genomic ◽  
Bacterial Genomes ◽  
Genomic Analyses ◽  
Experimental Laboratory ◽  
Bacterial Genes

ABSTRACT Prophages are common in many bacterial genomes. Distinguishing putatively viable prophages from nonviable sequences can be a challenge, since some prophages are remnants of once-functional prophages that have been rendered inactive by mutational changes. In some cases, a putative prophage may be missed due to the lack of recognizable prophage loci. The genome of a marine roseobacter, Roseovarius nubinhibens ISM (hereinafter referred to as ISM), was recently sequenced and was reported to contain no intact prophage based on customary bioinformatic analysis. However, prophage induction experiments performed with this organism led to a different conclusion. In the laboratory, virus-like particles in the ISM culture increased more than 3 orders of magnitude following induction with mitomycin C. After careful examination of the ISM genome sequence, a putative prophage (ISM-pro1) was identified. Although this prophage contains only minimal phage-like genes, we demonstrated that this “hidden” prophage is inducible. Genomic analysis and reannotation showed that most of the ISM-pro1 open reading frames (ORFs) display the highest sequence similarity with Rhodobacterales bacterial genes and some ORFs are only distantly related to genes of other known phages or prophages. Comparative genomic analyses indicated that ISM-pro1-like prophages or prophage remnants are also present in other Rhodobacterales genomes. In addition, the lysis of ISM by this previously unrecognized prophage appeared to increase the production of gene transfer agents (GTAs). Our study suggests that a combination of in silico genomic analyses and experimental laboratory work is needed to fully understand the lysogenic features of a given bacterium.

scholarly journals Coevolution ofaah: Adps-Like Gene with the Host Bacterium Revealed by Comparative Genomic Analysis

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Liyan Ping ◽  
Matthias Platzer ◽  
Gaiping Wen ◽  
Nicolas Delaroque
Keyword(s):  
Stop Codon ◽  
Sequence Similarity ◽  
General Pattern ◽  
Genomic Analysis ◽  
Dna Binding Proteins ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Host Bacterium ◽  
High Sequence Similarity ◽  
Lepidopteran Larvae

A protein named AAH was isolated from the bacteriumMicrobacterium arborescensSE14, a gut commensal of the lepidopteran larvae. It showed not only a high sequence similarity to Dps-like proteins (DNA-binding proteins from starved cell) but also reversible hydrolase activity. A comparative genomic analysis was performed to gain more insights into its evolution. The GC profile of theaahgene indicated that it was evolved from a low GC ancestor. Its stop codon usage was also different from the general pattern of Actinobacterial genomes. The phylogeny ofdps-like proteins showed strong correlation with the phylogeny of host bacteria. A conserved genomic synteny was identified in some taxonomically related Actinobacteria, suggesting that the ancestor genes had incorporated into the genome before the divergence of Micrococcineae from other families. Theaahgene had evolved new function but still retained the typical dodecameric structure.

Evolutionary origins of eukaryotic sodium/proton exchangers

2005 ◽  
Vol 288 (2) ◽  
pp. C223-C239 ◽  
Author(s):  
Christopher L. Brett ◽  
Mark Donowitz ◽  
Rajini Rao
Keyword(s):  
Plasma Membrane ◽  
Drug Sensitivity ◽  
Phylogenetic Analyses ◽  
Subcellular Location ◽  
Monovalent Cation ◽  
Model Organisms ◽  
Sequence Length ◽  
Animal Cells ◽  
Cation Selectivity ◽  
Evolutionary Origins

More than 200 genes annotated as Na+/H+hydrogen exchangers (NHEs) currently reside in bioinformation databases such as GenBank and Pfam. We performed detailed phylogenetic analyses of these NHEs in an effort to better understand their specific functions and physiological roles. This analysis initially required examining the entire monovalent cation proton antiporter (CPA) superfamily that includes the CPA1, CPA2, and NaT-DC families of transporters, each of which has a unique set of bacterial ancestors. We have concluded that there are nine human NHE (or SLC9A) paralogs as well as two previously unknown human CPA2 genes, which we have named HsNHA1 and HsNHA2. The eukaryotic NHE family is composed of five phylogenetically distinct clades that differ in subcellular location, drug sensitivity, cation selectivity, and sequence length. The major subgroups are plasma membrane (recycling and resident) and intracellular (endosomal/TGN, NHE8-like, and plant vacuolar). HsNHE1, the first cloned eukaryotic NHE gene, belongs to the resident plasma membrane clade. The latter is the most recent to emerge, being found exclusively in vertebrates. In contrast, the intracellular clades are ubiquitously distributed and are likely precursors to the plasma membrane NHE. Yeast endosomal ScNHX1 was the first intracellular NHE to be described and is closely related to HsNHE6, HsNHE7, and HsNHE9 in humans. Our results link the appearance of NHE on the plasma membrane of animal cells to the use of the Na+/K+-ATPase to generate the membrane potential. These novel observations have allowed us to use comparative biology to predict physiological roles for the nine human NHE paralogs and to propose appropriate model organisms in which to study the unique properties of each NHE subclass.

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