scholarly journals Giant GAL gene clusters for the melibiose-galactose pathway in Torulaspora

2020 ◽  
Author(s):  
Anjan Venkatesh ◽  
Anthony L. Murray ◽  
Aisling Y. Coughlan ◽  
Kenneth H. Wolfe
Keyword(s):  
Gene Cluster ◽  
Glucose Transporter ◽  
Common Ancestor ◽  
Yeast Species ◽  
Gene Clusters ◽  
Yeast Strains ◽  
The Common ◽  
Almost All ◽  
Horizontal Transfers ◽  
Catabolism Pathway

AbstractIn many yeast species the three genes at the center of the galactose catabolism pathway, GAL1, GAL10 and GAL7, are neighbors in the genome and form a metabolic gene cluster. We report here that some yeast strains in the genus Torulaspora have much larger GAL clusters that include genes for melibiase (MEL1), galactose permease (GAL2), glucose transporter (HGT1), phosphoglucomutase (PGM1), and the transcription factor GAL4, in addition to GAL1, GAL10, and GAL7. Together, these 8 genes encode almost all the steps in the pathway for catabolism of extracellular melibiose (a disaccharide of galactose and glucose). We show that a progenitor 5-gene cluster containing GAL 7-1-10-4-2 was likely present in the common ancestor of Torulaspora and Zygotorulaspora. It added PGM1 and MEL1 in the ancestor of most Torulaspora species. It underwent further expansion in the T. pretoriensis clade, involving the fusion of three progenitor clusters in tandem and the gain of HGT1. These giant GAL clusters are highly polymorphic in structure, and subject to horizontal transfers, pseudogenization and gene losses. We identify recent horizontal transfers of complete GAL clusters from T. franciscae into one strain of T. delbrueckii, and from a relative of T. maleeae into one strain of T. globosa. The variability and dynamic evolution of GAL clusters in Torulaspora indicates that there is strong natural selection on the GAL pathway in this genus.

scholarly journals Relationships of the Escherichia coli O157, O111, and O55 O-Antigen Gene Clusters with Those of Salmonella enterica and Citrobacter freundii, Which Express Identical O Antigens

2004 ◽  
Vol 186 (19) ◽  
pp. 6536-6543 ◽  
Author(s):  
Gabrielle Samuel ◽  
John-Paul Hogbin ◽  
Lei Wang ◽  
Peter R. Reeves
Keyword(s):  
Escherichia Coli ◽  
Gene Cluster ◽  
Common Ancestor ◽  
Gene Clusters ◽  
Citrobacter Freundii ◽  
E Coli ◽  
Antigen Gene ◽  
O Antigen ◽  
The Common ◽  
O Antigens

ABSTRACT Escherichia coli O157, Salmonella enterica O30, and Citrobacter freundii F90 have identical O-antigen structures, as do E. coli O55 and S. enterica O50. The O-antigen gene cluster sequences for E. coli O157 and E. coli O55 have been published, and the genes necessary for O-antigen biosynthesis have been identified, although transferase genes for glycosidic linkages are only generic and have not been allocated to specific linkages. We determined sequences for S. enterica O30 and C. freundii F90 O-antigen gene clusters and compared them to the sequence of the previously described E. coli O157 cluster. We also determined the sequence of the S. enterica O50 O-antigen gene cluster and compared it to the sequence of the previously described E. coli O55 cluster. For both the S. enterica O30-C. freundii F90-E. coli O157 group and the S. enterica O50-E. coli O55 group of O antigens, the gene clusters have identical or nearly identical organizations. The two sets of gene clusters had comparable overall levels of similarity in their genes, which were lower than the levels determined for housekeeping genes for these species, which were 55 to 65% for the genes encoding glycosyltransferases and O-antigen processing proteins and 75 to 93% for the nucleotide-sugar pathway genes. Nonetheless, the similarity of the levels of divergence in the five gene clusters required us to consider the possibility that the parent gene cluster for each structure was in the common ancestor of the species and that divergence is faster than expected for the common ancestor hypothesis. We propose that the identical O-antigen gene clusters originated from a common ancestor, and we discuss some possible explanations for the increased rate of divergence that is seen in these genes.

scholarly journals Loss of plastid developmental genes coincides with a reversion to monoplastidy in hornworts

2022 ◽  
Author(s):  
Alexander Istvan MacLeod ◽  
Parth K Raval ◽  
Simon Stockhorst ◽  
Michael Knopp ◽  
Eftychios Frangedakis ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Nuclear Division ◽  
Developmental Pathways ◽  
Ancestral State ◽  
Plastid Division ◽  
Plastid Development ◽  
State Reconstruction ◽  
Transcriptomic Data ◽  
The Common ◽  
Almost All

The first plastid evolved from an endosymbiotic cyanobacterium in the common ancestor of the Archaeplastida. The transformative steps from cyanobacterium to organelle included the transfer of control over developmental processes; a necessity for the host to orchestrate, for example, the fission of the organelle. The plastids of almost all embryophytes divide independent from nuclear division, leading to cells housing multiple plastids. Hornworts, however, are monoplastidic (or near-monoplastidic) and their photosynthetic organelles are a curious exception among embryophytes for reasons such as the occasional presence of pyrenoids. Here we screened genomic and transcriptomic data of eleven hornworts for components of plastid developmental pathways. We find intriguing differences among hornworts and specifically highlight that pathway components involved in regulating plastid development and biogenesis were differentially lost in this group of bryophytes. In combination with ancestral state reconstruction, our data suggest that hornworts have reverted back to a monoplastidic phenotype due to the combined loss of two plastid division-associated genes: ARC3 and FtsZ2.

scholarly journals Conservation of a gene cluster reveals novel cercosporin biosynthetic mechanisms and extends production to the genus Colletotrichum

2017 ◽  
Author(s):  
Ronnie de Jonge ◽  
Malaika K. Ebert ◽  
Callie R. Huitt-Roehl ◽  
Paramita Pal ◽  
Jeffrey C. Suttle ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Gene Cluster ◽  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Pathogenic Fungi ◽  
Gene Clusters ◽  
Phylogenomic Analysis ◽  
First Case ◽  
Horizontal Transfers ◽  
Fungal Genus

AbstractSpecies in the genus Cercospora cause economically devastating diseases in sugar beet, maize, rice, soy bean and other major food crops. Here we sequenced the genome of the sugar beet pathogen C. beticola and found it encodes 63 putative secondary metabolite gene clusters, including the cercosporin toxin biosynthesis (CTB) cluster. We show that the CTB gene cluster has experienced multiple duplications and horizontal transfers across a spectrum of plant pathogenic fungi, including the wide host range Colletotrichum genus as well as the rice pathogen Magnaporthe oryzae. Although cercosporin biosynthesis has been thought to-date to rely on an eight gene CTB cluster, our phylogenomic analysis revealed gene collinearity adjacent to the established cluster in all CTB cluster-harboring species. We demonstrate that the CTB cluster is larger than previously recognized and includes cercosporin facilitator protein (CFP) previously shown to be involved with cercosporin auto-resistance, and four additional genes required for cercosporin biosynthesis including the final pathway enzymes that install the unusual cercosporin methylenedioxy bridge. Finally, we demonstrate production of cercosporin by Colletotrichum fioriniae, the first known cercosporin producer within this agriculturally important genus. Thus, our results provide new insight into the intricate evolution and biology of a toxin critical to agriculture and broaden the production of cercosporin to another fungal genus containing many plant pathogens of important crops worldwide.Significance StatementSpecies in the fungal genus Cercospora cause diseases in many important crops worldwide. Their success as pathogens is largely due to the secretion of cercosporin during infection. We report that the cercosporin toxin biosynthesis (CTB) cluster is ancient and was horizontally transferred to diverse fungal pathogens on an unprecedented scale. Since these analyses revealed genes adjacent to the established CTB cluster, we evaluated their role in C. beticola to show that four are necessary for cercosporin biosynthesis. Finally, we confirmed that the apple pathogen Colletotrichum fioriniae produces cercosporin, the first case outside the family Mycosphaerellaceae. Other Colletotrichum plant pathogens also harbor the CTB cluster, which points to a wider concern that this toxin may play in virulence and human health.

scholarly journals A Large Gene Cluster for the Clostridium cellulovorans Cellulosome

2000 ◽  
Vol 182 (20) ◽  
pp. 5906-5910 ◽  
Author(s):  
Yutaka Tamaru ◽  
Shuichi Karita ◽  
Atef Ibrahim ◽  
Helen Chan ◽  
Roy H. Doi
Keyword(s):  
Surface Layer ◽  
Dna Sequencing ◽  
Gene Cluster ◽  
Common Ancestor ◽  
Catalytic Domain ◽  
Gene Clusters ◽  
Scaffolding Protein ◽  
Clostridium Cellulovorans ◽  
Hydrophobic Protein ◽  
Large Gene

ABSTRACT A large gene cluster for the Clostridium cellulovoranscellulosome has been cloned and sequenced upstream and downstream of the cbpA and exgS genes (C.-C. Liu and R. H. Doi, Gene 211:39–47, 1998). Gene walking revealed that theengL gene cluster (Y. Tamaru and R. H. Doi, J. Bacteriol. 182:244–247, 2000) was located downstream of thecbpA-exgS genes. Further DNA sequencing revealed that this cluster contains the genes for the scaffolding protein CbpA, the exoglucanase ExgS, several endoglucanases of family 9, the mannanase ManA, and the hydrophobic protein HbpA containing a surface layer homology domain and a hydrophobic (or cohesin) domain. The sequence of the clustered genes iscbpA-exgS-engH-engK-hbpA-engL-manA-engM-engN and is about 22 kb in length. The engN gene did not have a complete catalytic domain, indicating that engN is a truncated gene. This large gene cluster is flanked at the 5′ end by a putative noncellulosomal operon consisting of nifV-orf1-sigX-regAand at the 3′ end by noncellulosomal genes with homology to transposase (trp) and malate permease (mle). Since gene clusters for the cellulosome are also found in C. cellulolyticum and C. josui, they seem to be typical of mesophilic clostridia, indicating that the large gene clusters may arise from a common ancestor with some evolutionary modifications.

scholarly journals RubisCO Gene Clusters Found in a Metagenome Microarray from Acid Mine Drainage

2013 ◽  
Vol 79 (6) ◽  
pp. 2019-2026 ◽  
Author(s):  
Xue Guo ◽  
Huaqun Yin ◽  
Jing Cong ◽  
Zhimin Dai ◽  
Yili Liang ◽  
...  
Keyword(s):  
Acid Mine Drainage ◽  
Gene Cluster ◽  
Molecular Phylogenetics ◽  
Mine Drainage ◽  
Calvin Cycle ◽  
Gene Clusters ◽  
Rrna Gene ◽  
Bisphosphate Carboxylase ◽  
Acid Mine ◽  
Horizontal Transfers

ABSTRACTThe enzyme responsible for carbon dioxide fixation in the Calvin cycle, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), is always detected as a phylogenetic marker to analyze the distribution and activity of autotrophic bacteria. However, such an approach provides no indication as to the significance of genomic content and organization. Horizontal transfers of RubisCO genes occurring in eubacteria and plastids may seriously affect the credibility of this approach. Here, we presented a new method to analyze the diversity and genomic content of RubisCO genes in acid mine drainage (AMD). A metagenome microarray containing 7,776 large-insertion fosmids was constructed to quickly screen genome fragments containing RubisCO form I large-subunit genes (cbbL). Forty-sixcbbL-containing fosmids were detected, and six fosmids were fully sequenced. To evaluate the reliability of the metagenome microarray and understand the microbial community in AMD, the diversities ofcbbLand the 16S rRNA gene were analyzed. Fosmid sequences revealed that the form I RubisCO gene cluster could be subdivided into form IA and IB RubisCO gene clusters in AMD, because of significant divergences in molecular phylogenetics and conservative genomic organization. Interestingly, the form I RubisCO gene cluster coexisted with the form II RubisCO gene cluster in one fosmid genomic fragment. Phylogenetic analyses revealed that horizontal transfers of RubisCO genes may occur widely in AMD, which makes the evolutionary history of RubisCO difficult to reconcile with organismal phylogeny.

scholarly journals Juvenile hormone III skipped bisepoxide is widespread in true bugs (Hemiptera: Heteroptera)

2021 ◽  
Vol 8 (2) ◽  
pp. 202242
Author(s):  
Keiji Matsumoto ◽  
Toyomi Kotaki ◽  
Hideharu Numata ◽  
Tetsuro Shinada ◽  
Shin G. Goto
Keyword(s):  
Juvenile Hormone ◽  
Common Ancestor ◽  
Ultra Performance Liquid Chromatography ◽  
Insect Development ◽  
Methyl Farnesoate ◽  
True Bugs ◽  
Focal Species ◽  
Chemically Modified ◽  
The Common ◽  
Almost All

Juvenile hormone (JH) plays important roles in almost every aspect of insect development and reproduction. JHs are a group of acyclic sesquiterpenoids, and their farnesol backbone has been chemically modified to generate a homologous series of hormones in some insect lineages. JH III (methyl farnesoate, 10,11-epoxide) is the most common JH in insects, but Lepidoptera (butterflies and moths) and ‘higher’ Diptera (suborder: Brachycera; flies) have developed their own unique JHs. Although JH was first proposed in the hemipteran suborder Heteroptera (true bugs), the chemical identity of the heteropteran JH was only recently determined. Furthermore, recent studies revealed the presence of a novel JH, JH III skipped bisepoxide (JHSB 3 ), in some heteropterans, but its taxonomic distribution remains largely unknown. In the present study, we investigated JHSB 3 production in 31 heteropteran species, covering almost all heteropteran lineages, through ultra-performance liquid chromatography coupled with tandem mass spectrometry. We found that all of the focal species produced JHSB 3 , indicating that JHSB 3 is widespread in heteropteran bugs and the evolutionary occurrence of JHSB 3 ascends to the common ancestor of Heteroptera.

scholarly journals Gene cluster conservation provides insight into cercosporin biosynthesis and extends production to the genus Colletotrichum

2018 ◽  
Vol 115 (24) ◽  
pp. E5459-E5466 ◽  
Author(s):  
Ronnie de Jonge ◽  
Malaika K. Ebert ◽  
Callie R. Huitt-Roehl ◽  
Paramita Pal ◽  
Jeffrey C. Suttle ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Gene Cluster ◽  
Plant Pathogens ◽  
Pathogenic Fungi ◽  
Gene Clusters ◽  
Cercospora Beticola ◽  
Phylogenomic Analysis ◽  
Food Crops ◽  
Horizontal Transfers ◽  
Insight Into

Species in the genus Cercospora cause economically devastating diseases in sugar beet, maize, rice, soy bean, and other major food crops. Here, we sequenced the genome of the sugar beet pathogen Cercospora beticola and found it encodes 63 putative secondary metabolite gene clusters, including the cercosporin toxin biosynthesis (CTB) cluster. We show that the CTB gene cluster has experienced multiple duplications and horizontal transfers across a spectrum of plant pathogenic fungi, including the wide-host range Colletotrichum genus as well as the rice pathogen Magnaporthe oryzae. Although cercosporin biosynthesis has been thought to rely on an eight-gene CTB cluster, our phylogenomic analysis revealed gene collinearity adjacent to the established cluster in all CTB cluster-harboring species. We demonstrate that the CTB cluster is larger than previously recognized and includes cercosporin facilitator protein, previously shown to be involved with cercosporin autoresistance, and four additional genes required for cercosporin biosynthesis, including the final pathway enzymes that install the unusual cercosporin methylenedioxy bridge. Lastly, we demonstrate production of cercosporin by Colletotrichum fioriniae, the first known cercosporin producer within this agriculturally important genus. Thus, our results provide insight into the intricate evolution and biology of a toxin critical to agriculture and broaden the production of cercosporin to another fungal genus containing many plant pathogens of important crops worldwide.

scholarly journals Postcranial skeletal pneumaticity and air-sacs in the earliest pterosaurs

2009 ◽  
Vol 5 (4) ◽  
pp. 557-560 ◽  
Author(s):  
Richard J. Butler ◽  
Paul M. Barrett ◽  
David J. Gower
Keyword(s):  
Respiratory System ◽  
Common Ancestor ◽  
Late Triassic ◽  
Air Sacs ◽  
The Common ◽  
Respiratory Systems ◽  
Almost All

Patterns of postcranial skeletal pneumatization (PSP) indicate that pterosaurs possessed components of a bird-like respiratory system, including a series of ventilatory air-sacs. However, the presence of PSP in the oldest known pterosaurs has not been unambiguously demonstrated by previous studies. Here we provide the first unequivocal documentation of PSP in Late Triassic and earliest Jurassic pterosaurs. This demonstrates that PSP and, by inference, air-sacs were probably present in the common ancestor of almost all known pterosaurs, and has broader implications for the evolution of respiratory systems in bird-line archosaurs, including dinosaurs.

scholarly journals Bilaterally symmetric axes with rhizoids composed the rooting structure of the common ancestor of vascular plants

2017 ◽  
Vol 373 (1739) ◽  
pp. 20170042 ◽  
Author(s):  
Alexander J. Hetherington ◽  
Liam Dolan
Keyword(s):  
Vascular Plants ◽  
Common Ancestor ◽  
Terrestrial Ecosystem ◽  
Bilateral Symmetry ◽  
Land Plant ◽  
Land Plants ◽  
Free Living ◽  
Rhynie Chert ◽  
The Common ◽  
Almost All

There are two general types of rooting systems in extant land plants: gametophyte rhizoids and sporophyte root axes. These structures carry out the rooting function in the free-living stage of almost all land plant gametophytes and sporophytes, respectively. Extant vascular plants develop a dominant, free-living sporophyte on which roots form, with the exception of a small number of taxa that have secondarily lost roots. However, fossil evidence indicates that early vascular plants did not develop sporophyte roots. We propose that the common ancestor of vascular plants developed a unique rooting system—rhizoidal sporophyte axes. Here we present a synthesis and reinterpretation of the rootless sporophytes of Horneophyton lignieri , Aglaophyton majus , Rhynia gwynne-vaughanii and Nothia aphylla preserved in the Rhynie chert. We show that the sporophyte rooting structures of all four plants comprised regions of plagiotropic (horizontal) axes that developed unicellular rhizoids on their underside. These regions of axes with rhizoids developed bilateral symmetry making them distinct from the other regions which were radially symmetrical. We hypothesize that rhizoidal sporophyte axes constituted the rooting structures in the common ancestor of vascular plants because the phylogenetic positions of these plants span the origin of the vascular lineage. This article is part of a discussion meeting issue ‘The Rhynie cherts: our earliest terrestrial ecosystem revisited’.

Fibrinolytic Activity of the Arterial Wall

1969 ◽  
Vol 21 (01) ◽  
pp. 001-011 ◽  
Author(s):  
K Onoyama ◽  
K Tanaka
Keyword(s):  
Carotid Artery ◽  
Fibrinolytic Activity ◽  
Arterial Wall ◽  
Aortic Wall ◽  
Internal Carotid ◽  
Atheromatous Plaque ◽  
Human Fibrinogen ◽  
The Media ◽  
The Common ◽  
Almost All

SummaryThe tissue fibrinolysis was studied in 550 specimens of 7 kinds of arteries from 80 fresh cadavers, using Astrup’s biochemical method and Todd’s histochemical method with human fibrinogen.In the microscopically normal aortic wall, almost all specimens had the fibrinolytic activity which was the strongest in the adventitia and the weakest in the media.The fibrinolytic activity seemed to be localized in the endothelium.The stronger activity lay in the adventitia of the aorta and the pulmonary artery and all layers of the cerebral artery.The activity of the intima and media of the macroscopically normal areas seemed to be stronger in the internal carotid artery than in the common carotid artery.Mean fibrinolytic activity of the macroscopically normal areas seemed to decrease with age in the intima and the media of the thoracic aorta and seemed to be low in the cases with a high atherosclerotic index.The fibrinolytic activities of all three layers of the fibrous thickened aorta seemed to decrease, and those of the media and the adventitia of the atheromatous plaque to increase.The fibrinolytic activity of the arterial wall might play some role in the progress of atherosclerosis.

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