The Genome Portal of the Department of Energy Joint Genome Institute

Grigoriev, Igor V.; Nordberg, Henrik; Shabalov, Igor; Aerts, Andrea; Cantor, Mike; Goodstein, David; Kuo, Alan; Minovitsky, Simon; Nikitin, Roman; Ohm, Robin A.; Otillar, Robert; Poliakov, Alexander; Ratnere, Igor; Riley, Robert; Smirnova, Tatyana I.; Rokhsar, Daniel S.; Dubchak, Inna

doi:10.1093/nar/gkr947

Cited by 467 publications

(408 citation statements)

References 23 publications

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“…For JGI data that are available publicly, we obtained from "MycoCosm," JGI fungal portal (36,37), by choosing annotated "Gene Catalog proteins," if listed, or the largest protein file in the list. Finally, we downloaded two fungi data from the "Multicellularity" study by Broad Institute the (38).…”

Section: Methodsmentioning

confidence: 99%

A genome Tree of Life for the Fungi kingdom

Choi

Kim

2017

Proc. Natl. Acad. Sci. U.S.A.

131

108

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Fungi belong to one of the largest and most diverse kingdoms of living organisms. The evolutionary kinship within a fungal population has so far been inferred mostly from the gene-information–based trees (“gene trees”), constructed commonly based on the degree of differences of proteins or DNA sequences of a small number of highly conserved genes common among the population by a multiple sequence alignment (MSA) method. Since each gene evolves under different evolutionary pressure and time scale, it has been known that one gene tree for a population may differ from other gene trees for the same population depending on the subjective selection of the genes. Within the last decade, a large number of whole-genome sequences of fungi have become publicly available, which represent, at present, the most fundamental and complete information about each fungal organism. This presents an opportunity to infer kinship among fungi using a whole-genome information-based tree (“genome tree”). The method we used allows comparison of whole-genome information without MSA, and is a variation of a computational algorithm developed to find semantic similarities or plagiarism in two books, where we represent whole-genomic information of an organism as a book of words without spaces. The genome tree reveals several significant and notable differences from the gene trees, and these differences invoke new discussions about alternative narratives for the evolution of some of the currently accepted fungal groups.

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Section: Methodsmentioning

confidence: 99%

A genome Tree of Life for the Fungi kingdom

Choi

Kim

2017

Proc. Natl. Acad. Sci. U.S.A.

131

108

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“…Several gene databanks were searched, including National Center for Biotechnology Information (blast. ncbi.nlm.nih.gov/Blast.cgi), The Genome Portal of the Department of Energy Joint Genome Institute (JGI) (75), Compagen (76), The UniProt Consortium (77), and The Origins of Multicellularity Sequencing Project, Broad Institute of Harvard and MIT (www.broadinstitute.org/). Query sequences used to search genomes for CaM were vertebrate (NP_001008160.1), brown rot fungus (JGI Genome, Pospl1Protein Id 117693), or a diatom (XP_002295755.1).…”

Section: Methodsmentioning

confidence: 99%

Conserved properties of individual Ca ²⁺ -binding sites in calmodulin

Halling

Liebeskind

Hall

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

100

113

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Calmodulin (CaM) is a Ca 2+ -sensing protein that is highly conserved and ubiquitous in eukaryotes. In humans it is a locus of life-threatening cardiomyopathies. The primary function of CaM is to transduce Ca 2+ concentration into cellular signals by binding to a wide range of target proteins in a Ca 2+ -dependent manner. We do not fully understand how CaM performs its role as a highfidelity signal transducer for more than 300 target proteins, but diversity among its four Ca 2+ -binding sites, called EF-hands, may contribute to CaM's functional versatility. We therefore looked at the conservation of CaM sequences over deep evolutionary time, focusing primarily on the four EF-hand motifs. Expanding on previous work, we found that CaM evolves slowly but that its evolutionary rate is substantially faster in fungi. We also found that the four EF-hands have distinguishing biophysical and structural properties that span eukaryotes. These results suggest that all eukaryotes require CaM to decode Ca 2+ signals using four specialized EFhands, each with specific, conserved traits. In addition, we provide an extensive map of sites associated with target proteins and with human disease and correlate these with evolutionary sequence diversity. Our comprehensive evolutionary analysis provides a basis for understanding the sequence space associated with CaM function and should help guide future work on the relationship between structure, function, and disease.calcium signaling | EF-hand | structure | evolution | protein

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“…The expression of aCA2 and aCA3 is quite low but higher than that of aCA4 to aCA8. The physiological role of the aCAs is unknown.Arabidopsis has six bCA genes (Moroney et al, 2001), and other plants with sequenced genomes have a similar number of bCA genes (Grigoriev et al, 2012;Kawahara et al, 2013). CAs are highly expressed and can account for up to 1% of the soluble protein in a leaf (Tobin, 1970), with the bCAs being the most highly expressed CA genes in leaves (Fett and Coleman, 1994;Schmid et al, 2005;Fabre et al, 2007;Winter et al, 2007;Hu et al, 2010).…”

mentioning

confidence: 99%

The Cytoplasmic Carbonic Anhydrases βCA2 and βCA4 Are Required for Optimal Plant Growth at Low CO₂

et al. 2016

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Carbonic anhydrases (CAs) are zinc metalloenzymes that interconvert CO 2 and HCO 3 2 . In plants, both a-and b-type CAs are present. We hypothesize that cytoplasmic bCAs are required to modulate inorganic carbon forms needed in leaf cells for carbonrequiring reactions such as photosynthesis and amino acid biosynthesis. In this report, we present evidence that bCA2 and bCA4 are the two most abundant cytoplasmic CAs in Arabidopsis (Arabidopsis thaliana) leaves. Previously, bCA4 was reported to be localized to the plasma membrane, but here, we show that two forms of bCA4 are expressed in a tissue-specific manner and that the two proteins encoded by bCA4 localize to two different regions of the cell. Comparing transfer DNA knockout lines with wild-type plants, there was no reduction in the growth rates of the single mutants, bca2 and bca4. However, the growth rate of the double mutant, bca2bca4, was reduced significantly when grown at 200 mL L 21 CO 2 . The reduction in growth of the double mutant was not linked to a reduction in photosynthetic rate. The amino acid content of leaves from the double mutant showed marked reduction in aspartate when compared with the wild type and the single mutants. This suggests the cytoplasmic CAs play an important but not previously appreciated role in amino acid biosynthesis.Carbonic anhydrases (CAs) are zinc metalloenzymes that catalyze the interconversion of CO 2 and HCO 3 2 . Flowering plants possess members of the aCA, bCA, and gCA families. While all three CA families contain zinc, they clearly have evolved independently (Hewett-Emmett and Tashian, 1996). Most aCAs are monomeric, although there are notable exceptions (Whittington et al., 2001;Hilvo et al., 2008;Suzuki et al., 2010Suzuki et al., , 2011Cuesta-Seijo et al., 2011). The aCA active site contains a single zinc molecule coordinated by three His residues and a water molecule (Liljas et al., 1972). bCAs also contain a zinc active site, although the coordinating molecules are two Cys residues, a His, and a water molecule (Bracey et al., 1994). The active unit of the bCA is a dimer where the active site is located at the interface of the two monomers (Kimber and Pai, 2000). In contrast, gCAs are trimers that have their active site zinc ion situated at the interface of two subunits coordinated by His residues from both subunits (Kisker et al., 1996;Iverson et al., 2000).In Arabidopsis (Arabidopsis thaliana), there are three gCA proteins and two g-like proteins that interact to form an extra structure of complex I of the mitochondrial electron transport chain (Perales et al., 2004;Sunderhaus et al., 2006). Although not active in vitro, gCA has been shown to bind inorganic carbon (Martin et al., 2009), affect complex I levels, plant growth, and gas-exchange rates when deleted (Perales et al., 2004;Soto et al., 2015), and cause plant sterility when ectopically overexpressed ). Arabidopsis has eight aCA genes, but only aCA1, aCA2, and aCA3 appear to be expressed in leaf tissue. aCA1 has been reported to be localized to the c...

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The Genome Portal of the Department of Energy Joint Genome Institute

Cited by 467 publications

References 23 publications

A genome Tree of Life for the Fungi kingdom

A genome Tree of Life for the Fungi kingdom

Conserved properties of individual Ca ²⁺ -binding sites in calmodulin

The Cytoplasmic Carbonic Anhydrases βCA2 and βCA4 Are Required for Optimal Plant Growth at Low CO₂

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The Genome Portal of the Department of Energy Joint Genome Institute

Cited by 467 publications

References 23 publications

A genome Tree of Life for the Fungi kingdom

A genome Tree of Life for the Fungi kingdom

Conserved properties of individual Ca 2+ -binding sites in calmodulin

The Cytoplasmic Carbonic Anhydrases βCA2 and βCA4 Are Required for Optimal Plant Growth at Low CO2

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Product

Resources

About

Conserved properties of individual Ca ²⁺ -binding sites in calmodulin

The Cytoplasmic Carbonic Anhydrases βCA2 and βCA4 Are Required for Optimal Plant Growth at Low CO₂