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Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
...recently reported in Asgard archaea (Leão et al. 2024). The DISARM system comprises drmABC, a MTase (drmMI, N6 adenine-specific MTase or drmMII, C5 cytosine-specific DNA MTase), and drmD or drmE (Ofir et al. 2018). The Freyarchaeia system includes drmA, drmB, drmC, drmMII, drmE, and drmD (helicase similar...
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Research: Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals
- Ulrike Böhme,
- Thomas D. Otto,
- James A. Cotton,
- Sascha Steinbiss,
- Mandy Sanders,
- Samuel O. Oyola,
- Antoine Nicot,
- Sylvain Gandon,
- Kailash P. Patra,
- Colin Herd,
- Ellen Bushell,
- Katarzyna K. Modrzynska,
- Oliver Billker,
- Joseph M. Vinetz,
- Ana Rivero,
- Chris I. Newbold,
- and Matthew Berriman
Genome Res. April 2018 28: 547-560; Published in Advance March 2, 2018, doi:10.1101/gr.218123.116
...could not be ascribed (Supplemental Table S1), but a possible new member of the AP2 family of transcription factors (PRELSG_1134000, PGAL8A_00142800) (Supplemental Fig. S4A) was found in both species. We also found a six-cysteine protein, a protein phosphatase, and an AMP-specific ABC transporter...
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Method: An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics
- Ulrich Omasits,
- Adithi R. Varadarajan,
- Michael Schmid,
- Sandra Goetze,
- Damianos Melidis,
- Marc Bourqui,
- Olga Nikolayeva,
- Maxime Québatte,
- Andrea Patrignani,
- Christoph Dehio,
- Juerg E. Frey,
- Mark D. Robinson,
- Bernd Wollscheid,
- and Christian H. Ahrens
Genome Res. December 2017 27: 2083-2095; Published in Advance November 15, 2017, doi:10.1101/gr.218255.116
...is supported by class 1a peptides (MQB277 track, Supplemental Fig. S7).View larger version: In this window In a new window Figure 5. Protein evidence for single amino acid variations (SAAVs). (A) Genomic region encoding an ABC transporter (BH_RS05910). RefSeq and Ensembl annotate it as a pseudogene, Genoscope...
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Resource: The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen
- Pooja K. Strope,
- Daniel A. Skelly,
- Stanislav G. Kozmin,
- Gayathri Mahadevan,
- Eric A. Stone,
- Paul M. Magwene,
- Fred S. Dietrich,
- and John H. McCusker
Genome Res. May 2015 25: 762-774; Published in Advance April 3, 2015, doi:10.1101/gr.185538.114
...The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen Pooja K. Strope 1 , Daniel A. Skelly 2 , Stanislav G. Kozmin 1 , Gayathri Mahadevan 1...
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ARTICLE: Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes
- Toshiaki Fukui,
- Haruyuki Atomi,
- Tamotsu Kanai,
- Rie Matsumi,
- Shinsuke Fujiwara,
- and Tadayuki Imanaka
Genome Res. March 2005 15: 352-363; Published in Advance February 14, 2005, doi:10.1101/gr.3003105
...the deduced primary structures, among which 261 CDSs are unique to T. kodakaraensis with no significant homology to any known sequences to date. We identified 186 multigene families, and the largest family is the ATP-binding subunit of ABC transporters, containing 36 members, as is the case in other...
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Research: Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution
- Herwig Bachmann,
- Marjo J.C. Starrenburg,
- Douwe Molenaar,
- Michiel Kleerebezem,
- and Johan E.T. van Hylckama Vlieg
Genome Res. January 2012 22: 115-124; Published in Advance November 11, 2011, doi:10.1101/gr.121285.111
...Transcriptional regulator, Rgg/GadR/MutR family Upstream 60/27d 0.99/1d 163,848 x A>G LLKF_0160 Na+ driven multidrug efflux pump, MatE family I259T 107 1 341,612 x C>A LLKF_0350 Phosphonates ABC transporter, permease protein PhnB S260STOP 34 1 393,291 x G>T LLKF_0399 Oligopeptide ABC transporter, substrate...
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ARTICLE: The Complete Genome and Proteome of Mycoplasma mobile
- Jacob D. Jaffe,
- Nicole Stange-Thomann,
- Cherylyn Smith,
- David DeCaprio,
- Sheila Fisher,
- Jonathan Butler,
- Sarah Calvo,
- Tim Elkins,
- Michael G. FitzGerald,
- Nabil Hafez,
- Chinnappa D. Kodira,
- John Major,
- Shunguang Wang,
- Jane Wilkinson,
- Robert Nicol,
- Chad Nusbaum,
- Bruce Birren,
- Howard C. Berg,
- and George M. Church
Genome Res. August 2004 14: 1447-1461; doi:10.1101/gr.2674004
...sequence. Low coverage can be an indicator of low protein abundance. Another reason for failing to detect a protein or having low protein coverage can relate to difficulty in solubilizing a particular class of protein. We failed to detect several proteins annotated as ABC permease components and transport...
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METHODS: Comparing Bacterial Genomes Through Conservation Profiles
- Maria J. Martı́n,
- Javier Herrero,
- Alvaro Mateos,
- and Joaquin Dopazo
Genome Res. May 1, 2003 13: 991-998; Published in Advance April 14, 2003, doi:10.1101/gr.678303
...and maltodextrin; DPPF_ECOLI, which is part of the binding-protein–dependent transport system for dipeptides ( Abouhamad and Manson 1994 ), etc. Many of them belong to the family of ABC transporters (see additional information). View larger version: In this window In a new window Figure 3. Proportion Escherichia...
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ARTICLE: A Complete Sequence of the T. tengcongensis Genome
- Qiyu Bao,
- Yuqing Tian,
- Wei Li,
- Zuyuan Xu,
- Zhenyu Xuan,
- Songnian Hu,
- Wei Dong,
- Jian Yang,
- Yanjiong Chen,
- Yanfen Xue,
- Yi Xu,
- Xiaoqin Lai,
- Li Huang,
- Xiuzhu Dong,
- Yanhe Ma,
- Lunjiang Ling,
- Huarong Tan,
- Runsheng Chen,
- Jian Wang,
- Jun Yu,
- and Huanming Yang
Genome Res. May 1, 2002 12: 689-700; doi:10.1101/gr.219302
...categorized. Most of them are related to transposases (10 families; 54 copies) and ABC transporters (6 families; 13 copies). Others are unknown or hypothetical (11 families; 62 copies). The largest repeated sequence, TLR028 (3565-bp in length), is composed of two different transposases flanking a hypothetical...
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ARTICLE: Tandem Clusters of Membrane Proteins in Complete Genome Sequences
- Daisuke Kihara and
- Minoru Kanehisa
Genome Res. June 1, 2000 10: 731-743; doi:10.1101/gr.10.6.731
...-binding proteins in the complete genomes was also analyzed. Although this clustering was not statistically significant, it was useful to identify candidate membrane protein partners of isolated ATP-binding protein components in the ABC transporters. Possible implications of tandem cluster organization of membrane...

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