Login Register Cart 0
Generic placeholder image

Protein & Peptide Letters

Editor-in-Chief

ISSN (Print): 0929-8665
ISSN (Online): 1875-5305

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
Research Article

A Dual Leucine-rich Repeat in Proteins from the Eukaryotic SAR Group

Author(s): Norio Matsushima*, Dashdavaa Batkhishig, Purevjav Enkhbayar and Robert H. Kretsinger

Volume 30, Issue 7, 2023

Published on: 21 June, 2023

Page: [574 - 586] Pages: 13

DOI: 10.2174/0929866530666230519160439

Price: $65

Abstract

Background: Leucine-rich repeats (LRRs) occurring in tandem are 20 - 29 amino acids long. Eleven LRR types have been recognized; they include plant-specific (PS) type with the consensus of LxxLxLxxNxL SGxIPxxIxxLxx of 24 residues and SDS22-like type with the consensus of LxxLxLxxNxL xxIxxIxxLxx of 22 residues.

Objective: A viral LRR protein in metagenome data indicated that most of the LRRs (5/6 = 0.83) are represented by the consensus of LxxLDLxxTxV SGKLSDLxxLTN of 23 residues. This LRR shows a dual characteristic of PS and SDS22-like LRRs (called PS/SDS22-like LRR). A comprehensive similarity search was performed under the hypothesis that many proteins contain LRR domains consisting of only or mainly PS/SDS22-like LRR.

Methods: Sequence similarity search by the FASTA and BLAST programs was performed using the sequence of this PS/SDS22-like LRR domain as a query sequence. The presence of PS/SDS22-like LRR was screened within the LRR domains in known structures.

Results: Over 280 LRR proteins were identified from protists, fungi, and bacteria; ~ 40% come from the SAR group (the phyla Alveolate and Stramenopiles). The secondary structure analysis of PS/SDS22-like LRRs occurring sporadically in the known structures indicates three or four type patterns of secondary structures.

Conclusion: PS/SDS22-like LRR forms an LRR class with PS, SDS22-like and Leptospira-like LRRs. It appears that PS/SDS22-like LRR is a chameleon-like sequence. A duality of two LRR types brings diversity.

« Previous Next »
Graphical Abstract

[1]
Kobe, B.; Deisenhofer, J. The leucine-rich repeat: A versatile binding motif. Trends Biochem. Sci., 1994, 19(10), 415-421.
[http://dx.doi.org/10.1016/0968-0004(94)90090-6] [PMID: 7817399]
[2]
Bella, J.; Hindle, K.L.; McEwan, P.A.; Lovell, S.C. The leucine-rich repeat structure. Cell. Mol. Life Sci., 2008, 65(15), 2307-2333.
[http://dx.doi.org/10.1007/s00018-008-8019-0] [PMID: 18408889]
[3]
Matsushima, N.; Robert, H. Kretsinger. Leucine Rich Repeats: Sequences, structures, Ligand-Interactions and Evolution; LAMBERT Academic Publishing: Saarbrucken, Germany, 2016.
[4]
Kobe, B.; Kajava, A.V. The leucine-rich repeat as a protein recognition motif. Curr. Opin. Struct. Biol., 2001, 11(6), 725-732.
[http://dx.doi.org/10.1016/S0959-440X(01)00266-4] [PMID: 11751054]
[5]
Kajava, A.V.; Anisimova, M.; Peeters, N. Origin and evolution of GALA-LRR, a new member of the CC-LRR subfamily: From plants to bacteria? PLoS One, 2008, 3(2), e1694.
[http://dx.doi.org/10.1371/journal.pone.0001694] [PMID: 18301771]
[6]
Matsushima, N.; Miyashita, H.; Mikami, T.; Kuroki, Y. A nested leucine rich repeat (LRR) domain: The precursor of LRRs is a ten or eleven residue motif. BMC Microbiol., 2010, 10(1), 235-244.
[http://dx.doi.org/10.1186/1471-2180-10-235] [PMID: 20825685]
[7]
Matsushima, N.; Takatsuka, S.; Miyashita, H.; Kretsinger, R.H. Leucine rich repeat proteins: Sequences, mutations, structures and diseases. Protein Pept. Lett., 2019, 26(2), 108-131.
[http://dx.doi.org/10.2174/0929866526666181208170027] [PMID: 30526451]
[8]
Batkhishig, D.; Bilguun, K.; Enkhbayar, P.; Miyashita, H.; Kretsinger, R.H.; Matsushima, N. Super secondary structure consisting of a polyproline II helix and a beta-turn in leucine rich repeats in bacterial type III secretion system effectors. Protein J., 2018, 37(3), 223-236.
[http://dx.doi.org/10.1007/s10930-018-9767-9] [PMID: 29651716]
[9]
Batkhishig, D.; Enkhbayar, P.; Kretsinger, R.H.; Matsushima, N. A strong correlation between consensus sequences and unique super secondary structures in leucine rich repeats. Proteins, 2020, 88(7), 840-852.
[http://dx.doi.org/10.1002/prot.25876] [PMID: 31998983]
[10]
Batkhishig, D.; Enkhbayar, P.; Kretsinger, R.H.; Matsushima, N. A crucial residue in the hydrophobic core of the solenoid structure of leucine rich repeats. Biochim. Biophys. Acta. Proteins Proteomics, 2021, 1869(6), 140631.
[http://dx.doi.org/10.1016/j.bbapap.2021.140631] [PMID: 33631375]
[11]
Park, H.; Huxley-Jones, J.; Boot-Handford, R.P.; Bishop, P.N.; Attwood, T.K.; Bella, J. LRRCE: A leucine-rich repeat cysteine capping motif unique to the chordate lineage. BMC Genomics, 2008, 9(1), 599.
[http://dx.doi.org/10.1186/1471-2164-9-599] [PMID: 19077264]
[12]
Matsushima, N.; Miyashita, H.; Tamaki, S.; Kretsinger, R.H. Shrinking of repeating unit length in leucine-rich repeats from double-stranded DNA viruses. Arch. Virol., 2021, 166(1), 43-64.
[http://dx.doi.org/10.1007/s00705-020-04820-2] [PMID: 33052487]
[13]
Matsushima, N.; Kretsinger, R.H. Numerous variants of leucine rich repeats in proteins from nucleo-cytoplasmic large DNA viruses. Gene, 2022, 817, 146156.
[http://dx.doi.org/10.1016/j.gene.2021.146156] [PMID: 35032616]
[14]
Schulz, F.; Roux, S.; Paez-Espino, D.; Jungbluth, S.; Walsh, D.A.; Denef, V.J.; McMahon, K.D.; Konstantinidis, K.T.; Eloe-Fadrosh, E.A.; Kyrpides, N.C.; Woyke, T. Giant virus diversity and host interactions through global metagenomics. Nature, 2020, 578(7795), 432-436.
[http://dx.doi.org/10.1038/s41586-020-1957-x] [PMID: 31968354]
[15]
Matsushima, N.; Miyashita, H.; Mikami, T.; Yamada, K. A new method for the identification of leucine-rich repeats by incorporating protein second structure prediction. In: Bioinformatics: genome bioinformatics and computational biology; Tuteja, R., Ed.; NOVA Science Publisher: New York, 2011; pp. 61-88.
[16]
Matsushima, N.; Tanaka, T.; Enkhbayar, P.; Mikami, T.; Taga, M.; Yamada, K.; Kuroki, Y. Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors. BMC Genomics, 2007, 8(1), 124-143.
[http://dx.doi.org/10.1186/1471-2164-8-124] [PMID: 17517123]
[17]
Crooks, G.E.; Hon, G.; Chandonia, J.M.; Brenner, S.E. WebLogo: A sequence logo generator. Genome Res., 2004, 14(6), 1188-1190.
[http://dx.doi.org/10.1101/gr.849004] [PMID: 15173120]
[18]
El-Gebali, S.; Mistry, J.; Bateman, A.; Eddy, S.R.; Luciani, A.; Potter, S.C.; Qureshi, M.; Richardson, L.J.; Salazar, G.A.; Smart, A.; Sonnhammer, E.L.L.; Hirsh, L.; Paladin, L.; Piovesan, D.; Tosatto, S.C.E.; Finn, R.D. The Pfam protein families database in 2019. Nucleic Acids Res., 2019, 47(D1), D427-D432.
[http://dx.doi.org/10.1093/nar/gky995] [PMID: 30357350]
[19]
Blum, M.; Chang, H.Y.; Chuguransky, S.; Grego, T.; Kandasaamy, S.; Mitchell, A.; Nuka, G.; Paysan-Lafosse, T.; Qureshi, M.; Raj, S.; Richardson, L.; Salazar, G.A.; Williams, L.; Bork, P.; Bridge, A.; Gough, J.; Haft, D.H.; Letunic, I.; Marchler-Bauer, A.; Mi, H.; Natale, D.A.; Necci, M.; Orengo, C.A.; Pandurangan, A.P.; Rivoire, C.; Sigrist, C.J.A.; Sillitoe, I.; Thanki, N.; Thomas, P.D.; Tosatto, S.C.E.; Wu, C.H.; Bateman, A.; Finn, R.D. The InterPro protein families and domains database: 20 years on. Nucleic Acids Res., 2021, 49(D1), D344-D354.
[http://dx.doi.org/10.1093/nar/gkaa977] [PMID: 33156333]
[20]
Hirosawa, M.; Totoki, Y.; Hoshida, M.; Ishikawa, M. Comprehensive study on iterative algorithms of multiple sequence alignment. Bioinformatics, 1995, 11(1), 13-18.
[http://dx.doi.org/10.1093/bioinformatics/11.1.13] [PMID: 7796270]
[21]
Montgomerie, S.; Sundararaj, S.; Gallin, W.J.; Wishart, D.S. Improving the accuracy of protein secondary structure prediction using structural alignment. BMC Bioinformatics, 2006, 7(1), 301.
[http://dx.doi.org/10.1186/1471-2105-7-301] [PMID: 16774686]
[22]
Yang, Y.; Gao, J.; Wang, J.; Heffernan, R.; Hanson, J.; Paliwal, K.; Zhou, Y. Sixty-five years of the long march in protein secondary structure prediction: the final stretch? Brief. Bioinform., 2016, 19(3), bbw129.
[http://dx.doi.org/10.1093/bib/bbw129] [PMID: 28040746]
[23]
Tang, J.; Han, Z.; Sun, Y.; Zhang, H.; Gong, X.; Chai, J. Structural basis for recognition of an endogenous peptide by the plant receptor kinase PEPR1. Cell Res., 2015, 25(1), 110-120.
[http://dx.doi.org/10.1038/cr.2014.161] [PMID: 25475059]
[24]
Liu, P.; Hu, Z.; Zhou, B.; Liu, S.; Chai, J. Crystal structure of an LRR protein with two solenoids. Cell Res., 2013, 23(2), 303-305.
[http://dx.doi.org/10.1038/cr.2012.159] [PMID: 23147790]
[25]
Song, W.; Liu, L.; Wang, J.; Wu, Z.; Zhang, H.; Tang, J.; Lin, G.; Wang, Y.; Wen, X.; Li, W.; Han, Z.; Guo, H.; Chai, J. Signature motif-guided identification of receptors for peptide hormones essential for root meristem growth. Cell Res., 2016, 26(6), 674-685.
[http://dx.doi.org/10.1038/cr.2016.62] [PMID: 27229311]
[26]
Zhang, X.; Liu, W.; Nagae, T.T.; Takeuchi, H.; Zhang, H.; Han, Z.; Higashiyama, T.; Chai, J. Structural basis for receptor recognition of pollen tube attraction peptides. Nat. Commun., 2017, 8(1), 1331.
[http://dx.doi.org/10.1038/s41467-017-01323-8] [PMID: 29109411]
[27]
Chakraborty, S.; Pan, H.; Tang, Q.; Woolard, C.; Xu, G. The extracellular domain of pollen receptor kinase 3 is structurally similar to the SERK family of co-receptors. Sci. Rep., 2018, 8(1), 2796.
[http://dx.doi.org/10.1038/s41598-018-21218-y] [PMID: 29434276]
[28]
She, J.; Han, Z.; Kim, T.W.; Wang, J.; Cheng, W.; Chang, J.; Shi, S.; Wang, J.; Yang, M.; Wang, Z.Y.; Chai, J. Structural insight into brassinosteroid perception by BRI1. Nature, 2011, 474(7352), 472-476.
[http://dx.doi.org/10.1038/nature10178] [PMID: 21666666]
[29]
Faralla, C.; Bastounis, E.E.; Ortega, F.E.; Light, S.H.; Rizzuto, G.; Gao, L.; Marciano, D.K.; Nocadello, S.; Anderson, W.F.; Robbins, J.R.; Theriot, J.A.; Bakardjiev, A.I. Listeria monocytogenes InlP interacts with afadin and facilitates basement membrane crossing. PLoS Pathog., 2018, 14(5), e1007094.
[http://dx.doi.org/10.1371/journal.ppat.1007094] [PMID: 29847585]
[30]
Wang, J.; Li, H.; Han, Z.; Zhang, H.; Wang, T.; Lin, G.; Chang, J.; Yang, W.; Chai, J. Allosteric receptor activation by the plant peptide hormone phytosulfokine. Nature, 2015, 525(7568), 265-268.
[http://dx.doi.org/10.1038/nature14858] [PMID: 26308901]
[31]
Chen, H.; Kong, Y.; Chen, J.; Li, L.; Li, X.; Yu, F.; Ming, Z. Crystal structure of the extracellular domain of the receptor-like kinase TMK3 from Arabidopsis thaliana. Acta Crystallogr. F Struct. Biol. Commun., 2020, 76(8), 384-390.
[http://dx.doi.org/10.1107/S2053230X20010122] [PMID: 32744250]
[32]
Chebrek, R.; Leonard, S.; de Brevern, A.G.; Gelly, J.C. PolyprOnline: polyproline helix II and secondary structure assignment database. Database, 2014, bau102.
[http://dx.doi.org/10.1093/database/bau102]
[33]
Kabsch, W.; Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 1983, 22(12), 2577-2637.
[http://dx.doi.org/10.1002/bip.360221211] [PMID: 6667333]
[34]
Hutchinson, E.G.; Thornton, J.M. PROMOTIF-A program to identify and analyze structural motifs in proteins. Protein Sci., 1996, 5(2), 212-220.
[http://dx.doi.org/10.1002/pro.5560050204] [PMID: 8745398]
[35]
Heinig, M.; Frishman, D. STRIDE: A web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res., 2004, 32, W500-W502.
[http://dx.doi.org/10.1093/nar/gkh429]
[36]
Shapovalov, M.; Vucetic, S.; Dunbrack, R.L., Jr A new clustering and nomenclature for beta turns derived from high-resolution protein structures. PLOS Comput. Biol., 2019, 15(3), e1006844.
[http://dx.doi.org/10.1371/journal.pcbi.1006844] [PMID: 30845191]
[37]
Adl, S.M.; Bass, D.; Lane, C.E.; Lukeš, J.; Schoch, C.L.; Smirnov, A.; Agatha, S.; Berney, C.; Brown, M.W.; Burki, F.; Cárdenas, P.; Čepička, I.; Chistyakova, L.; Campo, J.; Dunthorn, M.; Edvardsen, B.; Eglit, Y.; Guillou, L.; Hampl, V.; Heiss, A.A.; Hoppenrath, M.; James, T.Y.; Karnkowska, A.; Karpov, S.; Kim, E.; Kolisko, M.; Kudryavtsev, A.; Lahr, D.J.G.; Lara, E.; Le, all, L.; Lynn, D.H.; Mann, D.G.; Massana, R.; Mitchell, E.A.D.; Morrow, C.; Park, J.S.; Pawlowski, J.W.; Powell, M.J.; Richter, D.J.; Rueckert, S.; Shadwick, L.; Shimano, S.; Spiegel, F.W.; Torruella, G.; Youssef, N.; Zlatogursky, V.; Zhang, Q. Revisions to the classification, nomenclature, and diversity of eukaryotes. J. Eukaryot. Microbiol., 2019, 66(1), 4-119.
[http://dx.doi.org/10.1111/jeu.12691] [PMID: 30257078]
[38]
Aranda, M.; Li, Y.; Liew, Y.J.; Baumgarten, S.; Simakov, O.; Wilson, M.C.; Piel, J.; Ashoor, H.; Bougouffa, S.; Bajic, V.B.; Ryu, T.; Ravasi, T.; Bayer, T.; Micklem, G.; Kim, H.; Bhak, J.; LaJeunesse, T.C.; Voolstra, C.R. Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle. Sci. Rep., 2016, 6(1), 39734.
[http://dx.doi.org/10.1038/srep39734] [PMID: 28004835]
[39]
Burki, F.; Kaplan, M.; Tikhonenkov, D.V.; Zlatogursky, V.; Minh, B.Q.; Radaykina, L.V.; Smirnov, A.; Mylnikov, A.P.; Keeling, P.J. Untangling the early diversification of eukaryotes: A phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista. Proc. Biol. Sci., 2016, 283(1823), 20152802.
[http://dx.doi.org/10.1098/rspb.2015.2802] [PMID: 26817772]
[40]
Chang, Y.; Wang, S.; Sekimoto, S.; Aerts, A.L.; Choi, C.; Clum, A.; LaButti, K.M.; Lindquist, E.A.; Yee Ngan, C.; Ohm, R.A.; Salamov, A.A.; Grigoriev, I.V.; Spatafora, J.W.; Berbee, M.L. Phylogenomic analyses indicate that early fungi evolved digesting cell walls of algal ancestors of land plants. Genome Biol. Evol., 2015, 7(6), 1590-1601.
[http://dx.doi.org/10.1093/gbe/evv090] [PMID: 25977457]
[41]
Hug, L.A.; Baker, B.J.; Anantharaman, K.; Brown, C.T.; Probst, A.J.; Castelle, C.J.; Butterfield, C.N.; Hernsdorf, A.W.; Amano, Y.; Ise, K.; Suzuki, Y.; Dudek, N.; Relman, D.A.; Finstad, K.M.; Amundson, R.; Thomas, B.C.; Banfield, J.F. A new view of the tree of life. Nat. Microbiol., 2016, 1(5), 16048.
[http://dx.doi.org/10.1038/nmicrobiol.2016.48] [PMID: 27572647]
[42]
Brown, C.T.; Hug, L.A.; Thomas, B.C.; Sharon, I.; Castelle, C.J.; Singh, A.; Wilkins, M.J.; Wrighton, K.C.; Williams, K.H.; Banfield, J.F. Unusual biology across a group comprising more than 15% of domain bacteria. Nature, 2015, 523(7559), 208-211.
[http://dx.doi.org/10.1038/nature14486] [PMID: 26083755]
[43]
Dombrowski, N.; Teske, A.P.; Baker, B.J. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat. Commun., 2018, 9(1), 4999.
[http://dx.doi.org/10.1038/s41467-018-07418-0] [PMID: 30479325]
[44]
Parks, D.H.; Chuvochina, M.; Waite, D.W.; Rinke, C.; Skarshewski, A.; Chaumeil, P.A.; Hugenholtz, P. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol., 2018, 36(10), 996-1004.
[http://dx.doi.org/10.1038/nbt.4229] [PMID: 30148503]
[45]
Sharrar, A.M.; Flood, B.E.; Bailey, J.V.; Jones, D.S.; Biddanda, B.A.; Ruberg, S.A.; Marcus, D.N.; Dick, G.J. Novel large sulfur bacteria in the metagenomes of groundwaterfed chemosynthetic microbial mats in the Lake Huron Basin. Front. Microbiol., 2017, 8, 791.
[http://dx.doi.org/10.3389/fmicb.2017.00791] [PMID: 28533768]
[46]
Fomenkov, A.; Sun, Z.; Vincze, T.; Dubinina, G.; Orlova, M.; Tarlachkov, S.V.; Anton, B.P.; Grabovich, M.Y.; Roberts, R.J. Complete genome sequence of the freshwater bacterium Beggiatoa leptomitoformis Strain D-401. Genome Announc., 2018, 6(17), e00311-18.
[http://dx.doi.org/10.1128/genomeA.00311-18] [PMID: 29700149]
[47]
Zhou, Z.; Tran, P.Q.; Kieft, K.; Anantharaman, K. Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation. ISME J., 2020, 14(8), 2060-2077.
[http://dx.doi.org/10.1038/s41396-020-0669-4] [PMID: 32393808]
[48]
Brooks, B.; Olm, M.R.; Firek, B.A.; Baker, R.; Geller-McGrath, D.; Reimer, S.R.; Soenjoyo, K.R.; Yip, J.S.; Dahan, D.; Thomas, B.C.; Morowitz, M.J.; Banfield, J.F. The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms. Microbiome, 2018, 6(1), 112-112.
[http://dx.doi.org/10.1186/s40168-018-0493-5] [PMID: 29925423]
[49]
Zhou, Z.; Liu, Y.; Xu, W.; Pan, J.; Luo, Z.H.; Li, M. Genome- and community- level interaction insights into carbon utilization and element cycling functions of Hydrothermarchaeota in hydrothermal sediment. mSystems, 2020, 5(1), e00795-19.
[http://dx.doi.org/10.1128/mSystems.00795-19] [PMID: 31911466]
[50]
Fomenkov, A.; Vincze, T.; Grabovich, M.Y.; Dubinina, G.; Orlova, M.; Belousova, E.; Roberts, R.J. Whole-genome sequence and Methylome analysis of the freshwater colorless sulfur bacterium Thioflexothrix psekupsii D3. Genome Announc., 2017, 5(35), e00904-17.
[http://dx.doi.org/10.1128/genomeA.00904-17] [PMID: 28860255]
[51]
Kojima, H.; Ogura, Y.; Yamamoto, N.; Togashi, T.; Mori, H.; Watanabe, T.; Nemoto, F.; Kurokawa, K.; Hayashi, T.; Fukui, M. Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence supplemented with proteomic evidence. ISME J., 2015, 9(5), 1166-1176.
[http://dx.doi.org/10.1038/ismej.2014.209] [PMID: 25343513]
[52]
Berger, S.; Shaw, D.R.; Berben, T.; Ouboter, H.T. Current production by non-methanotrophic bacteria enriched from an anaerobic methane-oxidizing microbial community. Biofilm., 2021, 3, 100054.
[http://dx.doi.org/10.1016/j.bioflm.2021.100054]
[53]
Anantharaman, K.; Brown, C.T.; Hug, L.A.; Sharon, I.; Castelle, C.J.; Probst, A.J.; Thomas, B.C.; Singh, A.; Wilkins, M.J.; Karaoz, U.; Brodie, E.L.; Williams, K.H.; Hubbard, S.S.; Banfield, J.F. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat. Commun., 2016, 7(1), 13219.
[http://dx.doi.org/10.1038/ncomms13219] [PMID: 27774985]
[54]
Kantor, R.S.; Huddy, R.J.; Iyer, R.; Thomas, B.C.; Brown, C.T.; Anantharaman, K.; Tringe, S.; Hettich, R.L.; Harrison, S.T.L.; Banfield, J.F. Genome-resolved meta-omics ties microbial dynamics to process performance in biotechnology for thiocyanate degradation. Environ. Sci. Technol., 2017, 51(5), 2944-2953.
[http://dx.doi.org/10.1021/acs.est.6b04477] [PMID: 28139919]
[55]
Miura, T.; Kusada, H.; Kamagata, Y.; Hanada, S.; Kimura, N. Genome sequence of the multiple-β-lactam-antibiotic-resistant bacterium Acidovorax sp. Strain MR-S7. Genome Announc., 2013, 1(4), e00412-13.
[http://dx.doi.org/10.1128/genomeA.00412-13] [PMID: 23814112]
[56]
Ide, H.; Ishii, K.; Fujitani, H.; Tsuneda, S. Draft genome sequence of Acidovorax sp. strain NB1, isolated from a nitrite-oxidizing enrichment culture. Microbiol. Resour. Announc., 2019, 8(33), e00547-19.
[http://dx.doi.org/10.1128/MRA.00547-19] [PMID: 31416864]
[57]
Bernard, K.A.; Pacheco, A.L.; Burdz, T.; Wiebe, D.; Bernier, A.M. Assignment of provisionally named CDC group NO-1 strains derived from animal bite wounds and other clinical sources, to genera nova in the family Comamonadaceae: description of Vandammella animalimorsus gen. nov., sp. nov. and Franklinella schreckenbergeri gen. nov., sp. nov. Int. J. Syst. Evol. Microbiol., 2022, 72(2), 005247.
[http://dx.doi.org/10.1099/ijsem.0.005247] [PMID: 35171091]
[58]
Heo, J.; Cho, H.; Hong, S.B.; Kim, J.S.; Kwon, S.W.; Kim, S.J. Ottowia oryzae sp. nov., isolated from Andong sikhye, a Korean traditional rice beverage. Int. J. Syst. Evol. Microbiol., 2018, 68(10), 3096-3100.
[http://dx.doi.org/10.1099/ijsem.0.002935] [PMID: 30102146]
[59]
Heo, J.; Cho, H.Y.; Heo, I.; Hong, S.B.; Kim, J.S.; Kwon, S.W.; Kim, S.J. Pulveribacter suum gen. nov., sp. nov., isolated from a pig farm dust collector. Int. J. Syst. Evol. Microbiol., 2019, 69(7), 1864-1869.
[http://dx.doi.org/10.1099/ijsem.0.003082] [PMID: 31046896]
[60]
Engelberts, J.P.; Robbins, S.J.; de Goeij, J.M.; Aranda, M.; Bell, S.C.; Webster, N.S. Characterization of a sponge microbiome using an integrative genome-centric approach. ISME J., 2020, 14(5), 1100-1110.
[http://dx.doi.org/10.1038/s41396-020-0591-9] [PMID: 31992859]
[61]
Dudek, N.K.; Sun, C.L.; Burstein, D.; Kantor, R.S.; Aliaga Goltsman, D.S.; Bik, E.M.; Thomas, B.C.; Banfield, J.F.; Relman, D.A. Novel microbial diversity and functional potential in the marine mammal oral microbiome. Curr. Biol., 2017, 27(24), 3752-3762.e6.
[http://dx.doi.org/10.1016/j.cub.2017.10.040] [PMID: 29153320]
[62]
Abendroth, C.; Latorre-Pérez, A.; Porcar, M.; Simeonov, C.; Luschnig, O.; Vilanova, C.; Pascual, J. Shedding light on biogas: Phototrophic biofilms in anaerobic digesters hold potential for improved biogas production. Syst. Appl. Microbiol., 2020, 43(1), 126024.
[http://dx.doi.org/10.1016/j.syapm.2019.126024] [PMID: 31708159]
[63]
Ali, M.; Shaw, D.R.; Albertsen, M.; Saikaly, P.E. Comparative genome-centric analysis of freshwater and marine ANAMMOX cultures suggests functional redundancy in nitrogen removal processes. Front. Microbiol., 2020, 11, 1637.
[http://dx.doi.org/10.3389/fmicb.2020.01637] [PMID: 32733431]
[64]
Tian, R.; Ning, D.; He, Z.; Zhang, P.; Spencer, S.J.; Gao, S.; Shi, W.; Wu, L.; Zhang, Y.; Yang, Y.; Adams, B.G.; Rocha, A.M.; Detienne, B.L.; Lowe, K.A.; Joyner, D.C.; Klingeman, D.M.; Arkin, A.P.; Fields, M.W.; Hazen, T.C.; Stahl, D.A.; Alm, E.J.; Zhou, J. Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity. Microbiome, 2020, 8(1), 51.
[http://dx.doi.org/10.1186/s40168-020-00825-w] [PMID: 32252814]
[65]
Campanaro, S.; Treu, L.; Rodriguez-R, L.M.; Kovalovszki, A.; Ziels, R.M.; Maus, I.; Zhu, X.; Kougias, P.G.; Basile, A.; Luo, G.; Schlüter, A.; Konstantinidis, K.T.; Angelidaki, I. New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters. Biotechnol. Biofuels, 2020, 13(1), 25.
[http://dx.doi.org/10.1186/s13068-020-01679-y] [PMID: 32123542]
[66]
Momper, L.; Jungbluth, S.P.; Lee, M.D.; Amend, J.P. Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community. ISME J., 2017, 11(10), 2319-2333.
[http://dx.doi.org/10.1038/ismej.2017.94] [PMID: 28644444]
[67]
Wrighton, K.C.; Thomas, B.C.; Sharon, I.; Miller, C.S.; Castelle, C.J.; VerBerkmoes, N.C.; Wilkins, M.J.; Hettich, R.L.; Lipton, M.S.; Williams, K.H.; Long, P.E.; Banfield, J.F. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science, 2012, 337(6102), 1661-1665.
[http://dx.doi.org/10.1126/science.1224041] [PMID: 23019650]
[68]
Zhang, L.; Hu, J.; Han, X.; Li, J.; Gao, Y.; Richards, C.M.; Zhang, C.; Tian, Y.; Liu, G.; Gul, H.; Wang, D.; Tian, Y.; Yang, C.; Meng, M.; Yuan, G.; Kang, G.; Wu, Y.; Wang, K.; Zhang, H.; Wang, D.; Cong, P. A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. Nat. Commun., 2019, 10(1), 1494.
[http://dx.doi.org/10.1038/s41467-019-09518-x] [PMID: 30940818]
[69]
Bowman, J.L.; Kohchi, T.; Yamato, K.T.; Jenkins, J.; Shu, S.; Ishizaki, K.; Yamaoka, S.; Nishihama, R.; Nakamura, Y.; Berger, F.; Adam, C.; Aki, S.S.; Althoff, F.; Araki, T.; Arteaga-Vazquez, M.A.; Balasubrmanian, S.; Barry, K.; Bauer, D.; Boehm, C.R.; Briginshaw, L.; Caballero-Perez, J.; Catarino, B.; Chen, F.; Chiyoda, S.; Chovatia, M.; Davies, K.M.; Delmans, M.; Demura, T.; Dierschke, T.; Dolan, L.; Dorantes-Acosta, A.E.; Eklund, D.M.; Florent, S.N.; Flores-Sandoval, E.; Fujiyama, A.; Fukuzawa, H.; Galik, B.; Grimanelli, D.; Grimwood, J.; Grossniklaus, U.; Hamada, T.; Haseloff, J.; Hetherington, A.J.; Higo, A.; Hirakawa, Y.; Hundley, H.N.; Ikeda, Y.; Inoue, K.; Inoue, S.; Ishida, S.; Jia, Q.; Kakita, M.; Kanazawa, T.; Kawai, Y.; Kawashima, T.; Kennedy, M.; Kinose, K.; Kinoshita, T.; Kohara, Y.; Koide, E.; Komatsu, K.; Kopischke, S.; Kubo, M.; Kyozuka, J.; Lagercrantz, U.; Lin, S.S.; Lindquist, E.; Lipzen, A.M.; Lu, C.W.; De Luna, E.; Martienssen, R.A.; Minamino, N.; Mizutani, M.; Mizutani, M.; Mochizuki, N.; Monte, I.; Mosher, R.; Nagasaki, H.; Nakagami, H.; Naramoto, S.; Nishitani, K.; Ohtani, M.; Okamoto, T.; Okumura, M.; Phillips, J.; Pollak, B.; Reinders, A.; Rövekamp, M.; Sano, R.; Sawa, S.; Schmid, M.W.; Shirakawa, M.; Solano, R.; Spunde, A.; Suetsugu, N.; Sugano, S.; Sugiyama, A.; Sun, R.; Suzuki, Y.; Takenaka, M.; Takezawa, D.; Tomogane, H.; Tsuzuki, M.; Ueda, T.; Umeda, M.; Ward, J.M.; Watanabe, Y.; Yazaki, K.; Yokoyama, R.; Yoshitake, Y.; Yotsui, I.; Zachgo, S.; Schmutz, J. Insights into land plant evolution garnered from the Marchantia polymorpha Genome. Cell, 2017, 171(2), 287-304.e15.
[http://dx.doi.org/10.1016/j.cell.2017.09.030] [PMID: 28985561]
[70]
McEwan, P.A.; Scott, P.G.; Bishop, P.N.; Bella, J. Structural correlations in the family of small leucine-rich repeat proteins and proteoglycans. J. Struct. Biol., 2006, 155(2), 294-305.
[http://dx.doi.org/10.1016/j.jsb.2006.01.016] [PMID: 16884925]
[71]
Mondo, S.J.; Dannebaum, R.O.; Kuo, R.C.; Louie, K.B.; Bewick, A.J.; LaButti, K.; Haridas, S.; Kuo, A.; Salamov, A.; Ahrendt, S.R.; Lau, R.; Bowen, B.P.; Lipzen, A.; Sullivan, W.; Andreopoulos, B.B.; Clum, A.; Lindquist, E.; Daum, C.; Northen, T.R.; Kunde-Ramamoorthy, G.; Schmitz, R.J.; Gryganskyi, A.; Culley, D.; Magnuson, J.; James, T.Y.; O’Malley, M.A.; Stajich, J.E.; Spatafora, J.W.; Visel, A.; Grigoriev, I.V. Widespread adenine N6-methylation of active genes in fungi. Nat. Genet., 2017, 49(6), 964-968.
[http://dx.doi.org/10.1038/ng.3859] [PMID: 28481340]
[72]
Hillmann, F.; Forbes, G.; Novohradská, S.; Ferling, I.; Riege, K.; Groth, M.; Westermann, M.; Marz, M.; Spaller, T.; Winckler, T.; Schaap, P.; Glöckner, G. Multiple roots of fruiting body formation in Amoebozoa. Genome Biol. Evol., 2018, 10(2), 591-606.
[http://dx.doi.org/10.1093/gbe/evy011] [PMID: 29378020]
[73]
Schönknecht, G.; Chen, W.H.; Ternes, C.M.; Barbier, G.G.; Shrestha, R.P.; Stanke, M.; Bräutigam, A.; Baker, B.J.; Banfield, J.F.; Garavito, R.M.; Carr, K.; Wilkerson, C.; Rensing, S.A.; Gagneul, D.; Dickenson, N.E.; Oesterhelt, C.; Lercher, M.J.; Weber, A.P.M. Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote. Science, 2013, 339(6124), 1207-1210.
[http://dx.doi.org/10.1126/science.1231707] [PMID: 23471408]
[74]
Ward, L.M.; Lingappa, U.F.; Grotzinger, J.P.; Fischer, W.W. Microbial mats in the Turks and Caicos Islands reveal diversity and evolution of phototrophy in the Chloroflexota order Aggregatilineales. Environ. Microbiol., 2020, 15(1), 9.
[http://dx.doi.org/10.1186/s40793-020-00357-8] [PMID: 33902735]
[75]
Park, Y.; Maeng, S.; Damdintogtokh, T.; Zhang, J.; Kim, M.K.; Srinivasan, S.; Kim, M.K. Spirosoma profusum sp. nov., and Spirosoma validum sp. nov., radiation-resistant bacteria isolated from soil in South Korea. Antonie van Leeuwenhoek, 2021, 114(7), 1155-1164.
[http://dx.doi.org/10.1007/s10482-021-01585-9] [PMID: 33969460]
[76]
Kusolkumbot, P.; Kim, S.G.; Suwannachart, C. Complete genome sequence of Spirosoma sp. strain KCTC 42546, isolated from a reservoir in South Korea. Microbiol. Resour. Announc., 2020, 9(38), e00694-20.
[http://dx.doi.org/10.1128/MRA.00694-20] [PMID: 32943563]
[77]
Choy, M.S.; Moon, T.M.; Ravindran, R.; Bray, J.A.; Robinson, L.C.; Archuleta, T.L.; Shi, W.; Peti, W.; Tatchell, K.; Page, R. SDS22 selectively recognizes and traps metal-deficient inactive PP1. Proc. Natl. Acad. Sci. USA, 2019, 116(41), 20472-20481.
[http://dx.doi.org/10.1073/pnas.1908718116] [PMID: 31548429]
[78]
Heroes, E.; Van der Hoeven, G.; Choy, M.S.; Garcia, J.P.; Ferreira, M.; Nys, M.; Derua, R.; Beullens, M.; Ulens, C.; Peti, W.; Van Meervelt, L.; Page, R.; Bollen, M. Structure-guided exploration of SDS22 interactions with protein phosphatase PP1 and the splicing factor BCLAF1. Structure, 2019, 27(3), 507-518.e5.
[http://dx.doi.org/10.1016/j.str.2018.12.002] [PMID: 30661852]
[79]
Jumper, J.; Evans, R.; Pritzel, A.; Green, T.; Figurnov, M.; Ronneberger, O.; Tunyasuvunakool, K.; Bates, R.; Žídek, A.; Potapenko, A.; Bridgland, A.; Meyer, C.; Kohl, S.A.A.; Ballard, A.J.; Cowie, A.; Romera-Paredes, B.; Nikolov, S.; Jain, R.; Adler, J.; Back, T.; Petersen, S.; Reiman, D.; Clancy, E.; Zielinski, M.; Steinegger, M.; Pacholska, M.; Berghammer, T.; Bodenstein, S.; Silver, D.; Vinyals, O.; Senior, A.W.; Kavukcuoglu, K.; Kohli, P.; Hassabis, D. Highly accurate protein structure prediction with AlphaFold. Nature, 2021, 596(7873), 583-589.
[http://dx.doi.org/10.1038/s41586-021-03819-2] [PMID: 34265844]
[80]
Li, W.; Kinch, L.N.; Karplus, P.A.; Grishin, N.V. ChSeq: A database of chameleon sequences. Protein Sci., 2015, 24(7), 1075-1086.
[http://dx.doi.org/10.1002/pro.2689] [PMID: 25970262]
[81]
Ghozlane, A.; Joseph, A.P.; Bornot, A.; Brevern, A.G. Analysis of protein chameleon sequence characteristics. Bioinformation, 2009, 3(9), 367-369.
[http://dx.doi.org/10.6026/97320630003367] [PMID: 19759809]
[82]
Miyashita, H.; Kuroki, Y.; Kretsinger, R.H.; Matsushima, N. Horizontal gene transfer of plant-specific leucine-rich repeats between plants and bacteria. Nat. Sci., 2013, 5(5), 580-598.
[http://dx.doi.org/10.4236/ns.2013.55074]

Rights & Permissions Print Cite
© 2024 Bentham Science Publishers | Privacy Policy